Identifying and tracking proteins through the marine water column: insights into the inputs and preservation mechanisms of protein in sediments

Abstract

Proteins generated during primary production represent an important fraction of marine organic nitrogen and carbon, and have the potential to provide organism-specific information in the environment. The Bering Sea is a highly productive system dominated by seasonal blooms and was used as a model system for algal proteins to be tracked through the water column and incorporated into detrital sedimentary material. Samples of suspended and sinking particles were collected at multiple depths along with surface sediments on the continental shelf and deeper basin of the Bering Sea. Modified standard proteomic preparations were used in conjunction with high pressure liquid chromatography-tandem mass spectrometry to identify the suite of proteins present and monitor changes in their distribution. In surface waters 207 proteins were identified, decreasing through the water column to 52 proteins identified in post-bloom shelf surface sediments and 24 proteins in deeper (3490 m) basin sediments. The vast majority of identified proteins in all samples were diatom in origin, reflecting their dominant contribution of biomass during the spring bloom. Identified proteins were predominantly from metabolic, binding/structural, and transport-related protein groups. Significant linear correlations were observed between the number of proteins identified and the concentration of total hydrolysable amino acids normalized to carbon and nitrogen. Organelle-bound, transmembrane, photosynthetic, and other proteins involved in light harvesting were preferentially retained during recycling. These findings suggest that organelle and membrane protection represent important mechanisms that enhance the preservation of protein during transport and incorporation into sediments.

INTRODUCTION

As the building blocks of proteins, amino acids represent the largest portion of characterized biochemicals in most marine environments, and are important contributors to both carbon and nitrogen pools (Burdige and Martens, 1988; Hedges, 1991; Benner et al., 1992; Lee et al., 2000). Estimates suggest that amino acids make up 2–30% of organic carbon and 15–42% of organic nitrogen in coastal and deep ocean sediments (Wakeham et al., 1997; Keil, 1999). Evidence from solid state N-15 NMR spectroscopy shows that the majority of organic nitrogen present in dissolved and particulate marine organic matter contains amide bonds, like those that occur in proteins (McCarthy et al., 1997; Knicker, 2000; Zang et al., 2001). In several cases, protein products as well as intact proteins have been observed in deep ocean waters (Tanoue, 1992; Suzuki et al., 1997; Dong et al., 2010).

Traditional approaches of measuring hydrolysable amino acids (THAAs) in environmental samples as a proxy for total protein material destroy the amide bond, and thus the inherent source information encoded in the protein's amino acid sequence is lost. Our aim is to link the observed THAA distributions to the defined amino acid sequences of identifiable proteins. This will enhance the information obtained between the biosynthetic building blocks of macromolecular organic nitrogen and the geochemical fate of their protein products. The recent characterization of the marine diatom Thalassiosira pseudonana genome (Armbrust et al., 2004; Oudot-Le Secq et al., 2007) and now the proteome (Nunn et al., 2009) provided insight into the biochemical pathways utilized by marine diatoms. In addition, it presents the opportunity to track the distribution of proteins from this major algal contributor in natural settings.

With primary production rates up to 570 g C m⁻² y⁻¹, the Bering Sea is perhaps the most productive region in the world (Sambrotto et al., 1986; McRoy et al., 1987; Walsh et al., 1989). As in many high latitude systems, diatoms dominate spring production (Banahan and Goering, 1986; Springer et al., 1996), leading to a carbon export flux in the range of 10 mmol C m⁻² day⁻¹ (Chen et al., 2003). This combination of high productivity of known algal communities and rapid transport to sediments make the Bering Sea an ideal system to study the early diagenetic fate of algal proteins in marine systems.

Here we link proteomic approaches with geochemical cycling to examine the environmental fate of proteins in a system where diatoms provide the bulk of new organic matter. We have merged traditional protein buffer extraction and gel electrophoresis purification techniques with mass spectrometry-based proteomics in order to identify individual proteins in these complex environmental samples. The goal of this study was to track proteins derived from the spring diatom bloom in the Bering Sea through the water column to eventual incorporation into the sedimentary organic nitrogen pool. In doing so, we have the opportunity to identify potential mechanism(s) which regulate the distributions observed during the initial stages of diagenesis.

METHODS

Bering Sea sample collection

All suspended particles from filtration, particle trap, and sediment samples were collected on the Bering Sea outer shelf and basin during the Bering Sea Ecosystem Study (BEST) cruises in the spring and summer of 2009 (Fig. 1). Particulate and trap samples were collected at multiple depths during the spring diatom bloom as ice retreated; samples included both suspended and sinking material inclusive of chlorophyll maximum to bottom waters (Table 1). Suspended particles, collected by Niskin bottles, were filtered onto 47 mm combusted glass fiber filters (GF/Fs) at three depths: chlorophyll max (4 m), 50 m, and 100 m. Sinking particles were collected from 12 hour trap deployments (40 m, 60 m, and 100 m) at the same location as suspended particles. No preservatives were used with particle trap cups prefilled with brine solution prior to deployment. After collection, 100 mL aliquots of the particle trap samples were filtered onto combusted 25 mm GF/Fs. Undisturbed sediments were collected using a multicore on both the outer shelf and in the deeper basin (3490 m) before the spring phytoplankton bloom and two months after the bloom to allow sampling of recently arrived material at the sediment-water interface (Table 1). Visible phytodetritus was present post-bloom on the surface of both shelf and basin sediments. Surface material (0–1 cm) was removed and samples were frozen and stored at −70°C until analysis.

Figure 1.

Map of Bering Sea and sample locations. Samples include: (1) shelf surface sediment during ice cover prior to the spring phytoplankton bloom; (2) water column suspended particles and sinking particle trap material during the spring phytoplankton bloom; (3) shelf sediments subsequent to the spring phytoplankton bloom and (4) basin surface sediments.

Table 1.

Station locations and bulk properties of suspended particles (POC), trap material and sediments of Bering Sea samples. Carbon and total hydrolysable amino acid (THAA) concentrations are μg/L for suspended particles, μg/hr for trap material, and μg/g for sediments. PBS = Post-bloom Shelf; PBB = Post-bloom Basin; OWS = Over-wintered Shelf.

Sample	Date	Lat (N)	Long (W)	Depth (m)	°C	C (μg/L)	C:N Ratio	THAA (μg)
Chl Max POC	4/30/2009	59.9	176.1	4	−0.79	1172	6.2	520.0
50m POC	4/30/2009	59.9	176.1	50	−0.05	114.4	3.5	14.2
100m POC	4/30/2009	59.9	176.1	100	0.71	126.1	3.9	9.0
40m Trap	4/30/2009	59.9	176.1	40	−0.76	225	4.1	4.6
60m Trap	4/30/2009	59.9	176.1	60	0.45	5314	4.0	4.0
100m Trap	4/30/2009	59.9	176.1	1.00	1.00	365	8.1	2.9
PBS	7/5/2009	59.6	175.2	136	1.08	10200	7.9	846.9
PBB	6/26/2009	57.5	175.2	3490	3.67	11600	7.5	687.8
OWS	4/9/2009	59.9	171.6	101	−0.15	10500	8.2	725.4

Amino acid analysis

To provide a metric for comparison of protein content and more traditional measures, total hydrolysable amino acids (THAAs) were quantified and analyzed in parallel with protein identification. Individual amino acids were identified and quantified by gas chromatography (GC) and GC mass spectrometry (GC/MS) using the EZFaast method (Phenomonex) which uses derivatization of AAs with propyl chloroformate and propanol for sensitive detection (see Waldhier et al., 2010 for a comparison of methods). Briefly, suspended particles, particle traps, and sediment samples were hydrolyzed for 4 hours at 110 °C (Cheng et al., 1975; Cowie and Hedges, 1992) with 6 M analytical-grade HCl and L-γ-Methylleucine as the recovery standard. Following hydrolysis and derivatization, amino acids were quantified using an Agilent 6890 capillary GC with samples injected at 250 °C and separated via a DB-5MS (0.25 mm ID, 30 m) column with H₂ as the carrier gas. The oven was ramped from an initial temperature of 110 °C to 280 °C at 10 °C per minute followed by a 5 minute hold. For amino acid identification, the GC was coupled to an Agilent 5973N mass spectrometer run under the same conditions with helium as the carrier gas and acquisition of spectra over the 50–600 Da range. Bovine serum albumin (BSA) was analyzed in parallel to correct for responses among individual amino acids and calculation of molar ratios. Amino acids were normalized to percent carbon or nitrogen using bulk samples analyzed by standard combustion methods.

Protein extraction

To extract proteins from suspended particle and particle trap samples, filters were sliced into sections, fully submerged in 3 mL of extraction buffer, (7 M urea, 2 M thiourea, 0.01 M Tris-HCl, 1 mM EDTA, 10% v/v glycerol, 2% w/v CHAPS, 0.2% w/v ampholytes, 2 mM Tributyl phosphine, see Kan et al., 2005) and pulse sonicated on ice with a Branson 250 Sonifier sonication probe at 20 kHz for 1 minute. The sonication probe was in full contact with filters and particulate material to enhance extraction. The extraction process of sonication in concentrated urea denaturing solution was very similar to past studies on marine particulate proteins identified from multiple cell types by proteomic mass spectrometry (Dong et al. 2010). Extracted material was then centrifuged for 5 min (5,000 × g) to remove particles. For suspended and sinking particles, protein extraction efficiencies were estimated by comparing Bradford Assay protein concentrations of protein extracts to total hydrolysable amino acids (THAAs) ofwhole samples as a proxy for total protein. The extraction efficiencies for chlorophyll max, 50 m, and 100 m suspended particulate samples (Bradford Assay Protein Concentration/THAA concentration) were 105%, 81%, and 90% respectively.

For sediment protein extraction, known weights of sediment were treated with 500 μL of extraction buffer in 1.5 mL Eppendorf tubes and pulse sonicated for one minute on ice. The entire sediment+extract buffer mixture was then loaded onto gel-prep cell tubes for isolation and molecular weight class separation of proteins. Amounts of protein material loaded onto gels were determined by measuring the concentration of THAAs in filter extracts and sediment buffer mixtures as a proxy for total protein. The extraction efficiencies (THAA concentration of extract/THAA concentration of sediment) were consistent, ranging from 11–12% for shelf and basin sediments. The extraction protocol and efficiency is described in greater detail in Moore et al. (2012, in press).

To purify extracts and separate proteins based on molecular weight (MW), 1 mL of extract from each sample was loaded onto individual preparatory electrophoresis tubes (prep-gel: 17% Acrylamide/Bis, 0.125 Tris-HCl) for one dimensional separation. Gels were covered with running buffer (0.25 M Tris, 0.192 M glycine, 0.1% SDS, pH 8.3; 180 V) and run until the ion front traveled 7 cm from the top of the gel. After electrophoresis, gels were washed and cut into five molecular weight ranges (<10, 10–25, 25–50, 50–100, and >100 kDa) based on prior separations of MW standards (Kaleidoscope) using identical gels.

In-gel protein digestion

Before enzymatic digestion, gel MW sections were cut into 2 × 2 mm slices to increase surface area for enzyme and chemical access. Pieces were covered with 100 mM ammonium bicarbonate and rinsed for 15 min to hydrate gel sections, and then rinsed for 15 minutes in acetonitrile to dehydrate gel sections and remove detergents and other chemical interferences. The rinse cycle was repeated five times and gel sections then were dried by speed-vac for 45 min. Subsequent reduction, alkylation, and digestion followed standard procedure by Shevchenko et al. (1996). Digests were dried and volumes were adjusted to give a final protein concentration of 1 μg protein/10 μL based upon THAA concentrations and measured recoveries.

Mass spectrometry and database searching

Proteins were identified via shotgun proteomics with samples introduced into the ion trap (LTQ Velos) mass spectrometer (Thermo Fisher) via NanoAcquity high performance liquid chromatography (HPLC, Waters) (Nunn et al., 2010). New analytical and trapping columns were packed in-house prior to batch analyses of Bering Sea samples in order to ensure no proteins were carried over from previous cell lysate proteomic experiments. Analytical columns were made using 11 cm long, 75 μm i.d. fused silica capillaries packed with C18 particles (Magic C18AQ, 100 Å, 5 μm; Michrom, Bioresources) preceded by a 2 cm long, 100 μm i.d. trapping-column (Magic C18AQ, 200 Å, 5 μm; Michrom). Samples were loaded onto the trapping column with a flow rate of 4 μl min⁻¹ (7 min), and then entered the analytical column at a flow rate of 250 nL min⁻¹ (total run time 100 min). Peptides were eluted using an acidified (formic acid, 0.1% v/v) water-acetonitrile linear gradient (5 to 35% acetonitrile in 60 min), and ionized in atmospheric pressure before entering the mass spectrometer. Following a survey of the ions that entered the ion trap (MS¹), the fourteen most intense ions from scans having either +2, +3, +4, or +5 charge states were selected for collision induced dissociation (CID) and tandem mass spectral (MS²) detection (for review see Nunn and Timperman, 2007). Sample digests were analyzed using full scan (m/z 350–2000), followed by gas phase fractionation with repeat analyses over multiple narrow, but overlapping mass to charge ranges (e.g. m/z 350–444, 444–583, 583–825, 825–1600) (Yi et al., 2002; Nunn et al., 2006; Scherl et al. 2008).

Mass spectra were interpreted and searched using an in-house copy of SEQUEST on a Beowolf-stlye computer cluster with 800 dedicated processing cores and 22 terabytes of storage (Eng et al., 1994; Eng et al., 2008). All data searches were performed with no assumption of proteolytic enzyme (e.g. trypsin) specificity to allow for identification of the maximal number of protein degradation products. Fixed modifications were set for 57 Da on cysteine (resulting from IAM alkylation step) and 16 Da on methionine via oxidation. Each tandem mass spectrum was then searched against a protein sequence database to correlate predicted peptide fragmentation patterns with observed sample ions. To objectively validate peptide and protein identifications, two statistical evaluations using PeptideProphet and ProteinProphet were used to provide probability based scores (Keller et al., 2002; Nesvizhskii et al., 2003). Probability thresholds for positive identifications of proteins and peptides were strictly set at 90% confidence on ProteinProphet and PeptideProphet for SEQUEST search results. Mass spectra from all samples were searched against a database (referred to as “Thaps database”) containing the proteomes of Thalassiosira pseudonana (marine diatom), Prochlorococcus marinus (marine cyanobacterium), and Pelagibacter ubique (marine bacterium belonging to the SAR11 clade). The proteomes of P. marinus and P. ubique were included to account for potential input of bacterial proteins through the water column. The Thaps database was chosen after extensive comparison revealed that larger databases, including the NCBI non-redundant database containing over 11.9 million protein sequences, did not enhance the number of protein identifications, added limited species diversity to identified proteins, and had 95% functional agreement between Thaps and larger database identified peptides from Bering Sea sediment (Moore et al., 2012 in press). False discovery rate was calculated to be 0.5% for Thaps database searches.

A second separate database search was conducted to investigate correlations with a highly diverse assemblage of microbial peptides. This database included the proteome of T. pseudonana, plus the Global Ocean Survey (GOS) Combined Assembly Protein database (Rusch et al., 2007; Yooseph et al., 2007; Community Cyberinfrastructure for Advanced Marine Microbial Ecology Research and Analysis, CAMERA, downloaded on 29 September 2008). Although the GOS database has over 6,000,000 marine microbial proteins sequenced from genomic data, limited functional data are available. In this combined database inclusive of Thaps and GOS sequences, proteins from T. pseudonana account for approximately 0.1% of the total protein sequences, suggesting that randomly identified false spectra correlation to a T. pseudonana peptide was highly unlikely. Searches using the GOS/Thaps database were only completed on the post bloom surface sediments where microbial products were expected to be most prevalent. The GOS/Thaps-searches were also limited because they were computationally intensive, consuming over 720 hours of search time (~1 month), even on the large computer cluster used. The intent of this search was to seek identifiable bacterial proteins in sediments which were expected to have high levels of microbial recycling.

RESULTS

Protein distribution

Using a mass-spectrometry based approach, 207 proteins were identified in suspended particles from the chl-max of the Bering Sea (Table 2, Fig. 2A). Substantially fewer proteins were identified in suspended particles at 50 m (11 proteins) and 100 m (22 proteins). The number of identified proteins in the particle traps decreased from 136 at 40 m to 53 at 60 m, and 82 at 100 m. In post-bloom shelf sediment 52 proteins were identified, with slightly less than half the number of identifications in post-bloom basin and over-wintered shelf sediment. The majority of identified proteins at depth were also identified in the chlorophyll max, representing transport down the water column (Fig. 3). Sequence coverage, defined as the percentage of a specific protein sequence observed using tandem mass spectrometry, was highest on average in the chl-max and lowest in 50m POC.

Table 2.

The number of total proteins identified in suspended particles (POC), particle traps, and sediments. Species distribution is based on database identifications originating from diatoms, (T. pseudonana), an autotrophic bacteria (P. marinus), or the pelagic bacteria (P. ubique).

Sample	Total Proteins Identified	T. pseudonana	P. marinus	P. ubique
Chl-max POC	207	200	3	4
50m POC	11	10	0	1
100m POC	22	19	0	3
40m Trap	136	129	5	2
60m Trap	53	52	1	0
100m Trap	82	79	3	0
PBS	52	49	1	2
PBB	24	21	1	2
OWS	23	22	1	0

Figure 2.

Profiles of (A) Number of proteins identified; (B) THAA/OC from each sample; (C) THAA-N/PN from each sample (Sediment samples graphed by residence time: OWS = Over-wintered Shelf; PBS = Post-bloom Shelf; PBB = Post-bloom Basin).

Figure 3.

Protein molecular weight vs. sequence coverage plots for each sample. Solid data points represent proteins that were identified in chl-max, open data points represent proteins that were not identified in chl-max. One ~400 kDa protein (sequence coverage: 1%) in PBB plot has been excluded for ease of comparison.

The vast majority of peptides observed in all samples correlated to diatom proteins (Table 2). In the two samples with the highest number of protein identifications, chl-max particles and the 40 m particle trap, there were 200 and 129 diatom proteins, respectively, plus seven bacterial identifications in each sample. Overall, the number of observed bacterial proteins accounts for 5% of the total identifications, with the remaining 95% of identifications correlating to a diatom origin. Post-bloom shelf sediment mass spectra searched against the larger combined Thaps/GOS database yielded no unique bacterial protein identifications with confidence. The majority of identified bacterial protein amino acid sequences overlapped with the amino acid sequences of T. pseudonana proteins as well.

As the number of identified proteins declined with increasing depth, the functional distribution of observed proteins changed. Protein categorization by gene ontology (Ashburner et al., 2000) revealed that metabolic proteins made up the largest functional group in chl-max particles at 63%, followed by structure/binding proteins at 18%, and transport proteins at 13% (Table 3). A more even distribution of proteins among the metabolic, structure/binding, and transport groups was observed in 50 m and 100 m suspended particles. In all particle trap and sediment samples, metabolic proteins make up the largest group. Within the metabolic category, translation proteins were the largest subgroup in the chl-max at 17% followed by photosynthesis/carbon fixation proteins at 15% (Table 3). Deeper in the water column, photosynthesis/carbon fixation proteins accounted for 7% to 25% of identified proteins in suspended particles and particle traps; this fraction increased slightly in post-bloom shelf sediment to 26%, then considerably increased to 46% in post-bloom basin sediment and 52% in over-wintered shelf sediment. Conversely, the proportion of transport proteins decreased from water column suspended particles and traps to post-bloom basin and over-wintered shelf sediment. The percentage of proteins classified as structural or binding proteins did not change to the same degree as photosynthesis or transport proteins.

Table 3.

The distribution of proteins observed in particles and sediments categorized by major cellular function as defined by Gene Ontology (Metabolic, Structure/Binding, or Transport). Total proteins observed are categorized as percentage of each by subgroup.

Chl-max POC IDs	207
% Metabolic	131 (63.3%)	% Structure/Binding	37 (17.9%)	% Transport	27 (13.0%)
Translation	35 (16.9%)	Binding, DNA/RNA	13 (6.3%)	Ion Transport	19 (9.2%)
Photosynthesis	30 (14.5%)	Binding, Protein	8 (3.9%)	Transport, General	8 (3.9%)
Biosynthesis	18 (8.7%)	Protein Folding	7 (3.4%)
Cellular Processing	29 (14.0%)	Binding, Molecule	6 (2.9%)
Glycolysis	11 (5.3%)	Structural	3 (1.4%)
Oxidation Reduction	8 (3.9%)

50m POC IDs	11
% Metabolic	3 (27.3%)	%Structure/Binding	2 (18.2%)	% Transport	5 (45.5%)
Photosynthesis	2 (18.2%)	Binding, Protein	1 (9.1%)	Ion Transport	4 (36.4%)
Translation	1 (9.1%)	Structural	1 (9.1%)	Transport, General	1 (9.1%)

100m POC IDs	22
% Metabolic	8 (36.4%)	% Structure/Binding	7 (31.8%)	% Transport	7 (31.8%)
Photosynthesis	5 (22.7%)	Binding	5 (22.7%)	Ion Transport	5 (22.7%)
Cell Processing	3 (13.6%)	Structure	2 (9.1%)	Transport, General	2 (9.1%)

40m Trap IDs	136
% Metabolic	82 (60.3%)	% Structure/Binding	25 (18.4%)	% Transport	24 (17.6%)
Photosynthesis	24 (17.6%)	Binding, DNA/RNA	9 (6.6%)	Ion Transport	19 (14.0%)
Translation	16 (11.8%)	Binding, Protein	7 (5.1%)	Transport, General	5 (3.7%)
Biosynthesis	12 (8.8%)	Protein Folding	3 (2.2%)
Glycolysis	10 (7.4%)	Structure	3 (2.2%)
Cellular Processing	16 (11.8%)	Binding, Molecule	3 (2.2%)
Oxidation Reduction	4 (2.9%)

60m Trap IDs	53
% Metabolic	34 (64.2%)	% Structure/Binding	8 (15.1%)	% Transport	10 (18.9%)
Photosynthesis	13 (24.5%)	Binding, DNA/RNA	2 (3.8%)	Ion Transport	6 (11.3%)
Glycolysis	6 (11.3%)	Binding, Protein	3 (5.7%)	Transport, General	4 (7.5%)
Cellular Metabolism	5 (9.4%)	Protein Folding	2 (3.8%)
Translation	4 (7.5%)	Structure	1 (1.9%)
Biosynthesis	3 (5.7%)
Cellular Processing	3 (5.7%)

100m Trap IDs	82
% Metabolic	39 (47.6%)	% Structure/Binding	12 (14.6%)	% Transport	18 (22.0%)
Translation	15 (18.3%)	Binding	7 (8.5%)	Ion Transport	16 (19.5%)
Photosynthesis	6 (7.3%)	Protein Folding	3 (3.7%)	Transport, General	2 (2.4%)
Glycolysis	6 (7.3%)	Structure	2 (2.4%)
Cellular Metabolism	5 (6.1%)
Cellular Processing	5 (6.1%)
Biosynthesis	2 (2.4%)

Post-bloom Shelf IDs	53
% Metabolic	21 (39.6%)	% Structure/Binding	14 (26.4%)	% Transport	17 (32.1%)
Photosynthesis	14 (26.4%)	Binding, DNA/RNA	6 (11.3%)	Ion Transport	12 (22.6%)
Cellular Processing	4 (7.5%)	Structure	4 (7.5%)	Transport, General	5 (9.4%)
Translation	3 (5.7%)	Binding, Protein	4 (7.5%)

Post-bloom Basin IDs	24
% Metabolic	17 (70.8%)	% Structure/Binding	4 (16.7%)	% Transport	2 (8.3%)
Photosynthesis	11 (45.8%)	Binding, DNA/RNA	2 (8.3%)	Ion Transport	2 (8.3%)
Cellular Processing	4 (16.7%)	Structure	1 (4.2%)
Translation	2 (8.3%)	Membrane	1 (4.2%)

Over-wintered Shelf IDs	23
% Metabolic	16 (69.6%)	% Structure/Binding	5 (21.7%)	% Transport	2 (8.7%)
Photosynthesis	12 (52.2%)	Binding, DNA/RNA	3 (13.0%)	Ion Transport	2 (8.7%)
Translation	2 (8.7%)	Binding, Protein	1 (4.3%)
Cellular Processing	2 (8.7%)	Structure	1 (4.3%)

The comparison of protein abundance with more traditional measures found that THAAs decreased from the chl-max (520 μg/L) to 50 m suspended particles (14.2 μg/L), with a much smaller reduction from 50 m to 100 m (9.0 μg/L) (Table 1, Figure 2). Sediment trap THAAs decreased more steadily with depth than seen in suspended particles, not unlike identified proteins. Post-bloom shelf sediment had greater THAA concentrations than post-bloom basin sediment and over-wintered shelf sediment. Hydrophobic amino acids (Leu, Gly, Ala, Phe, Ile, Val) were the most represented amino acids in all samples, making up 56% of the average amino acid distribution in THAAs and 47% of the amino acid distribution of identified protein amino acid sequences (Fig. 4, Appendix 2).

Figure 4.

The distribution of non polar, polar uncharged, and polar charged amino acids among (A) total hydrolysable amino acids; (B) tabulated amino acids of identified proteins; (C) tabulated amino acids of TMHMM modeled transmembrane regions within identified proteins. Identified protein amino acids and THAAs show very similar distribution, while transmembrane regions have greater proportion of non polar amino acids.

Molecular weight distribution of surviving proteins

To compare the potential for selective loss of individual proteins based on molecular weight, identified proteins were grouped into five molecular weight ranges (<10, 10–25, 25–50, 50–100, >100 kDa) based on two categories. The first category was the predicted molecular weight of intact proteins as identified using mass spectrometry. The second was the molecular weight range in which each protein was observed following gel purification. Proteins identified in their anticipated gel molecular weight range can be categorized as “expected” since molecular weights were in agreement. In contrast, proteins observed by gel electrophoresis to be outside their predicted molecular weight range were categorized as “observed” in order to denote the disparity between gel mobility and expected molecular weight (Fig. 5). Of the proteins grouped by “expected” molecular weight, the vast majority of proteins identified in particles, traps, and sediments were in the intermediate size ranges (10–25, 25–50, 50–100 kDa) expected for many cellular proteins (Fig. 5A). The group with the most identifications comprises those proteins in particles and traps from 25–50 kDa. This changed as the proportion of 25–50 kDa proteins decreased in sediments compared to water particles and traps. The majority of “observed” proteins in suspended particles and particle traps were found to have greater than expected molecular weights (“observed larger”) based on gel migratory behavior (Fig. 5B). The proportion of proteins with lower than expected molecular weights (“observed smaller”) increased in sediments, especially post-bloom basin and over-wintered shelf sediments.

Figure 5.

The percentage of identified proteins in each sample within molecular weight groups verses identified proteins with altered properties. A) The expected distribution of identified proteins in samples; (B) The distribution of proteins identified in each gel section: black bars represent the percentage of proteins identified in the expected gel section molecular weight range, grey bars represent “observed large” proteins, white bars represent “observed small” proteins.

DISCUSSION

Through the identification of unique peptide sequences, we are able to demonstrate that proteins derived from primary production are able to survive the degradation processes during initial transit to the sediment water interface. Over 70% of all proteins identified in suspended particles at depth, and over 80% of proteins identified in particle traps were also detected in the diatom dominated chlorophyll maximum. The importance of proteins derived from primary producers extended to both shelf sediment samples, representing >80% of identified proteins, and basin sediments where 67% of identified proteins were identical to those observed in the chl-max. Diatoms may contribute organic matter to sediments because they are encapsulated in high-density silica frustules that can rapidly transport OM to depth (Dunne et al., 2005; Ragueneau, et al., 2006; Miki et al., 2009). Multiple fucoxanthin chlorophyll a/c binding proteins (FCPs), important light harvesting complex proteins in diatoms and other marine algae (Grossman et al., 1995; Lang and Kroth, 2001; Nunn et al., 2009), were observed in all sediment samples. The presence of these proteins is not completely unexpected; FCPs are central in the light harvesting complex, representing the most abundant protein class discovered in mid-exponential growth T. pseudonana (Nunn et al., 2009) and later observed to remain after extensive microbial attack in a controlled month-long degradation experiment (Nunn et al, 2010) . Since diatoms dominate spring bloom production in the Bering Sea, and their density and aggregation result in sinking after bloom termination (Smetacek et al., 1985), it is very likely that diatoms are the source of algal-derived light harvesting proteins to Bering Sea sediments.

The discovery of diatom and algal specific proteins in ocean basin sediments reveals that, despite the intensive recycling processes active in oceanic waters, highly organized macromolecules such as proteins can be transported intact from their biosynthetic origins in surface waters to sediments. While fewer proteins were identified in this study than Dong et al. (2010), greater statistical rigor was applied by way of PeptideProphet and ProteinProphet to identify peptides and proteins in the system with greater confidence. In addition, the diatom/algal proteins identified were not only observed over the shallow productive continental shelf, but also in the deeper ocean surface sediments, suggesting that seasonal primary production in the Bering Sea is also an important contributor to deeper environments. Given that diatom sinking rates can range from 40 m per day to over 100 m per day (Smetacek, 1985 and references therein), the sinking time for bloom material to the shelf sediment-water interface (101–136 m) would be on the order of days, while sinking time over the basin (3490 m) would be on the order of weeks. Recent laboratory studies by Nunn et al., (2010) found that a subset of diatom proteins can be retained over a 23 day degradation period, which could encompass the potential sinking time of bloom material to sediments and initial sedimentary recycling. Many more proteins were identified in sinking sediment trap material than in suspended particle samples (Table 2), reinforcing previous observations that sinking material has a distinct composition compared to suspended particles (Sheridan et al., 2002; Abramson et al., 2010). To our knowledge, this is the first demonstration that intracellular, cytosolic and soluble proteins can be transported to depth from sources in the upper water column. These factors suggest that in the Bering Sea and other diatom-dominated systems, the large size and density of diatoms is central to transport, burial, and eventual preservation of sedimentary proteins from a range cellular compartments.

It has long been observed that as marine organic matter becomes more degraded, there is a decrease in the ratios of total hydrolysable amino acids to organic carbon (THAA/OC), and THAA-nitrogen to particulate nitrogen (THAA-N/PN) (e.g. Cowie and Hedges, 1994 and references therein). Here, these two ratios were used to normalize amino acid amounts across multiple sample types, and compare amino acid concentrations with the number of identifiable proteins in each sample. Plotting the number of identified proteins against the ratios of THAA/OC and THAA-N/PN, strong correlations are observed for both carbon and nitrogen (Fig. 6A, B). The correlation between protein identifications and THAA-N/PN is particularly strong, displaying the importance of protein to marine organic nitrogen (Brown, 1991; Lourenco et al., 1998). These relationships also show that over a wide range of concentrations, THAAs present in particles and even surface sediments likely include a portion of intact proteins, with the number of identified proteins reflecting the extent to which proteins have been degraded during diagenesis. In the case of this study where diatoms are the primary source material, the relationship likely reflects the freshness of produced organic matter and retention of diatom proteins.

Figure 6.

(A) The number of identified proteins plotted against THAA/OC; (B) Identified proteins plotted against THAA-N/PN with linear regressions displayed for each.

Arranging samples in order of decreasing THAA-N/PN values, sample clusters are formed: chl-max particles > all particle traps > deeper suspended particles and surface sediment, which likely represents increasing degradation status (Fig. 6B). This order also generally reflects the amount of identifiable proteins in each sample and average sequence coverage of identified proteins in most samples. Fewer identifiable proteins and similar THAA-N/PN proxies from suspended particles suggest a similar “degraded” status for proteins compared to those found in the sediments. This may reflect the length of time since organic matter production (Hartnett et al., 1998) as well as the potential importance of sorption to sediment for protein preservation (Collins, 1995; Mayer, 1999). The enhanced sedimentation rates of large aggregates could control the fraction of proteins present in surface sediments.

In addition to the absolute number of identified proteins and THAAs, the diversity of different protein groups based on cellular function declined in deeper waters and with residence time in surface sediments. Metabolic proteins made up the largest group in all samples except for the 50 m suspended particle sample (Table 3). Within the metabolic protein category, photosynthetic and carbon fixation proteins represent the largest percentage of proteins remaining in sedimentary material. Recent work by Nunn et al. (2010) highlighted factors that might influence the preservation of such proteins over short time scales. Several characteristic traits were proposed to encourage protein stability and/or longevity including organelle compartmentalization, transmembrane-spanning domains, initial cellular abundance, glycan modifications, and aggregation. Several of these mechanisms can be considered in the context of Bering Sea protein preservation.

Compartmentalization and preservation potential

Proteins are not uniformly distributed in cells, but typically associated with various cellular compartments which might influence preservation and help explain the observed distribution shifts of protein cellular functions through water column loss. Gel electrophoresis has been shown to enhance liberation of membrane bound proteins (Coughenour et al., 2004) allowing improved identification of organelle proteins in addition to molecular weight separation. To examine the possibility of organelle preservation, protein compartments were assigned to sub-cellular locations based on the T. pseudonana proteome using the TargetP 1.1 Server (Emanuelsson et al., 2007) and uniprot.org (Jain et al., 2009).

The proportion of membrane compartmentalized proteins discovered in sediments (i.e. chloroplast and mitochondrial proteins) increased from post-bloom shelf sediment to both post-bloom basin and over-wintered shelf sediments, while the proportion of secretory proteins decreased. Similarly, the percentage of identified proteins with transmembrane regions, as modeled by TMHMM Server v. 2.0 (Krogh et al., 2001) increased in deeper particles and sediments (Table 4). These observations suggest that soluble secretory proteins, with no added organelle membrane protection, are more susceptible to microbial recycling during sinking to deep basin sediments or longer residence time in over-wintered shelf sediments compared to post bloom shelf sediments. Similar patterns were recently seen in laboratory incubations (Nunn et al. 2010) with the preferential preservation of organelle enclosed proteins. This includes the important light harvesting FCP proteins which are enclosed in 4 membrane layers of the thylakoid and chloroplast (Westermann and Rhiel, 2005). Previous work has shown proteins enclosed in crude membrane extracts are degraded more slowly compared to soluble proteins (Nagata et al., 1998), and protein sequences derived from conserved membrane/envelope proteins were previously identified from Gulf of Mexico DOM (Powell et al. 2005). These lines of evidence point to physical protection through membrane associations as a factor in the survival of marine proteins.

Table 4.

The average isoelectric point (pI), number and relative abundance of high abundance diatom proteins¹, number and percentage of transmembrane proteins, percent transmembrane amino acids from each sample, and number and percentage of transmembrane proteins located in the chloroplast. Transmembrane regions predicted by TMHMM server v. 2.0.

Sample	pI	High Abundance Proteins	Membrane Proteins	Percent Transmembrane AAs	Transmembrane Proteins in Chloroplast
Chl Max	6.5	59 (29%)	25 (12%)	2	17 (68%)
50m POC	5.6	8 (80%)	2 (18%)	16	2 (100%)
100m POC	6.8	13 (59%)	6 (27%)	8	4 (67%)
40m Trap	6.2	48 (37%)	20 (15%)	3	15 (75%)
60m Trap	5.5	30 (58%)	5 (9%)	2	5 (100%)
100m Trap	6.6	32 (41%)	16 (20%)	5	13 (81%)
PBS	6.9	23 (47%)	15 (28%)	9	12 (80%)
PBB	6.8	9 (43%)	9 (38%)	9	8 (89%)
OWS	6.8	12 (55%)	10 (44%)	14	9 (90%)

¹high abundance proteins were defined as the top 1% of proteins based on proteome analysis (Nunn et al., 2009)

Implications of identified proteins on THAA distribution

Although early reports found that the relative distribution of particulate amino acids show only minor changes with ocean depth (Wakeham et al., 1984; Müller et al., 1986), or as algae are subject to degradation (Nguyen and Harvey, 1997), amino acid distributions have been used as a metric for degradation state (Dauwe and Middelburg, 1998 and references therein). Given that the amino acid distribution of most proteins is very similar (Brooks et al., 2002), such changes are small. We can compare total THAAs among all sample types with amino acids tabulated from the sequences of identified proteins and those amino acids associated only with transmembrane regions of proteins (Fig. 4A–C). Grouped for ease of comparison into major functional groups, the distribution of amino acids tabulated from identified proteins shows remarkable similarity to THAAs among suspended, sinking, and sedimentary material. The proportion of hydrophobic amino acids was highest for transmembrane proteins among all sample types (71–73% non-polar), and may reflect hydrophobic interactions previously observed as stabilizing forces for proteins in particulate material and organic rich sediments (Nguyen and Harvey, 2001) and kerogens (Nguyen and Harvey, 2003).

Protein abundance and identification

The array of possible marine proteins is vast, as reflected by the breadth of the GOS protein database (Yooseph et al., 2007). Identification of proteins by data-dependent ion selection of peptides during HPLC-MS/MS is inherently biased to more abundant peptides in complex matrices and thus proteins in low concentrations may remain below detection limits. This suggests that the most abundant proteins present in diatom cells are more likely to be available for identification after long term microbial attack. To test this, proteins ranked in the top ~1% of abundance based on the proteome analysis of Nunn et al., (2009) were classified as high abundance proteins, while the remaining proteins in the T. pseudonana proteome were grouped as low abundance proteins. The proportion of high abundance proteins increases among identified proteins with depth from bloom material to sinking trap material to sediments (Table 4). The percentage of high abundance proteins was also greater in over-wintered shelf sediment than either post-bloom or deeper shelf sediment samples. This suggests that initial abundance of individual proteins in living cells influences the potential for their detection after substantial losses via degradation. Once a protein reaches the sediment, preservation mechanisms such as aggregation (Nguyen and Harvey, 2001; 2003), particle (Nagata and Kirchman, 1996), or mineral sorption (Mayer, 1994; 1999; Hedges and Keil, 1999), are likely to extend its longevity.

Protein molecular weight

An important caveat to the identification of proteins is that absolute molecular weight is not measured, and thus proteins which are retained in the system might represent non-native forms. Indeed, covalent modifications have been previously proposed as one mechanism for protein preservation in older sediments (Cronin and Morris, 1981; Benner et al, 1992; Nguyen and Harvey, 2003). Given the molecular weight distribution of low, intermediate, and high molecular weight proteins in the T. pseudonana proteome (Armbrust et al., 2004; Nunn et al., 2009), the observed electrophoretic behavior among a subset of identified proteins suggests that changes to the original sequence (or charge) are common and can lead to higher than expected molecular weights based on mobility within a gel (Fig. 5B). While aggregation has been proposed previously as one mechanism (Nguyen and Harvey, 2001; 2003), the denaturing conditions used here suggest that covalent modifications or charge alterations are also operative. The fact that there were also a significant number of proteins which appear to have lower molecular weights than expected suggests that partial hydrolysis is active as well (i.e. Pantoja and Lee, 1999).

Bacterial proteins in sediment

In the Bering Sea as in other ocean environments, microbial processes act as the primary catalyst for organic matter recycling. Although estimated bacterial biomass present in sediments is far lower than that derived from primary production, proteins associated with active microbial populations undoubtedly are present. Mass spectra collected from Bering Sea shelf post-bloom sediments searched against the T. pseudonana/GOS Combined Assembly Protein database yielded only two bacterial protein identifications at the 90% confidence level: 1) a vacuolar proton inorganic pyrophosphatase and 2) translation elongation factor 1 alpha. The spectra that correlated to peptides from the GOS database from these two proteins also correlated with known T. pseudonana peptides, demonstrating that in many cases different species have homologous peptide sequences.

Challenges with identifying bacterial proteins noted in the soil literature include high diversity of known and unknown bacterial proteins resulting in incomplete bacterial protein databases and individual proteins being below detection limits (Graves and Haystead, 2002; Quince et al., 2008; Bastida et al., 2009). Furthermore, bacterial proteins may be masked by co-extracted sedimentary material (Criquet et al., 2002) confounding the issue of detection limits missing highly diverse low abundance proteins. Nevertheless, proteomic studies on soil organic matter have revealed functional information on microbial communities and particle bound material (Schulze et al, 2005; Benndorf et al., 2007). Bacteria appear principally as catalysts in this first examination of protein distributions during organic matter recycling in marine systems, with phytoplankton derived material as the confirmed source of proteins in Bering Sea sediments. Simple estimations based on typical bacterial cell abundance in marine sediments (~10⁹ cells g⁻¹; Griffiths, et al., 1978; Deming and Colwell, 1982; Harvey, et al., 1984; Luna, et al., 2002; Kopke, et al., 2005) and average protein content per cell (24 fg cell⁻¹, Zubkov et al., 1999) indicate that bacteria likely contribute a small fraction to the total protein pool examined here.

CONCLUSIONS

This is the first study to apply an MS-based proteomics approach to follow the environmental fate of phytoplankton specific proteins present during bloom, transport, and initial incorporation into sediments. The survival of algal derived proteins appears selective, with compartmentalized and cell membrane proteins demonstrating greater longevity after genesis and short-term recycling in the water column. The correlation between identifiable proteins and THAA-N/PN suggests that proteins are not all rapidly hydrolyzed but may represent a predictable fraction of organic nitrogen present in organic matter. While database and detection limit challenges hinder the identification of bacterial proteins, phytoplankton proteins appear to be important contributors to Bering Sea sedimentary THAAs.

Figure 7.

The relative distribution of proteins identified from the cellular compartments of diatoms. Each section shows the percent contribution of proteins originating from a specific compartment. Cellular compartments include: chloroplast, secretory, nucleus, mitochondria, and a group of proteins that are from undefined or unknown compartments. The sizes of each circle is scaled to the number of proteins identified in each sample.

APPENDIX 1

Summary list of all proteins identified in each sample. Includes identified species, biological function, cellular compartment (Comp): C = Chloroplast; S = Secretory; M = Mitochondria; N = Nucleus; U = Uncharacterized Compartment), molecular weight (MW), isoelectric point (pI) sequence coverage, percent sequence coverage (Seq Cov).

Chl Max
Protein		Annotation	Species	Function	Comp	MW	pI	SC
26S proteasome AAA-ATPase subunit RPT3	jgi	24475	Thalassiosira pseudonana	Photosynthesis	S	42455	6.0	4.8
30S ribosomal protein S1	jgi	15259	Thalassiosira pseudonana	Translation	S	31770	4.6	7.7
30S ribosomal protein S11	gi	118411211	Thalassiosira pseudonana	Translation	C	13821	11.3	13.8
30S ribosomal protein S18	gi	118411132	Thalassiosira pseudonana	Translation	C	8155	10.8	31.9
30S ribosomal protein S3	gi	118411197	Thalassiosira pseudonana	Translation	C	24091	9.2	6.1
30S ribosomal protein S7	gi	118411217	Thalassiosira pseudonana	Translation	C	17730	10.5	21.2
30S ribosomal protein S8	gi	118411204	Thalassiosira pseudonana	Translation	C	14805	9.4	8.3
3-deoxy-7-phosphoheptulonate synthase	jgi	2790	Thalassiosira pseudonana	Biosynthesis	C	53939	6.0	13.2
3-phosphoshikimate 1-carboxyvinyltransferase	jgi	33008	Thalassiosira pseudonana	Transport	S	47333	4.6	5.6
40S ribosomal protein S17	jgi	37809	Thalassiosira pseudonana	Translation	C	14145	10.0	9.8
40S ribosomal protein S5	jgi	29955	Thalassiosira pseudonana	Translation	S	24397	6.9	6.0
40S ribosomal protein S9	jgi	268651	Thalassiosira pseudonana	Binding rRNA	S	21764	10.2	8.9
40S ribosomal protein SA p40	jgi	21871	Thalassiosira pseudonana	Translation	S	27261	5.9	18.9
50S ribosomal protein L11	gi	118411123	Thalassiosira pseudonana	Translation	C	14880	9.7	9.2
50S ribosomal protein L14	gi	118411201	Thalassiosira pseudonana	Translation	C	13433	10.3	27.3
50S ribosomal protein L16	gi	118411198	Thalassiosira pseudonana	Translation	C	15581	11.0	10.2
50S ribosomal protein L2	gi	118411193	Thalassiosira pseudonana	Translation	C	30675	10.9	6.5
50S ribosomal protein L21	gi	118411174	Thalassiosira pseudonana	Binding RNA	C	12433	10.1	8.6
50S ribosomal protein L3	gi	118411190	Thalassiosira pseudonana	Translation	C	22012	10.1	19.3
60 kDa chaperonin	gi	118411188	Thalassiosira pseudonana	Binding Protein	C	57361	5.2	15.6
60s Acidic ribosomal protein	jgi	3463	Thalassiosira pseudonana	Translation	S	27213	4.6	6.1
6-phosphogluconate dehydrogenase	jgi	33343	Thalassiosira pseudonana	Dehydrogenase	S	53348	5.6	10.8
Abnormal wing discs CG2210-PA	jgi	6290	Thalassiosira pseudonana	Biosynthesis	u	17236	5.5	30.3
Acetyl-CoA carboxylase	jgi	6770	Thalassiosira pseudonana	Metabolic Process	c	228295	5.0	2.3
Acidic ribosomal phosphoprotein P0	jgi	25812	Thalassiosira pseudonana	Biosynthesis Ribosome	S	34116	4.8	3.7
Actin A	jgi	25772	Thalassiosira pseudonana	Binding Protein	S	41791	5.0	19.9
Adenosinetriphosphatase	jgi	40156	Thalassiosira pseudonana	Transport Proton	S	39935	7.6	20.2
ALA dehydratase	jgi	5240	Thalassiosira pseudonana	Biosynthesis	S	40419	5.0	7.4
Aminotransferase AGD2	jgi	31394	Thalassiosira pseudonana	Transport	S	44264	4.8	11.5
Arginyl-tRNA synthetase	jgi	40028	Thalassiosira pseudonana	translation	S	66081	4.9	2.7
			Candidatus
ArgJ family protein	gi	71083219	Pelagibacter ubique	Biosynthesis	S	43114	9.5	3.4
Aromatic amino acid family biosynthesis-related protein	jgi	268552	Thalassiosira pseudonana	Biosynthesis	C	66486	5.0	3.8
ATP binding / protein binding	jgi	23102	Thalassiosira pseudonana	Binding Protein	S	59170	5.3	5.3
ATP synthase CF0 B chain subunit I	gi	118411110	Thalassiosira pseudonana	Transport Proton	C	20029	9.8	8.4
ATP synthase CF0 B' chain subunit II	gi	118411109	Thalassiosira pseudonana	Transport Proton	C	17373	4.6	29.5
ATP synthase CF1 alpha chain	gi	118411112	Thalassiosira pseudonana	Transport Ion	C	53989	5.0	35.0
ATP synthase CF1 beta chain	gi	118411134	Thalassiosira pseudonana	Transport Ion	C	51143	4.7	51.1
ATP synthase CF1 delta chain	gi	118411111	Thalassiosira pseudonana	Transport Ion	C	21077	9.2	8.0
ATP/ADP translocator	jgi	39143	Thalassiosira pseudonana	Transport	M	32254	9.4	4.0
ATPase, E1–E2 type	jgi	262679	Thalassiosira pseudonana	Transport Cation	S	99192	5.6	1.5
ATP-dependent clp protease ATP-binding subunit	gi	118411220	Thalassiosira pseudonana	Catalysis	C	102150	6.5	1.5
ATP-sulfurylase	jgi	1326	Thalassiosira pseudonana	Metabolic Process	S	45362	5.2	2.0
BiP	jgi	27656	Thalassiosira pseudonana	Cell Morphogenesis	C	70451	4.7	27.6
Catalytic	jgi	41733	Thalassiosira pseudonana	Biosynthesis	C	71455	5.4	9.3
CbbX protein homolog	jgi	40193	Thalassiosira pseudonana	Biosynthesis	C	35036	5.3	25.1
CDC48/ATPase	jgi	267952	Thalassiosira pseudonana	Binding ATP	S	89464	4.8	4.4
cell division protein FtsH2	jgi	31930	Thalassiosira pseudonana	Binding Zn	C	61956	5.1	11.9
Cell division protein FtsH-like protein	gi	118411141	Thalassiosira pseudonana	Proteolysis	C	70206	5.1	15.9
CG11154-PA, isoform A	jgi	41256	Thalassiosira pseudonana	Transport Proton	U	53388	5.1	50.8
CG17332-PA, isoform A isoform 1	jgi	263135	Thalassiosira pseudonana	Transport Proton	U	33233	5.7	5.4
Chloroplast 1-hydroxy-2-methyl-2-(E)-butenyl-4-diphosphate synthase precursor	jgi	29228	Thalassiosira pseudonana	Biosynthesis	C	75736	4.9	2.6
Chloroplast clp protease P	jgi	1738	Thalassiosira pseudonana	Proteolysis	C	28223	4.8	11.1
Chloroplast coproporphyrinogen III oxidase	jgi	31012	Thalassiosira pseudonana	Biosynthesis	C	34001	5.4	5.7
Chloroplast cysteine synthase 1 precursor	jgi	31829	Thalassiosira pseudonana	Metabolic Process	C	33261	5.1	6.9
Chloroplast light harvesting protein isoform 12	jgi	270092	Thalassiosira pseudonana	Photosynthesis	C	18463	4.6	6.2
Chloroplast light harvesting protein isoform 12	jgi	33606	Thalassiosira pseudonana	Photosynthesis	C	26078	5.5	13.5
Chloroplast light harvesting protein isoform 15	jgi	2845	Thalassiosira pseudonana	Photosynthesis	C	21873	5.1	5.4
Chloroplast O-acetyl-serine lyase	jgi	267987	Thalassiosira pseudonana	Metabolic Process	C	38072	5.7	4.8
Chorismate synthase	jgi	38964	Thalassiosira pseudonana	Biosynthesis	C	44051	5.5	4.9
CPN60 protein	jgi	23329	Thalassiosira pseudonana	Binding Protein	C	59177	4.7	5.6
Cytochrome b559 alpha chain	gi	118411160	Thalassiosira pseudonana	Photosynthesis	C	9514	5.6	25.0
Cytochrome c-550	gi	118411100	Thalassiosira pseudonana	Electron Transport	C	17841	7.7	11.0
Cytochrome f	gi	118411137	Thalassiosira pseudonana	Photosynthesis	C	33988	8.2	28.3
Cytosolic ribosomal protein S8	jgi	29825	Thalassiosira pseudonana	Translation	S	22604	10.5	7.5
D-3-phosphoglycerate dehydrogenase	jgi	25130	Thalassiosira pseudonana	Oxidoreductase	C	50144	6.4	4.3
Diaminopimelate decarboxylase	gi	71083118	Candidatus Pelagibacter ubique	Biosynthesis, amino acid	S	45589	9.9	4.5
DNA binding	jgi	29950	Thalassiosira pseudonana	Binding DNA	C	15300	11.3	8.1
Domain specific binding protein 14-3-3	jgi	26146	Thalassiosira pseudonana	Binding Protein	S	27869	4.6	23.1
Elongation factor 2	jgi	269148	Thalassiosira pseudonana	Translation	S	91887	6.0	4.2
Elongation factor alpha-like protein	jgi	41829	Thalassiosira pseudonana	Translation	S	49969	8.7	10.6
Endoplasmic reticulum membrane fusion protein	jgi	40348	Thalassiosira pseudonana	Transcription	S	74221	4.7	2.4
Enolase	jgi	40771	Thalassiosira pseudonana	Glycolysis	S	46744	4.9	21.1
Enolase 2	jgi	40391	Thalassiosira pseudonana	Glycolysis	S	46547	4.8	21.1
Enoyl-acyl carrier reductase	jgi	32860	Thalassiosira pseudonana	Oxidation Reduction	S	32813	5.1	25.0
ENSANGP00000020417	jgi	354	Thalassiosira pseudonana	Binding, DNA	M	41939	6.9	4.3
Eukaryotic translation initiation factor 4A2 isoform 2	jgi	9716	Thalassiosira pseudonana	Binding DNA	S	42405	5.6	19.5
F0F1 ATP synthase subunit alpha	gi	33862007	Prochlorococcus marinus	Transport Proton	S	54306	4.9	4.6
F0F1 ATP synthase subunit beta	gi	33861994	Prochlorococcus marinus	Transport Proton	S	51948	5.0	13.3
F0F1 ATP synthase subunit beta	gi	71082935	Candidatus Pelagibacter ubique	Transport Proton	S	50696	4.9	9.7
Ferredoxin component	jgi	29842	Thalassiosira pseudonana	Oxidoreductase	C	18511	8.9	6.7
Ferredoxin-dependent glutamate synthase	jgi	269900	Thalassiosira pseudonana	Metabolic Process	C	178531	5.4	5.6
FeS assembly protein SufD	jgi	268364	Thalassiosira pseudonana	Binding Protein	S	31963	5.2	5.8
Formylglycineamide ribotide amidotransferase	jgi	30301	Thalassiosira pseudonana	Catalysis	S	143746	5.0	1.4
Fructose-1,6-bisphosphate aldolase precursor	jgi	428	Thalassiosira pseudonana	Glycolysis Metabolic	S	39810	4.8	19.7
Fructose-bisphosphatase	jgi	264556	Thalassiosira pseudonana	Process Carbohydrate	C	33667	5.3	5.1
Fucoxanthin chlorophyl a/c protein	jgi	38667	Thalassiosira pseudonana	Photosynthesis	C	21807	4.8	17.6
Fucoxanthin chlorophyl a/c protein	jgi	38715	Thalassiosira pseudonana	Photosynthesis	C	20718	4.9	19.3
Fucoxanthin chlorophyll a/c protein	jgi	38494	Thalassiosira pseudonana	Photosynthesis	C	20354	4.5	17.5
Fucoxanthin chlorophyll a/c protein	jgi	42962	Thalassiosira pseudonana	Photosynthesis	C	21515	5.1	18.4
Fucoxanthin chlorophyll a/c binding protein	jgi	12097	Thalassiosira pseudonana	Photosynthesis	C	27330	4.8	8.2
Fucoxanthin chlorophyll a/c binding protein	jgi	264921	Thalassiosira pseudonana	Photosynthesis	c	22205	4.6	8.6
Fucoxanthin chlorophyll a/c binding protein	jgi	268127	Thalassiosira pseudonana	Photosynthesis	C	22628	4.8	17.1
Fucoxan thin-chlorophyll a/c light-harvesting protein	jgi	33018	Thalassiosira pseudonana	Photosynthesis	C	21786	5.4	4.0
G protein beta subunit	jgi	26063	Thalassiosira pseudonana	rRNA Processing	S	35960	6.2	23.0
GDP-mannose dehydratase	jgi	40586	Thalassiosira pseudonana	Catalysis	S	40412	5.9	4.2
Geranyl-geranyl reductase	jgi	10234	Thalassiosira pseudonana	Electron Transport	C	47230	5.9	20.0
Glucose-6-phosphate isomerase	jgi	38266	Thalassiosira pseudonana	Glycolysis	S	61689	5.9	2.7
Glutamate 1-semialdehyde 2,1-aminomutase	jgi	575	Thalassiosira pseudonana	Binding Phosphate	S	43658	5.5	7.1
Glutamine synthetase	jgi	26051	Thalassiosira pseudonana	Biosynthesis	C	45620	5.2	5.8
Glyceraldehyde-3-phosphate dehydrogenase	jgi	28334	Thalassiosira pseudonana	Glycolysis	C	36574	6.1	8.4
Glyceraldehyde-3-phosphate dehydrogenase precursor	jgi	31383	Thalassiosira pseudonana	Glycolysis	S	39587	5.3	29.6
Glycolaldehydetransferase	jgi	21175	Thalassiosira pseudonana	Transport	M	71708	5.0	25.6
Heat shock protein 60	jgi	38191	Thalassiosira pseudonana	Folding Protein	S	58525	4.8	6.8
Heat shock protein 70	jgi	269120	Thalassiosira pseudonana	Folding Protein	S	71187	4.8	10.1
Heat shock protein 83	jgi	268500	Thalassiosira pseudonana	Folding Protein	S	86014	4.6	1.8
Heat shock protein Hsp90	jgi	6285	Thalassiosira pseudonana	Folding Protein	S	80242	4.7	7.5
Histone H2A.1	jgi	19793	Thalassiosira pseudonana	Binding DNA	N	13053	10.4	7.3
Histone H4	jgi	3184	Thalassiosira pseudonana	Binding DNA	N	11384	11.5	41.7
Hsp70-type chaperone	gi	118411189	Thalassiosira pseudonana	Transcription	C	65339	4.8	7.0
HSP90-like protein	jgi	22766	Thalassiosira pseudonana	Folding Protein	S	80966	4.7	2.0
Hypothetical protein	jgi	26224	Thalassiosira pseudonana	n.a.	S	31116	8.9	7.7
Hypothetical protein	jgi	38221	Thalassiosira pseudonana	n.a.	U	14645	5.6	9.3
Hypothetical Protein	jgi	23918	Thalassiosira pseudonana	n.a.	C	31192	4.8	11.3
Hypothetical Protein	jgi	24512	Thalassiosira pseudonana	n.a.	C	41414	6.0	4.8
Hypothetical Protein	jgi	6441	Thalassiosira pseudonana	n.a.	S	26822	5.4	49.8
Hypothetical protein AN1993.2	jgi	31424	Thalassiosira pseudonana	Transport	S	45198	6.2	3.8
Hypothetical protein CBG01077	jgi	22792	Thalassiosira pseudonana	Transport	S	22486	6.7	13.9
Hypothetical protein CBG08717	jgi	269322	Thalassiosira pseudonana	Transport Proton	S	58009	5.8	19.4
Hypothetical protein DDB0218359	jgi	24710	Thalassiosira pseudonana	n.a.	C	46717	4.6	3.8
Hypothetical protein DEHA0F19712g	jgi	27352	Thalassiosira pseudonana	Binding DNA	N	13064	10.3	16.7
Hypothetical protein FG01081.1	jgi	25949	Thalassiosira pseudonana	Translation	U	20124	9.8	7.9
Hypothetical protein LOC496448	jgi	269540	Thalassiosira pseudonana	Binding Protein	S	192707	5.5	0.9
Importin alpha 1	jgi	43097	Thalassiosira pseudonana	Transport Protein	S	60533	4.9	3.2
Inorganic diphosphatase/magnesium ion binding/pyrophosphatase	jgi	269348	Thalassiosira pseudonana	Metabolic Process Phosphate	S	29982	4.8	5.5
Integrin beta 4 binding protein	jgi	29782	Thalassiosira pseudonana	Binding Ribosome	S	27279	5.0	9.4
Isocitrate/isopropylmalate dehydrogenase	jgi	5293	Thalassiosira pseudonana	Oxidoreductase	S	40667	4.6	12.5
Ketol-acid reductoisomerase	jgi	23228	Thalassiosira pseudonana	Oxidation Reduction	C	58240	5.1	8.6
L4/L1	jgi	22610	Thalassiosira pseudonana	Translation	S	40991	10.3	7.7
Magnesium-chelatase subunit I	gi	118411138	Thalassiosira pseudonana	Photosynthesis	C	39500	5.0	6.5
Malate dehydrogenase	jgi	20726	Thalassiosira pseudonana	Oxidoreductase	S	36724	6.3	7.4
Manganese superoxide dismutase	jgi	32874	Thalassiosira pseudonana	Metabolic Process	M	27061	5.5	14.8
Molecular chaperone DnaK	jgi	269240	Thalassiosira pseudonana	Morphogenesis, Cell	S	72207	5.0	2.4
Molecular chaperone DnaK2, heat shock protein hsp70-2	gi	33862260	Prochlorococcus marinus	Folding Protein	S	68202	4.8	2.7
Myo-inositol dehydrogenase precursor	jgi	1049	Thalassiosira pseudonana	Biosynthesis	S	48134	5.0	6.2
Nucleoside diphosphate kinase	jgi	31091	Thalassiosira pseudonana	Biosynthesis	C	16597	5.8	17.2
Nucleoside diphosphate kinase	jgi	12070	Thalassiosira pseudonana	Biosynthesis	C	16917	8.3	18.8
Oxygen-evolving enhancer protein 1 precursor	jgi	34830	Thalassiosira pseudonana	Photosynthesis	C	29136	5.2	27.3
PAaA	jgi	24864	Thalassiosira pseudonana	Transport Proton	S	29661	5.6	5.5
phosphatase 1, catalytic subunit, beta isoform 1	jgi	2538	Thalassiosira pseudonana	hydrolase	S	35512	5.0	4.7
Phosphoadenosine-phosphosulphate reductase	jgi	24887	Thalassiosira pseudonana	Metabolic Process	C	49035	5.0	3.9
Phosphofructokinase	jgi	22213	Thalassiosira pseudonana	Glycolysis	C	43797	5.7	2.7
Phosphoglucomutase, cytoplasmic (Glucose phosphomutase)	jgi	268621	Thalassiosira pseudonana	Binding Mg	S	60470	4.8	2.5
Phosphoglycerate kinase precursor	jgi	35712	Thalassiosira pseudonana	Glycolysis	C	42256	5.0	24.5
Phosphoglycerate mutase 1	jgi	27850	Thalassiosira pseudonana	Glycolysis	C	32465	6.1	4.1
Phosphoribulokinase	jgi	4376	Thalassiosira pseudonana	Biosynthesis	C	42389	4.9	7.2
Phosphoserine transaminase	jgi	3018	Thalassiosira pseudonana	Metabolic Process	C	55763	5.3	2.5
Photosystem I ferredoxin-binding protein	gi	118411153	Thalassiosira pseudonana	Photosynthesis	C	15518	9.6	56.8
Photosystem I protein F	gi	118411168	Thalassiosira pseudonana	Photosynthesis	C	20362	8.9	20.0
Photosystem I protein L	gi	118411163	Thalassiosira pseudonana	Photosynthesis	C	15704	9.3	5.4
Photosystem II 10 kDa phosphoprotein	gi	118411116	Thalassiosira pseudonana	Photosynthesis	C	7388	6.0	21.2
Photosystem II 11 kD protein	jgi	3258	Thalassiosira pseudonana	Photosystem	C	19602	9.6	6.3
Photosystem II chlorophyll A core antenna apoprotein	gi	118411113	Thalassiosira pseudonana	Photosynthesis	C	56408	6.5	14.5
Photosystem II chlorophyll A core antenna apoprotein CP43	gi	118411149	Thalassiosira pseudonana	Photosynthesis	C	51845	7.7	4.7
Photosystem II protein Y	gi	118411171	Thalassiosira pseudonana	Photosynthesis	C	4006	12.5	22.2
Photosystem II reaction center protein D1	gi	118411180	Thalassiosira pseudonana	Photosystem	C	39699	5.3	6.7
Photosystem II reaction center protein D2	gi	118411148	Thalassiosira pseudonana	Photosystem	C	39064	5.6	12.5
Photosystem II stability/assembly factor HCF136	jgi	38769	Thalassiosira pseudonana	Photosystem	C	40327	5.2	32.5
Phytanoyl-CoA dioxygenase	jgi	2770	Thalassiosira pseudonana	Oxygenase	S	33971	6.6	4.4
Phytoene dehydrogenase and related proteins	jgi	10233	Thalassiosira pseudonana	Electron Transport	C	75519	5.6	2.7
Polyprenyl synthetase	jgi	268480	Thalassiosira pseudonana	Biosynthesis	C	36015	4.8	4.1
Proteasomal ATPase	jgi	32037	Thalassiosira pseudonana	Binding DNA	C	45065	8.7	4.7
Protein product unnamed	jgi	37976	Thalassiosira pseudonana	Folding, Protein	U	17068	8.8	6.7
Pyridine nucleotide-disulphide oxidoreductase, class I	jgi	24399	Thalassiosira pseudonana	Electron Transport	S	52509	5.4	4.2
Pyruvate dehydrogenase
E1 component beta subunit	jgi	32983	Thalassiosira pseudonana	Glycolysis	C	37156	5.4	3.5
Pyruvate kinase	jgi	4875	Thalassiosira pseudonana	Glycolysis	C	67221	5.2	4.5
Quinone oxidoreductase	jgi	32955	Thalassiosira pseudonana	Oxidation Reduction	C	32992	5.9	10.9
Ribosomal protein L12e	jgi	39424	Thalassiosira pseudonana	Translation	S	17412	9.1	14.6
Ribosomal protein L14	jgi	39499	Thalassiosira pseudonana	translation	C	14975	10.2	6.7
Ribosomal protein L19	jgi	268372	Thalassiosira pseudonana	Translation	S	21275	11.6	9.2
Ribosomal protein L5	jgi	802	Thalassiosira pseudonana	Translation	C	35283	8.6	3.9
Ribosomal protein PETRP-like	jgi	33241	Thalassiosira pseudonana	Translation	S	17754	10.3	8.1
Ribosomal protein S10	jgi	19501	Thalassiosira pseudonana	Translation	C	11912	9.4	8.7
Ribosomal protein S12	jgi	37628	Thalassiosira pseudonana	Binding RNA	C	12611	6.2	21.7
Ribosomal protein S18	jgi	26893	Thalassiosira pseudonana	Binding RNA	C	17159	10.8	28.8
Ribosomal protein S19	jgi	28425	Thalassiosira pseudonana	Translation	C	16703	9.0	8.8
Ribosomal protein S26e	jgi	20008	Thalassiosira pseudonana	Translation	S	10971	11.0	12.8
Ribosomal protein S3	jgi	28049	Thalassiosira pseudonana	Binding RNA	C	29161	9.3	9.6
Ribosomal protein S9	jgi	40312	Thalassiosira pseudonana	Translation	C	16088	10.2	5.6
Ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit	gi	118411104	Thalassiosira pseudonana	Photosynthesis	C	54325	6.2	35.1
Ribulose-1,5-bisphosphate carboxylase/oxygenase small subunit	gi	118411103	Thalassiosira pseudonana	Photosynthesis	C	15843	5.1	69.8
Rieske iron-sulfur protein precursor	jgi	38231	Thalassiosira pseudonana	Electron Transport	C	19151	5.5	5.0
Rieske iron-sulfur protein precursor	jgi	26131	Thalassiosira pseudonana	Electron Transport	C	19305	5.1	8.8
RsuA	jgi	269764	Thalassiosira pseudonana	Binding RNA	S	36568	6.2	4.0
Rubisco expression protein	gi	118411164	Thalassiosira pseudonana	Photosynthesis	C	32381	5.9	22.3
S-adenosyl methionine synthetase	jgi	21815	Thalassiosira pseudonana	Transport	S	50359	5.2	16.1
S-adenosyl-L-homocysteinas protein	jgi	28496	Thalassiosira pseudonana	Metabolic Process	S	52309	5.1	10.6
S-adenosyl-L-homocysteine hydrolase	gi	71082903	Candidatus Pelagibacter ubique	Metabolism, one carbon	S	47071	5.5	4.0
Structural constituent of ribosome	jgi	26137	Thalassiosira pseudonana	Translation	S	20867	9.8	5.4
Structural constituent of ribosome	jgi	262056	Thalassiosira pseudonana	Translation	S	14755	10.4	9.7
Structural constituent of ribosome	jgi	31084	Thalassiosira pseudonana	Translation	S	13713	9.9	17.4
Transaldolase	jgi	27187	Thalassiosira pseudonana	Metabolic Process Carbohydrate	S	34855	4.8	11.0
Translation elongation factor G	jgi	25629	Thalassiosira pseudonana	Translation	c	86389	5.0	16.6
Translation elongation factor Tu	gi	118411218	Thalassiosira pseudonana	Translation	c	44458	4.9	28.9
Triosephosphate isomerase/glyceraldehyde-3-phosphate dehydrogenase precursor	jgi	28239	Thalassiosira pseudonana	Metabolic Process	S	65308	5.6	4.9
Tubulin alpha-2 chain	jgi	29304	Thalassiosira pseudonana	Structural	S	49904	5.0	8.4
Tubulin beta chain	jgi	8069	Thalassiosira pseudonana	Structural	S	49497	4.9	3.3
Tubulin beta chain	jgi	31569	Thalassiosira pseudonana	Structural	S	49670	4.9	12.6
Ubiquinol-cytochrome-c reductase	jgi	36107	Thalassiosira pseudonana	Oxidoreductase	M	11977	5.4	9.3
Ubiquitin	jgi	40669	Thalassiosira pseudonana	Modification Protein	S	17567	9.9	18.3
Unknown	jgi	10417	Thalassiosira pseudonana	n.a.	S	22939	4.9	6.4
Unknown	jgi	30683	Thalassiosira pseudonana	Metabolic Process	u	26039	6.0	6.3
Unknown	jgi	39424	Thalassiosira pseudonana	Binding GTP	u	20905	6.8	25.6
Vacuolar ATP synthase 16 kDa proteolipid subunit	jgi	2233	Thalassiosira pseudonana	Transport Proton	S	16720	5.6	10.8
Vacuolar ATP synthase subunit A	jgi	37123	Thalassiosira pseudonana	Transport Proton	S	68343	5.0	7.6
Vacuolar ATPase B subunit	jgi	40522	Thalassiosira pseudonana	Transport Proton	S	56064	5.9	16.8
Vacuolar proton-inorganic pyrophosphatase	jgi	39520	Thalassiosira pseudonana	Transport Proton	S	70120	5.0	2.7
Vacuolar sorting receptor homolog	jgi	42545	Thalassiosira pseudonana	Binding Calcium	S	56362	4.9	3.1

50m POC
Protein		Annotation	Species	Function	Comp	MW	pI	SC
ABC transporter	gi	71083646	Candidatus Pelagibacter ubique	Transport	S	25649	6.1	4
Actin A	jgi	25772	Thalassiosira pseudonana	Binding Protein	S	41791	5.0	2.7
Adenosinetriphosphatase	jgi	40156	Thalassiosira pseudonana	Transport Proton	S	39935	7.6	3.5
ATP synthase CF1 alpha chain	gi	118411112	Thalassiosira pseudonana	Transport Ion	C	53989	5.0	4.6
ATP synthase CF1 beta chain	gi	118411134	Thalassiosira pseudonana	Transport Ion	C	51143	4.7	6.1
Cytochrome c-550	gi	118411100	Thalassiosira pseudonana	Electron Transport	C	17841	7.7	11
Fucoxanthin chlorophyll a/c binding protein	jgi	268127	Thalassiosira pseudonana	Photosynthesis	C	22628	4.8	14.8
Glyceraldehyde-3-phosphate dehydrogenase precursor	jgi	31383	Thalassiosira pseudonana	Glycolysis	C	39587	5.3	4
Hypothetical Protein	jgi	23918	Thalassiosira pseudonana	n.a.	S	31192	4.8	3.1
Ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit	gi	118411104	Thalassiosira pseudonana	Photosynthesis	C	54325	6.2	3.9
Tubulin beta chain	jgi	8069	Thalassiosira pseudonana	Structural	S	49497	4.9	2.7

100m POC
Protein		Annotation	Species	Function	Comp	MW	pI	SC
ABC transporter	gi	71083646	Candidatus Pelagibacter ubique	Transport	S	25649	6.1	6.6
Adenosinetriphosphatase	jgi	40156	Thalassiosira pseudonana	Transport Proton	S	39935	7.6	3.5
ATP synthase CF1 alpha chain	gi	118411112	Thalassiosira pseudonana	Transport Ion	C	53989	5.0	5
ATP synthase CF1 beta chain	gi	118411134	Thalassiosira pseudonana	Transport Ion	C	51143	4.7	8.4
CG11154-PA, isoform A	jgi	41256	Thalassiosira pseudonana	Transport Proton	U	53388	5.1	3
DNA binding	jgi	29950	Thalassiosira pseudonana	Binding DNA	C	15300	11.3	13.2
Fucoxanthin chlorophyl a/c protein	jgi	38667	Thalassiosira pseudonana	Photosynthesis	C	21807	4.8	6.8
Fucoxanthin chlorophyll a/c binding protein	jgi	268127	Thalassiosira pseudonana	Photosynthesis	C	22628	4.8	6.2
Glyceraldehyde-3-phosphate dehydrogenase precursor	jgi	31383	Thalassiosira pseudonana	Glycolysis	S	39587	5.3	4
Histone H2A.1	jgi	19793	Thalassiosira pseudonana	Binding DNA	N	13053	10.4	7.3
Histone H4	jgi	3184	Thalassiosira pseudonana	Binding DNA	N	11384	11.5	34
Hypothetical protein DEHA0F19712g	jgi	27352	Thalassiosira pseudonana	Binding DNA	N	13064	10.3	12.5
Photosystem II chlorophyll A core antenna apoprotein	gi	118411113	Thalassiosira pseudonana	Photosynthesis	C	56408	6.5	4.1
Photosystem II reaction center protein D2	gi	118411148	Thalassiosira pseudonana	Photosynthesis	C	39064	5.6	6.3
Protein product unnamed	jgi	27435	Thalassiosira pseudonana	Transcription	U	18469	6.3	7.7
Ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit	gi	118411104	Thalassiosira pseudonana	Photosynthesis	C	54325	6.2	16.3
Spermidine/putrescine-binding periplasmic protein	gi	71084024	Candidatus Pelagibacter ubique	Binding	S	40556	5.0	8.8
TRAP dicarboxylate transporter - DctP subunit	gi	71082971	Candidatus Pelagibacter ubique	Transport	S	42131	9.2	6.2
Tubulin alpha-2 chain	jgi	29304	Thalassiosira pseudonana	Structural	S	49904	5.0	5.3
Tubulin beta chain	jgi	8069	Thalassiosira pseudonana	Structural	S	49497	4.9	12.9
Ubiquitin	jgi	40669	Thalassiosira pseudonana	Modification Protein	S	17567	9.9	8.5
Vacuolar-type H+-pyrophosphatase	jgi	32586	Thalassiosira pseudonana	Transport Proton	S	67969	4.6	1.7

40m Trap
Protein		Annotation	Species	Function	Comp	MW	pI	SC
30S ribosomal protein S1	jgi	15259	Thalassiosira pseudonana	Binding RNA	C	31770	4.6	7.3
30S ribosomal protein S12	gi	118411216	Thalassiosira pseudonana	Translation	C	13914	11.6	6.5
30S ribosomal protein S18	gi	118411132	Thalassiosira pseudonana	Translation	C	8155	10.8	18.1
3-deoxy-7-phosphoheptulonate synthase	jgi	2790	Thalassiosira pseudonana	Biosynthesis	S	53939	6.0	9.9
40S ribosomal protein S5	jgi	29955	Thalassiosira pseudonana	Translation	R	24397	6.9	6
40S ribosomal protein S9	jgi	268651	Thalassiosira pseudonana	Binding rRNA	R	21764	10.2	11.6
40S ribosomal protein SA p40	jgi	21871	Thalassiosira pseudonana	Translation	R	27261	5.9	13.2
50S ribosomal protein L4	gi	118411191	Thalassiosira pseudonana	Translation	C	24203	10.2	7.9
50S ribosomal protein L5	gi	118411203	Thalassiosira pseudonana	Translation	C	27571	9.7	5.9
60 kDa chaperonin	gi	118411188	Thalassiosira pseudonana	Binding Protein	C	57361	5.2	5.3
6-phosphogluconate dehydrogenase	jgi	33343	Thalassiosira pseudonana	Dehydrogenase	S	53348	5.6	8.4
Acidic ribosomal phosphoprotein P0	jgi	25812	Thalassiosira pseudonana	Biosynthesis Ribosome	R	34116	4.8	3.7
Actin A	jgi	25772	Thalassiosira pseudonana	Binding Protein	S	41791	5.0	15.1
Adenosinetriphosphatase	jgi	40156	Thalassiosira pseudonana	Transport Proton	S	39935	7.6	7.4
Aminotransferase AGD2	jgi	31394	Thalassiosira pseudonana	Transport	M	44264	4.8	3.7
Argininosuccinate synthase	jgi	42719	Thalassiosira pseudonana	Biosynthesis	C	45938	5.3	2.9
Aromatic-ring hydroxylase	gi	33861317	Prochlorococcus marinus	Metabolic Process	S	49438	8.9	3.1
ATP binding / protein binding	jgi	23102	Thalassiosira pseudonana	Binding Protein	S	59170	5.3	5.3
ATP synthase CF0 B chain subunit I	gi	118411110	Thalassiosira pseudonana	Transport Proton	C	20029	9.8	16.8
ATP synthase CF0 B' chain subunit II	gi	118411109	Thalassiosira pseudonana	Transport Proton	C	17373	4.6	9.6
ATP synthase CF1 alpha chain	gi	118411112	Thalassiosira pseudonana	Transport Ion	C	53989	5.0	25.8
ATP synthase CF1 beta chain	gi	118411134	Thalassiosira pseudonana	Transport Ion	C	51143	4.7	36.5
ATP/ADP translocator	jgi	39143	Thalassiosira pseudonana	Transport	M	32254	9.4	3.6
ATP-dependent clp protease ATP-binding subunit	gi	118411220	Thalassiosira pseudonana	Catalysis	C	102150	6.5	1.5
ATP-dependent clp protease ATP-binding subunit	gi	33861644	Prochlorococcus marinus	n.a.	S	93370	5.5	2.6
ATP-sulfurylase	jgi	1326	Thalassiosira pseudonana	Metabolic Process	M	45362	5.2	4.9
BiP	jgi	27656	Thalassiosira pseudonana	Cell Morphogenesis	S	70451	4.7	20
CbbX protein homolog	jgi	40193	Thalassiosira pseudonana	Biosynthesis	C	35036	5.3	19.3
CDC48/ATPase	jgi	267952	Thalassiosira pseudonana	Binding ATP	S	89464	4.8	3.2
Cell division protein FtsH2	jgi	31930	Thalassiosira pseudonana	Binding Zn	C	61956	5.1	16
Cell division protein FtsH-like protein	gi	118411141	Thalassiosira pseudonana	Proteolysis	C	70206	5.1	9.8
CG11154-PA, isoform A	jgi	41256	Thalassiosira pseudonana	Transport Proton	U	53388	5.1	29
Chloroplast 1-hydroxy-2-methyl-2-(E)-butenyl-4-diphosphate synthase precursor	jgi	29228	Thalassiosira pseudonana	Biosynthesis	C	75736	4.9	2.6
Chloroplast ferredoxin dependent NADH oxireductase	jgi	25892	Thalassiosira pseudonana	Transport Electron	C	37819	5.9	2.4
Chloroplast light harvesting protein isoform 12	jgi	270092	Thalassiosira pseudonana	Photosynthesis	C	26078	5.5	11.2
Chloroplast light harvesting protein isoform 15	jgi	2845	Thalassiosira pseudonana	Photosynthesis	C	21873	5.1	5.4
Chorismate synthase	jgi	38964	Thalassiosira pseudonana	Biosynthesis	S	44051	5.5	3.2
Cobaltochelatase	jgi	26573	Thalassiosira pseudonana	Biosynthesis	S	148275	4.9	1
CPN60 protein	jgi	23329	Thalassiosira pseudonana	Binding Protein	M	59177	4.7	5.1
Cytochrome b559 alpha chain	gi	118411160	Thalassiosira pseudonana	Photosynthesis	C	9514	5.6	25
Cytochrome c-550	gi	118411100	Thalassiosira pseudonana	Transport Electron	C	17841	7.7	11
Cytochrome f	gi	118411137	Thalassiosira pseudonana	Photosynthesis	C	33988	8.2	19.1
DNA binding	jgi	29950	Thalassiosira pseudonana	Binding DNA	C	15300	11.3	8.1
Domain specific binding protein 14-3-3	jgi	26146	Thalassiosira pseudonana	Binding Protein Domain Specific	S	27869	4.6	7.3
Elongation factor 2	jgi	269148	Thalassiosira pseudonana	Translation	S	91887	6.0	4.2
Enolase 2	jgi	40391	Thalassiosira pseudonana	Glycolysis	S	46547	4.8	3.4
Enoyl-acyl carrier reductase	jgi	32860	Thalassiosira pseudonana	Oxidation Reduction	S	32813	5.1	8
Eukaryotic translation initiation factor 4A2 isoform 2	jgi	9716	Thalassiosira pseudonana	Binding Nucleic Acid	S	42405	5.6	20.6
F0F1 ATP synthase subunit alpha	gi	33862007	Prochlorococcus marinus	Transport Proton	S	54306	4.9	6.7
			Candidatus
F0F1 ATP synthase subunit beta	gi	71082935	Pelagibacter ubique	Transport Proton	S	50696	4.9	16.9
FeS assembly protein SufD	jgi	268364	Thalassiosira pseudonana	Binding Protein	S	31963	5.2	5.8
Fructose-1,6-bisphosphate aldolase precursor	jgi	428	Thalassiosira pseudonana	Glycolysis	S	39810	4.8	7.3
Fructose-bisphosphatase	jgi	264556	Thalassiosira pseudonana	Metabolic Process Carbohydrate	M	33667	5.3	5.1
Fucoxanthin chlorophyl a/c protein	jgi	38667	Thalassiosira pseudonana	Photosynthesis	C	21807	4.8	21.6
Fucoxanthin chlorophyll a /c protein	jgi	38494	Thalassiosira pseudonana	Photosynthesis	C	20354	4.5	18.4
Fucoxanthin chlorophyll a /c protein	jgi	42962	Thalassiosira pseudonana	Photosynthesis	C	21515	5.1	17.5
Fucoxanthin chlorophyll a/c binding protein	jgi	264921	Thalassiosira pseudonana	Photosynthesis	C	21263	5.0	5
Fucoxanthin chlorophyll a/c binding protein	jgi	268127	Thalassiosira pseudonana	Photosynthesis	C	22205	4.6	15.3
Fucoxanthin chlorophyll a/c binding protein	jgi	30385	Thalassiosira pseudonana	Photosynthesis	C	22628	4.8	35.7
GDP-mannose dehydratase	jgi	40586	Thalassiosira pseudonana	Catalysis	S	40412	5.9	3.3
Geranyl-geranyl reductase	jgi	10234	Thalassiosira pseudonana	Transport Electron	C	47230	5.9	7.3
Glucose-6-phosphate isomerase	jgi	38266	Thalassiosira pseudonana	Glycolysis	C	61689	5.9	4.9
Glutamate 1-semialdehyde 2,1-aminomutase	jgi	575	Thalassiosira pseudonana	Binding Phosphate	C	43658	5.5	3.2
Glutamine synthase	jgi	270138	Thalassiosira pseudonana	Biosynthesis	C	69172	5.2	1.8
Glutamine synthetase	jgi	26051	Thalassiosira pseudonana	Biosynthesis	C	45620	5.2	3.4
Glyceraldehyde-3-phosphate dehydrogenase	jgi	28334	Thalassiosira pseudonana	Glycolysis	M	36574	6.1	4.4
Glyceraldehyde-3-phosphate dehydrogenase precursor	jgi	31383	Thalassiosira pseudonana	Glycolysis	S	39587	5.3	27.2
Glycolaldehydetransferase	jgi	21175	Thalassiosira pseudonana	Transport	M	71708	5.0	26.1
Heat shock protein 60	jgi	38191	Thalassiosira pseudonana	Binding Protein	S	58525	4.8	2.9
Heat shock protein 70	jgi	269120	Thalassiosira pseudonana	Folding Protein	S	71187	4.8	16.4
Heat shock protein Hsp90	jgi	6285	Thalassiosira pseudonana	Folding Protein	S	80242	4.7	7.1
Histone H2A.1	jgi	19793	Thalassiosira pseudonana	Binding DNA	N	13053	10.4	7.3
Histone H4	jgi	3184	Thalassiosira pseudonana	Binding DNA	N	11384	11.5	35
Hsp70-type chaperone	gi	118411189	Thalassiosira pseudonana	Transcription	C	65339	4.8	2.3
Hypothetical Protein	jgi	23918	Thalassiosira pseudonana	n.a.	S	31192	4.8	36.5
Hypothetical protein CBG01077	jgi	22792	Thalassiosira pseudonana	Transport	S	22486	6.7	9
Hypothetical protein CBG08717	jgi	269322	Thalassiosira pseudonana	Transport Proton	S	58009	5.8	19.4
Hypothetical protein FG01081.1	jgi	25949	Thalassiosira pseudonana	Translation	U	20124	9.8	7.9
Hypothetical protein Synpcc7942_1497	jgi	4382	Thalassiosira pseudonana	n.a.	S	30101	5.6	5.3
Hypothetical protein UM03322.1	jgi	28443	Thalassiosira pseudonana	Translation	M	24676	10.2	5.1
Isocitrate/isopropylmalate dehydrogenase	jgi	5293	Thalassiosira pseudonana	Oxidoreductase	S	40667	4.6	5.9
Ketol-acid reductoisomerase	jgi	23228	Thalassiosira pseudonana	Oxidation Reduction	S	58240	5.1	7.3
L4/L1	jgi	22610	Thalassiosira pseudonana	Translation	R	40991	10.3	5
Malate dehydrogenase	jgi	20726	Thalassiosira pseudonana	Oxidoreductase	M	36724	6.3	3.4
Mitochondrial glyceraldehyde-3-phosphate dehydrogenase	jgi	28241	Thalassiosira pseudonana	Glycolysis	M	36243	5.9	9.5
Molecular chaperone DnaK2	gi	33862260	Prochlorococcus marinus	Folding Protein	S	68202	4.8	4.9
Myo-inositol dehydrogenase precursor	jgi	1049	Thalassiosira pseudonana	Biosynthesis	S	48134	5.0	4.2
Nitrate reductase	jgi	25299	Thalassiosira pseudonana	Transport Electron	S	101408	5.9	1
Oxidoreductase	jgi	8063	Thalassiosira pseudonana	Metabolic Process	C	36723	7.6	6.2
Oxygen-evolving enhancer protein 1 precursor	jgi	34830	Thalassiosira pseudonana	Photosynthesis	C	29136	5.2	26.2
Phosphoadenosine-phosphosulphate reductase	jgi	24887	Thalassiosira pseudonana	Metabolic Process	C	49035	5.0	3.9
Phosphofructokinase	jgi	22213	Thalassiosira pseudonana	Glycolysis	C	43797	5.7	2.7
Phosphoglycerate kinase precursor	jgi	35712	Thalassiosira pseudonana	Glycolysis	S	42256	5.0	26.8
Phosphoglycerate mutase 1	jgi	27850	Thalassiosira pseudonana	Glycolysis	C	32465	6.1	3.1
Phosphoribosyl-pyrophosphate synthetase	jgi	26109	Thalassiosira pseudonana	Biosynthesis	S	33425	8.4	3.2
Photosystem I ferredoxin-binding protein	gi	118411153	Thalassiosira pseudonana	Photosynthesis	C	15518	9.6	37.4
Photosystem I p700 chlorophyll A apoprotein A	gi	118411096	Thalassiosira pseudonana	Photosynthesis	C	83642	7.3	4.1
Photosystem I protein F	gi	118411168	Thalassiosira pseudonana	Photosynthesis	C	20362	8.9	8.1
Photosystem II 10 kDa phosphoprotein	gi	118411116	Thalassiosira pseudonana	Photosynthesis	C	7388	6.0	21.2
Photosystem II chlorophyll A core antenna apoprotein	gi	118411113	Thalassiosira pseudonana	Photosynthesis	C	56408	6.5	20.2
Photosystem II chlorophyll A core antenna apoprotein CP43	gi	118411149	Thalassiosira pseudonana	Photosynthesis	C	51845	7.7	12.1
Photosystem II PsbD protein D2	gi	33861713	Prochlorococcus marinus	Photosynthesis	C	39917	5.6	6.4
Photosystem II reaction center protein D1	gi	118411180	Thalassiosira pseudonana	Photosystem	C	39699	5.3	6.4
Photosystem II reaction center protein D2	gi	118411148	Thalassiosira pseudonana	Photosystem	C	39064	5.6	12.5
Photosystem II stability/assembly factor HCF136	jgi	38769	Thalassiosira pseudonana	Photosystem	C	40327	5.2	10.5
Protein product unnamed	jgi	262083	Thalassiosira pseudonana	n.a.	S	103903	6.1	2.6
Pyruvate kinase	jgi	40393	Thalassiosira pseudonana	Glycolysis	C	54650	5.9	2.5
Ribosomal protein L12e	jgi	39424	Thalassiosira pseudonana	Translation	R	17412	9.1	14.6
Ribosomal protein S13	jgi	26221	Thalassiosira pseudonana	Translation	C	17054	10.4	8.6
Ribosomal protein S18	jgi	26893	Thalassiosira pseudonana	Binding RNA	C	17159	10.8	27.4
Ribosomal protein S3	jgi	28049	Thalassiosira pseudonana	Binding RNA	C	29161	9.3	8.9
Ribosomal protein S9	jgi	40312	Thalassiosira pseudonana	Translation	C	16088	10.2	7.7
Ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit	gi	118411104	Thalassiosira pseudonana	Photosynthesis	C	54325	6.2	32.2
Ribulose-1,5-bisphosphate carboxylase/oxygenase small subunit	gi	118411103	Thalassiosira pseudonana	Photosynthesis	C	15843	5.1	19.4
RsuA	jgi	269764	Thalassiosira pseudonana	Binding RNA	S	36568	6.2	4
Rubisco expression protein	gi	118411164	Thalassiosira pseudonana	Photosynthesis	C	32381	5.9	4.9
S-adenosyl methionine synthetase	jgi	21815	Thalassiosira pseudonana	Transport	S	50359	5.2	6
S-adenosyl-L-homocysteinas protein	jgi	28496	Thalassiosira pseudonana	Metabolic Process	S	52309	5.1	12.7
			Candidatus
S-adenosyl-L-homocysteine hydrolase	gi	71082903	Pelagibacter ubique	Metabolic Process	S	47071	5.5	4
SDH1-1	jgi	42475	Thalassiosira pseudonana	Transport Electron	M	68963	5.7	2.2
Serine hydroxymethyltransferase	jgi	26031	Thalassiosira pseudonana	Metabolic Process	S	52999	6.5	1.9
Transaldolase	jgi	27187	Thalassiosira pseudonana	Metabolic Process Carbohydrate	S	34855	4.8	12.6
Translation elongation factor 1 alpha	jgi	3858	Thalassiosira pseudonana	Translation	S	47815	7.2	2.5
Translation elongation factor G	jgi	25629	Thalassiosira pseudonana	Translation	S	86389	5.0	9.2
Translation elongation factor Tu	gi	118411218	Thalassiosira pseudonana	Translation	C	44458	4.9	17.8
Tubulin alpha-2 chain	jgi	29304	Thalassiosira pseudonana	Structure	S	49904	5.0	11.9
Tubulin beta chain	jgi	31569	Thalassiosira pseudonana	Structure	S	49497	4.9	18.5
Tubulin beta chain	jgi	8069	Thalassiosira pseudonana	Structure	S	49670	4.9	3.3
Ubiquitin	jgi	40669	Thalassiosira pseudonana	Modification Protein	S	17567	9.9	8.5
Unknown	jgi	10417	Thalassiosira pseudonana	n.a.	S	22939	4.9	17.8
Vacuolar ATP synthase 16 kDa proteolipid subunit	jgi	2233	Thalassiosira pseudonana	Transport Proton	S	16720	5.6	10.8
Vacuolar ATP synthase subunit A	jgi	37123	Thalassiosira pseudonana	Transport Proton	S	68343	5.0	3.5
Vacuolar ATPase B subunit	jgi	40522	Thalassiosira pseudonana	Transport Proton	S	56064	5.9	23.9
Vacuolar proton translocating ATPase A subunit	jgi	40728	Thalassiosira pseudonana	Transport Proton	S	92414	5.3	1.6
Vacuolar-type H+-pyrophosphatase	jgi	32586	Thalassiosira pseudonana	Transport Proton	S	67969	4.6	1.7
Vitamin B6 biosynthesis protein	jgi	42612	Thalassiosira pseudonana	Biosynthesis	S	35430	6.0	9

60m Trap
Protein		Annotation	Species	Function	Comp	MW	pI	SC
30S ribosomal protein S1	jgi	15259	Thalassiosira pseudonana	Translation	R	31770	4.6	3.8
3-deoxy-7-phosphoheptulonate synthase	jgi	2790	Thalassiosira pseudonana	Biosynthesis	C	53939	6.0	4.8
3-phosphoshikimate 1-carboxyvinyltransferase	jgi	33008	Thalassiosira pseudonana	Transport	C	47333	4.6	3.1
6-phosphogluconate dehydrogenase	jgi	33343	Thalassiosira pseudonana	Dehydrogenase	S	53348	5.6	2
Actin A	jgi	25772	Thalassiosira pseudonana	Binding Protein	S	41791	5.0	9
Adenosinetriphosphatase	jgi	40156	Thalassiosira pseudonana	Transport Proton	S	39935	7.6	3.5
Aromatic-ring hydroxylase	gi	33861317	Prochlorococcus marinus	Photosynthesis	S	49438	8.9	3.1
ATP binding / protein binding	jgi	23102	Thalassiosira pseudonana	Binding Protein	S	59170	5.3	5.3
ATP synthase CF1 alpha chain	gi	118411112	Thalassiosira pseudonana	Transport Ion	C	53989	5.0	24.1
ATP synthase CF1 beta chain	gi	118411134	Thalassiosira pseudonana	Transport Ion	C	51143	4.7	38.4
ATP-sulfurylase	jgi	1326	Thalassiosira pseudonana	Metabolic Process	M	45362	5.2	2.9
BiP	jgi	27656	Thalassiosira pseudonana	Cell Morphogenesis	S	70451	4.7	4.5
CbbX protein homolog	jgi	40193	Thalassiosira pseudonana	Biosynthesis	C	35036	5.3	7.1
CG11154-PA, isoformA	jgi	41256	Thalassiosira pseudonana	Transport Proton	S	53388	5.1	33
CPN60 protein	jgi	23329	Thalassiosira pseudonana	Binding Protein	M	59177	4.7	2.9
Enolase 2	jgi	40391	Thalassiosira pseudonana	Glycolysis	S	46547	4.8	5.5
Eukaryotic translation initiation factor 4A2 isoform2	jgi	9716	Thalassiosira pseudonana	Binding DNA	S	42405	5.6	17.6
Fructose-1,6-bisphosphate aldolase precursor	jgi	428	Thalassiosira pseudonana	Glycolysis	S	39810	4.8	12.4
Fructose-bisphosphatase	jgi	264556	Thalassiosira pseudonana	Metabolic Process Carbohydrate	M	33667	5.3	5.1
Fucoxanthin chlorophyl a/c protein	jgi	38667	Thalassiosira pseudonana	Photosynthesis	C	21807	4.8	13.2
Fucoxanthin chlorophyll a /c protein	jgi	38494	Thalassiosira pseudonana	Photosynthesis	C	20354	4.5	13.7
Fucoxanthin chlorophyll a/c binding protein	jgi	264921	Thalassiosira pseudonana	Photosynthesis	C	22205	4.6	8.6
Fucoxanthin chlorophyll a/c binding protein	jgi	268127	Thalassiosira pseudonana	Photosynthesis	C	22628	4.8	27.6
Glutamine synthetase	jgi	26051	Thalassiosira pseudonana	Biosynthesis	C	45620	5.2	3.4
Glyceraldehyde-3-phosphate dehydrogenase	jgi	28334	Thalassiosira pseudonana	Glycolysis	S	36574	6.1	4.4
Glyceraldehyde-3-phosphate dehydrogenase precursor	jgi	31383	Thalassiosira pseudonana	Glycolysis	S	39587	5.3	10.4
Glycolaldehydetransferase	jgi	21175	Thalassiosira pseudonana	Transport	S	71708	5.0	4.4
Heat shock protein 60	jgi	38191	Thalassiosira pseudonana	Folding Protein	S	58525	4.8	5.2
Heat shock protein 70	jgi	269120	Thalassiosira pseudonana	Folding Protein	S	71187	4.8	10.3
Histone H2A.1	jgi	19793	Thalassiosira pseudonana	Binding DNA	N	13053	10.4	7.3
Hypothetical Protein	jgi	23918	Thalassiosira pseudonana	n.a.	S	31192	4.8	9.6
Hypothetical protein CBG08717	jgi	269322	Thalassiosira pseudonana	Transport Proton	S	58009	5.8	12.9
Isocitrate/isopropylmalate dehydrogenase	jgi	5293	Thalassiosira pseudonana	Oxidoreductase	S	40667	4.6	6.4
L4/L1	jgi	22610	Thalassiosira pseudonana	Translation	R	40991	10.3	4.2
Magnesium-chelatase subunit I	gi	118411138	Thalassiosira pseudonana	Photosynthesis	C	39500	5.0	5.1
Mitochondrial glyceraldehyde-3-phosphate dehydrogenase	jgi	28241	Thalassiosira pseudonana	Glycolysis	M	36243	5.9	6.2
Phosphoadenosine-phosphosulphate reductase	jgi	24887	Thalassiosira pseudonana	Metabolic Process	C	49035	5.0	3.9
Phosphoglycerate kinase precursor	jgi	35712	Thalassiosira pseudonana	Glycolysis	S	42256	5.0	15
Photosystem II 10 kDa phosphoprotein	gi	118411116	Thalassiosira pseudonana	Photosynthesis	C	7388	6.0	21.2
Photosystem II chlorophyll A core antenna apoprotein	gi	118411113	Thalassiosira pseudonana	Photosynthesis	C	56408	6.5	5.5
Photosystem II chlorophyll A core antenna apoprotein CP43	gi	118411149	Thalassiosira pseudonana	Photosynthesis	C	51845	7.7	3.4
Photosystem II reaction center protein D2	gi	118411148	Thalassiosira pseudonana	Photosystem	C	39064	5.6	6.3
Photosystem II stability/assembly factor HCF136	jgi	38769	Thalassiosira pseudonana	Photosystem	C	40327	5.2	7.3
Predicted translation elongation factor G	jgi	25629	Thalassiosira pseudonana	Translation	S	86389	5.0	6.6
Putative aminotransferase AGD2	jgi	31394	Thalassiosira pseudonana	Transport	M	44264	4.8	6.6
Putative S-adenosyl-L-homocysteinas protein	jgi	28496	Thalassiosira pseudonana	Metabolic Process	S	52309	5.1	6.2
Ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit	gi	118411104	Thalassiosira pseudonana	Photosynthesis	C	54325	6.2	12.2
Ribulose-1,5-bisphosphate carboxylase/oxygenase small subunit	gi	118411103	Thalassiosira pseudonana	Photosynthesis	C	15843	5.1	10.1
S-adenosyl methionine synthetase	jgi	21815	Thalassiosira pseudonana	Transport	S	50359	5.2	3.2
Transaldolase	jgi	27187	Thalassiosira pseudonana	Metabolic Process Carbohydrate	S	34855	4.8	4.1
Translation elongation factor Tu	gi	118411218	Thalassiosira pseudonana	Translation	C	44458	4.9	3.9
Tubulin alpha-2 chain	jgi	29304	Thalassiosira pseudonana	Structural	S	49904	5.0	2.2
Vacuolar ATPase B subunit	jgi	40522	Thalassiosira pseudonana	Transport Proton	S	56064	5.9	12.8

100m Trap
Protein		Annotation	Species	Function	Comp	MW	pI	SC
30S ribosomal protein S12	gi	118411216	Thalassiosira pseudonana	Translation	C	13914	11.6	6.5
3-deoxy-7-phosphoheptulonate synthase	jgi	2790	Thalassiosira pseudonana	Transport Electron	C	53939	6.0	1.9
40S ribosomal protein S17-like protein	jgi	37809	Thalassiosira pseudonana	Translation	C	14145	10.0	17.1
40S ribosomal protein S6	jgi	269779	Thalassiosira pseudonana	Translation	R	27587	11.0	3.7
40S ribosomal protein SA p40	jgi	21871	Thalassiosira pseudonana	Translation	R	27261	5.9	13.2
50S ribosomal protein L11	gi	118411123	Thalassiosira pseudonana	Translation	C	14880	9.7	9.2
50S ribosomal protein L4	gi	118411191	Thalassiosira pseudonana	Translation	C	24203	10.2	5.1
6-phosphogluconate dehydrogenase	jgi	33343	Thalassiosira pseudonana	Dehydrogenase	S	53348	5.6	6.9
Actin A	jgi	25772	Thalassiosira pseudonana	Binding Protein	S	41791	5.0	11.7
Adenosinetriphosphatase	jgi	40156	Thalassiosira pseudonana	Transport Proton	S	39935	7.6	3.5
Aromatic-ring hydroxylase	gi	33861317	Prochlorococcus marinus	Metabolic Process	S	49438	8.9	3.1
ATP synthase CF1 alpha chain	gi	118411112	Thalassiosira pseudonana	Transport Ion	C	53989	5.0	14.3
ATP synthase CF1 beta chain	gi	118411134	Thalassiosira pseudonana	Transport Ion	C	51143	4.7	14.1
ATPase, E1–E2 type	jgi	262679	Thalassiosira pseudonana	Transport Cation	S	99192	5.6	1.5
ATP-dependent clp protease ATP-binding subunit	gi	118411220	Thalassiosira pseudonana	Catalysis	C	102150	6.5	1.5
BiP	jgi	27656	Thalassiosira pseudonana	Cell Morphogenesis	S	70451	4.7	6.7
Cell division protein FtsH-like protein	gi	118411141	Thalassiosira pseudonana	Proteolysis	C	70206	5.1	1.9
CG11154-PA, isoform A	jgi	41256	Thalassiosira pseudonana	Transport Proton	S	53388	5.1	11.6
Chloroplast ferredoxin dependent NADH oxireductase	jgi	25892	Thalassiosira pseudonana	Transport Electron	C	37819	5.9	4.4
Cyc07-like protein	jgi	26046	Thalassiosira pseudonana	Translation	S	28811	9.6	13.1
Cytochrome b559 alpha chain	gi	118411160	Thalassiosira pseudonana	Photosynthesis	C	9514	5.6	10.7
Cytochrome b6	gi	118411154	Thalassiosira pseudonana	Transport Electron	C	23906	9.2	6
Cytochrome c-550	gi	118411100	Thalassiosira pseudonana	Transport Electron	C	17841	7.7	11
Cytochrome f	gi	118411137	Thalassiosira pseudonana	Photosynthesis	C	33988	8.2	4.1
DNA binding	jgi	29950	Thalassiosira pseudonana	Binding DNA	C	15300	11.3	13.2
Elongation factor alpha-like protein	jgi	41829	Thalassiosira pseudonana	Translation	S	49969	8.7	2.2
Eukaryotic translation initiation factor 4A2 isoform 2	jgi	9716	Thalassiosira pseudonana	Binding Nucleic Acid	S	42405	5.6	6
Fructose-1,6-bisphosphate aldolase precursor	jgi	428	Thalassiosira pseudonana	Glycolysis	S	39810	4.8	3
Fucoxanthin chlorophyll a /c protein	jgi	38494	Thalassiosira pseudonana	Photosynthesis	C	20354	4.5	11.6
Fucoxanthin chlorophyll a/c binding protein	jgi	264921	Thalassiosira pseudonana	Photosynthesis	C	22205	4.6	8.6
Fucoxanthin chlorophyll a/c binding protein	jgi	268127	Thalassiosira pseudonana	Photosynthesis	C	22628	4.8	11
Fucoxanthin-chlorophyll a/c light-harvesting protein	jgi	33018	Thalassiosira pseudonana	Photosynthesis	C	21786	5.4	4.5
GDP-mannose dehydratase	jgi	40586	Thalassiosira pseudonana	Catalysis	S	40412	5.9	3.3
Glutamine synthetase	jgi	26051	Thalassiosira pseudonana	Biosynthesis	C	45620	5.2	5.8
Glyceraldehyde-3-phosphate dehydrogenase	jgi	28334	Thalassiosira pseudonana	Glycolysis	M	36574	6.1	4.4
Glyceraldehyde-3-phosphate dehydrogenase precursor	jgi	31383	Thalassiosira pseudonana	Glycolysis	S	39587	5.3	8.8
Glycolaldehydetransferase	jgi	21175	Thalassiosira pseudonana	Transport	S	71708	5.0	4.4
Heat shock protein 70	jgi	269120	Thalassiosira pseudonana	Folding Protein	S	71187	4.8	2
Heat shock protein Hsp90	jgi	6285	Thalassiosira pseudonana	Folding Protein	S	80242	4.7	2
Histone H2A.1	jgi	19793	Thalassiosira pseudonana	Binding DNA	N	13053	10.4	7.3
Histone H4	jgi	3184	Thalassiosira pseudonana	Binding DNA	N	11384	11.5	30.1
Hypothetical protein	jgi	27167	Thalassiosira pseudonana	n.a.	U	27052	10.0	5.4
Hypothetical Protein	jgi	23918	Thalassiosira pseudonana	n.a.	S	31192	4.8	33.1
Hypothetical protein CBG08717	jgi	269322	Thalassiosira pseudonana	Transport Proton	S	58009	5.8	6.5
hypothetical protein FG01081.1	jgi	25949	Thalassiosira pseudonana	Translation	U	20124	9.8	7.9
Hypothetical proteinUM03322.1	jgi	28443	Thalassiosira pseudonana	Translation	R	24676	10.2	10.6
Inorganic diphosphatase/magnesium ion binding / pyrophosphatase	jgi	269348	Thalassiosira pseudonana	Metabolic Process Phosphate	C	29982	4.8	5.9
Molecular chaperone DnaK2	gi	33862260	Prochlorococcus marinus	Folding Protein	S	68202	4.8	2.5
Nitrate reductase	jgi	25299	Thalassiosira pseudonana	Transport Electron	S	101408	5.9	1
Oxygen-evolving enhancer protein 1 precursor	jgi	34830	Thalassiosira pseudonana	Photosynthesis	C	29136	5.2	8.4
Phosphoglycerate kinase precursor	jgi	35712	Thalassiosira pseudonana	Glycolysis	S	42256	5.0	4.5
Phosphoglycerate mutase 1	jgi	27850	Thalassiosira pseudonana	Glycolysis	S	32465	6.1	3.1
Phosphoribosyl-pyrophosphate synthetase	jgi	26109	Thalassiosira pseudonana	Biosynthesis	S	33425	8.4	3.2
Photosystem I protein PsaD	gi	33862134	Prochlorococcus marinus	Photosynthesis	C	15665	6.4	8.6
Photosystem II 10 kDa phosphoprotein	gi	118411116	Thalassiosira pseudonana	Photosynthesis	C	7388	6.0	21.2
Photosystem II chlorophyll A core antenna apoprotein	gi	118411113	Thalassiosira pseudonana	Photosynthesis	C	56408	6.5	2
Photosystem II chlorophyll A core antenna apoprotein CP43	gi	118411149	Thalassiosira pseudonana	Photosynthesis	C	51845	7.7	8.7
Photosystem II reaction center protein D1	gi	118411180	Thalassiosira pseudonana	Photosystem	C	39699	5.3	6.7
Photosystem II reaction center protein D2	gi	118411148	Thalassiosira pseudonana	Photosystem	C	39064	5.6	3.7
Photosystem II stability/assembly factor HCF136	jgi	38769	Thalassiosira pseudonana	Photosystem	C	40327	5.2	3.8
Predicted translation elongation factor G	jgi	25629	Thalassiosira pseudonana	Translation	S	86389	5.0	3.5
Protein product unnamed	jgi	29007	Thalassiosira pseudonana	Translation	M	18378	10.5	5.6
Putative ribosomal protein L12e	jgi	39424	Thalassiosira pseudonana	Translation	R	17412	9.1	9.1
Putative S-adenosyl-L-homocysteinas protein	jgi	28496	Thalassiosira pseudonana	Metabolic Process	S	52309	5.1	2.5
Pyruvate kinase	jgi	22345	Thalassiosira pseudonana	Glycolysis	C	57892	5.2	3.3
Ribosomal protein S3	jgi	28049	Thalassiosira pseudonana	Binding RNA	C	29161	9.3	13.3
Ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit	gi	118411104	Thalassiosira pseudonana	Photosynthesis	C	54325	6.2	17.3
Ribulose-1,5-bisphosphate carboxylase/oxygenase small subunit	gi	118411103	Thalassiosira pseudonana	Photosynthesis	C	15843	5.1	10.1
RsuA	jgi	269764	Thalassiosira pseudonana	Binding RNA	S	36568	6.2	4
S-adenosyl methionine synthetase	jgi	21815	Thalassiosira pseudonana	Transport	S	50359	5.2	3.2
Transaldolase	jgi	27187	Thalassiosira pseudonana	Metabolic Process Carbohydrate	S	34855	4.8	4.1
Translation elongation factor 1 alpha	jgi	3858	Thalassiosira pseudonana	Translation	S	47815	7.2	2.5
Translation elongation factor Tu	gi	118411218	Thalassiosira pseudonana	Translation	C	44458	4.9	6.1
Triosephosphate isomerase/glyceraldehyde-3-phosphate dehydrogenase precursor	jgi	28239	Thalassiosira pseudonana	Metabolic Process	S	65308	5.6	2.3
Tubulin alpha-2 chain	jgi	29304	Thalassiosira pseudonana	Structure	S	49904	5.0	2.2
Tubulin beta chain	jgi	8069	Thalassiosira pseudonana	Structure	S	49497	4.9	5.6
Ubiquitin	jgi	40669	Thalassiosira pseudonana	Modification Protein	S	17567	9.9	8.5
Vacuolar ATP synthase 16 kDa proteolipid subunit	jgi	2233	Thalassiosira pseudonana	Transport Proton	S	16720	5.6	10.8
Vacuolar ATP synthase subunit A	jgi	37123	Thalassiosira pseudonana	Transport Proton	S	68343	5.0	2.4
Vacuolar ATPase B subunit	jgi	40522	Thalassiosira pseudonana	Transport Proton	S	56064	5.9	3
Vacuolar proton translocating ATPase A subunit, putative	jgi	40728	Thalassiosira pseudonana	Transport Proton	S	92414	5.3	1.6
Vacuolar-type H+-pyrophosphatase	jgi	32586	Thalassiosira pseudonana	Transport Proton	S	67969	4.6	1.7

Post Bloom Shelf Sediment
Protein		Annotation	Species	Function	Comp	MW	pI	SC
3-deoxy-7-phosphoheptulonate synthase	jgi	2790	Thalassiosira pseudonana	Transport Electron	S	53939	6.0	2.5
6-phosphogluconate dehydrogenase	jgi	33343	Thalassiosira pseudonana	Dehydrogenase	S	53348	5.6	4.7
Actin A	jgi	25772	Thalassiosira pseudonana	Binding Protein	S	41791	5.0	9.0
Adenosinetriphosphatase	jgi	40156	Thalassiosira pseudonana	Transport Proton	S	39935	7.6	7.4
ATP synthase CF0 B' chain subunit II	gi	118411109	Thalassiosira pseudonana	Transport Proton	C	17373	4.6	9.0
ATP synthase CF1 alpha chain	gi	118411112	Thalassiosira pseudonana	Transport Ion	C	53989	5.0	10.1
ATP synthase CF1 beta chain	gi	118411134	Thalassiosira pseudonana	Transport Ion	C	51143	4.7	20.5
ATP/ADP translocator	jgi	39143	Thalassiosira pseudonana	Transport	M	32254	9.4	3.6
Cell wall surface anchor family protein	jgi	6962	Thalassiosira pseudonana	Structure	S	75600	9.7	4.9
CG11154-PA, isoform A	jgi	41256	Thalassiosira pseudonana	Transport Proton	U	53388	5.1	8.0
Chloroplast light harvesting protein isoform 15	jgi	2845	Thalassiosira pseudonana	Photosynthesis	C	21873	5.1	5.4
Cytochrome b6	gi	118411154	Thalassiosira pseudonana	Transport Electron	C	23906	9.2	6.0
DNA binding	jgi	29950	Thalassiosira pseudonana	Binding DNA	C	15300	11.3	13.2
DNA-directed RNA polymerase beta prime chain	gi	71083809	Candidatus Pelagibacter ubique	Translation	S	154411	8.8	1.4
Domain specific binding protein 14-3-3	jgi	26146	Thalassiosira pseudonana	Binding Protein Domain Specific	S	27869	4.6	7.3
Eukaryotic translation initiation factor 4A2 isoform2	jgi	9716	Thalassiosira pseudonana	Binding Nucleic Acid	S	42405	5.6	2.7
F0F1 ATP synthase subunit alpha	gi	33862007	Prochlorococcus marinus	Transport Proton	S	54306	4.9	4.6
F0F1 ATP synthase subunit beta	gi	71082935	Candidatus Pelagibacter ubique	Transport Proton	S	50696	4.9	10.0
Fucoxanthin chlorophyl a/c protein	jgi	38667	Thalassiosira pseudonana	Photosynthesis	C	21807	4.8	13.2
Fucoxanthin chlorophyll a /c protein	jgi	42962	Thalassiosira pseudonana	Photosynthesis	C	21515	5.1	6.5
Fucoxanthin chlorophyll a/c binding protein	jgi	268127	Thalassiosira pseudonana	Photosynthesis	C	22628	4.8	12.9
Glyceraldehyde-3-phosphate dehydrogenase precursor	jgi	31383	Thalassiosira pseudonana	Glycolysis	S	39587	5.3	9.1
Heat shock protein Hsp90	jgi	6285	Thalassiosira pseudonana	Folding Protein	S	80242	4.7	4.0
Histone 3	jgi	3183	Thalassiosira pseudonana	Binding DNA	C	15312	11.4	13.2
Histone H2A.1	jgi	19793	Thalassiosira pseudonana	Binding DNA	N	13053	10.4	18.5
Histone H4	jgi	3184	Thalassiosira pseudonana	Binding DNA	N	11384	11.5	42.7
Hypothetical protein CBG01077	jgi	22792	Thalassiosira pseudonana	Transport	S	22486	6.7	10.9
Hypothetical protein CBG08717	jgi	269322	Thalassiosira pseudonana	Transport Proton	U	58009	5.8	9.2
Hypothetical protein DEHA0F19712g	jgi	27352	Thalassiosira pseudonana	Binding DNA	N	13064	10.3	12.5
Hypothetical protein FG01081.1	jgi	25949	Thalassiosira pseudonana	Translation	U	20124	9.8	7.9
Manganese superoxide dismutase	jgi	32874	Thalassiosira pseudonana	Metabolic Process	M	27061	5.5	5.3
Photosystem I p700 chlorophyll A apoprotein A	gi	118411096	Thalassiosira pseudonana	Photosynthesis	C	83642	7.3	3.5
Photosystem I p700 chlorophyll A apoprotein B	gi	118411097	Thalassiosira pseudonana	Photosynthesis	C	82090	7.6	4.5
Photosystem I protein F	gi	118411168	Thalassiosira pseudonana	Photosynthesis	C	20362	8.9	8.1
Photosystem I protein L	gi	118411163	Thalassiosira pseudonana	Photosynthesis	C	15704	9.3	12.2
Photosystem II 10 kDa phosphoprotein	gi	118411116	Thalassiosira pseudonana	Photosynthesis	C	7388	6.0	21.2
Photosystem II chlorophyll A core antenna apoprotein	gi	118411113	Thalassiosira pseudonana	Photosynthesis	C	56408	6.5	18.9
Photosystem II chlorophyll A core antenna apoprotein CP43	gi	118411149	Thalassiosira pseudonana	Photosynthesis	C	51845	7.7	15.9
Photosystem II reaction center protein D1	gi	118411180	Thalassiosira pseudonana	Photosystem	C	39699	5.3	6.4
Photosystem II reaction center protein D2	gi	118411148	Thalassiosira pseudonana	Photosystem	C	39064	5.6	6.3
Rab family GTPase Rab8	jgi	33126	Thalassiosira pseudonana	Transport	S	20382	7.7	12.2
RAB small monomeric GTPase	jgi	35818	Thalassiosira pseudonana	Transport	S	20626	6.6	11.1
Ribosomal protein S18	jgi	26893	Thalassiosira pseudonana	Structure Ribosome	R	17159	10.8	13.7
Ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit	gi	118411104	Thalassiosira pseudonana	Photosynthesis	C	54325	6.2	25.3
S-adenosyl methionine synthetase	jgi	21815	Thalassiosira pseudonana	Transport	S	50359	5.2	3.2
Translation elongation factor 1 alpha	jgi	3858	Thalassiosira pseudonana	Translation	S	47815	7.2	2.5
Tubulin alpha-2 chain	jgi	29304	Thalassiosira pseudonana	Structure	S	49904	5.0	2.9
Tubulin beta chain	jgi	8069	Thalassiosira pseudonana	Structure	S	49497	4.9	11.5
Ubiquitin	jgi	40669	Thalassiosira pseudonana	Modification Protein	S	17567	9.9	22.2
Unknown	jgi	39299	Thalassiosira pseudonana	Binding GTP	U	20905	6.8	25.1
Vacuolar ATP synthase 16 kDa proteolipid subunit	jgi	2233	Thalassiosira pseudonana	Transport Proton	S	16720	5.6	10.8
Vacuolar proton-inorganic pyrophosphatase	jgi	39520	Thalassiosira pseudonana	Transport Proton	S	70120	5.0	2.4

Post Bloom Basin Sediment
Protein		Annotation	Species	Function	Comp	MW	pI	SC
ATP synthase CF1 beta chain	gi	118411134	Thalassiosira pseudonana	Transport Ion	C	51143	4.7	5.3
DNA-directed RNA polymerase subunit gamma	gi	33862040	Prochlorococcus marinus	Translation	S	72335	6.6	1.7
Fucoxanthin chlorophyl a/c protein	jgi	38667	Thalassiosira pseudonana	Photosynthesis	C	21807	4.8	6.8
Fucoxanthin chlorophyll a /c protein	jgi	38494	Thalassiosira pseudonana	Photosynthesis	C	20354	4.5	6.8
Fucoxanthin chlorophyll a/c binding protein	jgi	268127	Thalassiosira pseudonana	Photosynthesis	C	22628	4.8	6.2
Histone H2A.1	jgi	19793	Thalassiosira pseudonana	DNA Binding	N	13053	10.4	7.3
Histone H4	jgi	3184	Thalassiosira pseudonana	DNA Binding	N	11384	11.5	41.7
Hypothetical protein DDB0187116	jgi	25297	Thalassiosira pseudonana	Metabolic Process Lipid	U	369027	6.3	0.9
Intracellular membrane-associated calcium-independent phospholipase A2 gamma	jgi	23984	Thalassiosira pseudonana	Metabolic Process Lipid	S	92973	5.4	2.3
OmpA family protein	gi	71083303	Candidatus Pelagibacter ubique	Membrane	S	17499	9.6	5.7
Oxygen-evolving enhancer protein 1 precursor	jgi	34830	Thalassiosira pseudonana	Photosynthesis	S	29136	5.2	7.6
Photosystem I p700 chlorophyll A apoprotein A	gi	118411096	Thalassiosira pseudonana	Photosynthesis	C	83642	7.3	1.9
Photosystem I p700 chlorophyll A apoprotein B	gi	118411097	Thalassiosira pseudonana	Photosynthesis	C	82090	7.6	3.4
Photosystem II 10 kDa phosphoprotein	gi	118411116	Thalassiosira pseudonana	Photosynthesis	C	7388	6.0	21.2
Photosystem II chlorophyll A core antenna apoprotein	gi	118411113	Thalassiosira pseudonana	Photosynthesis	C	56408	6.5	18.7
Photosystem II chlorophyll A core antenna apoprotein CP43	gi	118411149	Thalassiosira pseudonana	Photosynthesis	C	51845	7.7	9.6
Photosystem II reaction center protein D1	gi	118411180	Thalassiosira pseudonana	Photosystem	C	39699	5.3	3.1
Photosystem II reaction center protein D2	gi	118411148	Thalassiosira pseudonana	Photosystem	C	39064	5.6	13.7
TFIID subunit	jgi	3021	Thalassiosira pseudonana	Transcription	N	55578	6.6	4.4
Transcription termination factor Rho	gi	71083054	Candidatus Pelagibacter ubique	Transcription	S	47060	8.4	2.6
Translation elongation factor 1 alpha	jgi	3858	Thalassiosira pseudonana	Translation	S	47815	7.2	2.5
Tubulin beta chain	jgi	8069	Thalassiosira pseudonana	Structure	U	49497	4.9	2.7
Ubiquitin	jgi	40669	Thalassiosira pseudonana	Modification Protein	S	17567	9.9	11.8
Vacuolar ATP synthase 16 kDa proteolipid subunit	jgi	2233	Thalassiosira pseudonana	Transport Proton	S	16720	5.6	10.8

Over Wintered Shelf Sediment
Protein		Annotation	Species	Function	Comp	MW	pI	SC
Actin A	jgi	25772	Thalassiosira pseudonana	Binding Protein	S	41791	5.0	7.2
ATP synthase CF1 beta chain	gi	118411134	Thalassiosira pseudonana	Transport Ion	C	51143	4.7	8.0
DNA-directed RNA polymerase subunit gamma	gi	33862040	Prochlorococcus marinus	Translation	S	72335	6.6	1.7
Fucoxanthin chlorophyl a/c protein	jgi	38667	Thalassiosira pseudonana	Photosynthesis	C	21807	4.8	6.8
Fucoxanthin chlorophyll a /c protein	jgi	42962	Thalassiosira pseudonana	Photosynthesis	C	21515	5.1	6.5
Fucoxanthin chlorophyll a/c binding protein	jgi	268127	Thalassiosira pseudonana	Photosynthesis	C	22628	4.8	6.2
Heat shock protein 70	jgi	269120	Thalassiosira pseudonana	Folding Protein	S	71187	4.8	4.1
Histone H2A.1	jgi	19793	Thalassiosira pseudonana	Binding DNA	N	13053	10.4	7.3
Histone H4	jgi	3184	Thalassiosira pseudonana	Binding DNA	N	11384	11.5	40.8
Hypothetical protein UM00510.1	jgi	261141	Thalassiosira pseudonana	Binging DNA	S	29752	8.9	4.4
Photosystem I p700 chlorophyll A apoprotein A	gi	118411096	Thalassiosira pseudonana	Photosynthesis	C	83642	7.3	1.9
Photosystem I p700 chlorophyll A apoprotein B	gi	118411097	Thalassiosira pseudonana	Photosynthesis	C	82090	7.6	2.9
Photosystem I protein L	gi	118411163	Thalassiosira pseudonana	Photosynthesis	C	15704	9.3	12.2
Photosystem II 10 kDa phosphoprotein	gi	118411116	Thalassiosira pseudonana	Photosynthesis	C	7388	6.0	21.2
Photosystem II chlorophyll A core antenna apoprotein	gi	118411113	Thalassiosira pseudonana	Photosynthesis	C	56408	6.5	5.9
Photosystem II chlorophyll A core antenna apoprotein CP43	-	118411149	Thalassiosira pseudonana	Photosynthesis	C	51845	7.7	6.4
Photosystem II reaction center protein D1	gi	118411180	Thalassiosira pseudonana	Photosystem	C	39699	5.3	3.1
Photosystem II reaction center protein D2	gi	118411148	Thalassiosira pseudonana	Photosystem	C	39064	5.6	6.3
Ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit	gi	118411104	Thalassiosira pseudonana	Photosynthesis	C	54325	6.2	11.0
Translation elongation factor 1 alpha	jgi	3858	Thalassiosira pseudonana	Translation	S	47815	7.2	2.5
Tubulin beta chain	jgi	8069	Thalassiosira pseudonana	Structure	u	49497	4.9	5.4
Ubiquitin	jgi	40669	Thalassiosira pseudonana	Modification Protein	S	17567	9.9	15.7
Vacuolar ATP synthase 16 kDa proteolipid subunit	jgi	2233	Thalassiosira pseudonana	Transport Proton	S	16720	5.6	10.8

APPENDIX 2

(A) Total hydrolyzable amino acid mole percent distribution of suspended particle, sediment trap, and sediment samples; (B) Tabulated amino acid mole percent distribution of identified proteins; (C) Tabulated amino acid mole percent distribution of identified protein transmembrane regions.

(A)
	Chl Max POC	50m POC	100m POC	40m Trap	60m Trap	100m Trap	PBS	PBB	OWS
Ala	11.11	11.80	12.21	9.11	10.01	9.66	7.67	7.57	7.20
Gly	7.82	13.12	16.11	9.52	10.02	11.37	17.06	16.93	17.17
Val	4.62	4.47	4.01	5.93	6.18	5.65	4.71	4.94	5.18
Leu	6.25	6.41	4.43	7.31	7.66	6.46	3.39	3.44	3.12
Ile	4.04	2.57	1.61	4.53	4.50	3.88	3.68	4.06	3.76
Thr	3.80	2.06	2.77	3.96	3.79	4.03	5.83	5.13	5.43
Pro	5.12	6.07	5.75	4.83	5.19	5.28	4.42	4.78	4.43
Asp/Asn	8.73	6.82	6.50	8.30	7.12	8.50	10.05	10.07	10.30
Phe	3.09	1.77	0.88	3.73	3.13	2.46	1.92	1.89	1.92
Glu/Gln	12.74	4.99	3.75	7.80	5.60	6.49	6.48	5.68	6.94
Lys	4.38	1.80	4.15	3.33	2.53	2.07	2.04	1.94	2.35
Tyr	2.80	4.73	8.68	3.85	4.24	4.16	2.86	0.87	3.00

(B)
	Chl Max POC	50m POC	100m POC	40m Trap	60m Trap	100m Trap	PBS	PBB	OWS
Leu	8.20	8.12	8.28	8.29	7.93	8.12	8.86	9.40	9.22
Gly	8.46	8.65	9.48	8.57	9.02	8.64	8.87	8.60	9.50
Ala	9.26	8.93	10.12	9.22	9.51	8.93	9.32	8.10	8.72
Phe	3.72	4.29	4.73	3.88	3.79	3.93	4.39	4.88	5.38
Ile	6.14	6.19	6.16	6.30	6.32	6.37	6.55	5.96	6.65
Val	7.46	7.36	7.27	7.43	7.69	7.52	6.89	7.00	6.56
Ser	6.31	7.27	5.94	6.06	6.00	6.05	6.52	7.45	5.92
His	1.62	1.82	1.49	1.66	1.43	1.71	1.91	2.49	2.50
Thr	5.76	6.15	6.25	5.77	5.80	5.96	5.73	5.65	5.57
Met	2.78	2.65	2.94	2.84	2.91	2.79	2.71	2.73	2.93
Trp	0.87	1.20	1.12	0.90	0.91	1.01	1.28	1.57	1.93
Tyr	2.80	2.90	3.04	2.81	2.82	2.90	2.94	2.67	2.99
Pro	4.25	4.43	3.95	4.10	4.09	4.22	3.93	4.25	4.48
Cys	1.31	1.29	1.04	1.23	1.22	1.24	1.13	0.97	1.00
Asn	3.97	3.66	3.54	3.85	3.73	3.84	3.56	4.01	4.00
Gln	3.23	3.19	3.62	3.28	3.13	3.18	3.42	3.19	3.30
Arg	4.82	4.81	4.57	4.76	4.68	4.83	4.83	5.24	4.60
Glu	6.93	6.16	5.58	7.05	6.94	6.74	6.11	5.86	5.52
Lys	6.06	5.23	5.38	6.04	5.66	6.13	5.70	4.78	4.47
Asp	6.05	5.72	5.50	5.96	6.42	5.87	5.34	5.18	4.77

(C)
	Chl Max POC	50m POC	100m POC	40m Trap	60m Trap	100m Trap	PBS	PBB	ows
Leu (L)	13.80	14.38	14.33	14.61	14.16	14.16	14.37	14.30	14.56
Gly (G)	12.49	13.05	12.54	12.94	13.48	12.09	12.46	12.33	12.63
Ala (A)	13.42	13.45	15.64	12.71	11.24	12.42	12.06	13.05	12.29
Phe (F)	9.63	9.32	8.79	9.78	10.11	9.62	9.46	10.01	10.02
Ile (I)	10.50	9.72	9.28	10.64	8.76	9.82	9.92	9.56	9.85
Val (V)	9.70	8.92	9.45	8.17	8.99	10.42	8.94	7.77	7.58
Ser (S)	6.28	7.59	7.82	5.92	6.07	5.95	5.89	5.45	5.56
His (H)	1.68	2.66	1.95	3.22	4.27	2.07	4.15	5.90	5.64
Thr (T)	5.10	3.46	4.40	3.68	3.60	4.74	4.21	3.66	3.79
Met (M)	2.80	4.13	4.56	4.08	3.37	4.14	3.75	3.75	3.70
Trp (W)	2.18	2.93	2.61	2.82	4.49	2.40	3.17	4.02	3.87
Tyr (Y)	3.60	3.20	2.28	3.45	3.82	3.54	3.75	3.40	3.54
Pro (P)	2.86	2.26	2.28	2.59	3.15	2.54	2.37	2.06	2.10
Cys (C)	1.93	1.73	1.14	1.61	1.80	1.94	1.62	1.52	1.60
Asn (N)	1.18	0.80	0.81	1.27	0.90	1.14	1.04	1.07	1.01
Gln (Q)	0.87	0.53	0.65	0.92	0.22	1.07	0.75	0.63	0.67
Arg (R)	0.62	0.40	0.33	0.52	0.45	0.67	0.81	0.54	0.59
Glu (E)	0.62	0.53	0.49	0.46	0.45	0.40	0.63	0.36	0.42
Lys (K)	0.37	0.53	0.16	0.40	0.45	0.40	0.40	0.54	0.42
Asp (D)	0.37	0.40	0.49	0.23	0.22	0.47	0.23	0.09	0.17