Table 2. Integral plasma membrane proteins detected by MS and their relative abundance in leaf and root tissue (q-value).
| AGI Code | Name | TAIR Description | MW | TMa | Uniq Peptb | Q-value (SD)c | No. of Specd | GVe |
| Transporters | ||||||||
| AT3G61430 | PIP1;1 | Aquaporin | 30897 | 5 | 1 | 0.60 | 12 | lR |
| AT2G45960 | PIP1;2 | Aquaporin | 30806 | 5 | 1 | 0.34 | 23 | LR |
| AT4G23400 | PIP1;5 | Aquaporin | 30855 | 5 | 1 | 1.00 | 2 | LR |
| AT3G53420 | PIP2;1 | Aquaporin | 30474 | 6 | 2 | 0.30 (0.01) | 151 | Lr |
| AT2G37170 | PIP2;2 | Aquaporin | 30662 | 6 | 3 | 0.73 (0.01) | 96 | lR |
| AT2G37180 | PIP2;3 | Aquaporin | 30638 | 6 | 1 | 1.00 | 2 | lR |
| AT5G60660 | PIP2;4 | Aquaporin | 31217 | 6 | 2 | 1.00 (0.00) | 59 | R |
| AT2G39010 | PIP2;6 | Aquaporin | 31258 | 7 | 2 | 0.00 (0.00) | 13 | L |
| AT4G35100 | PIP2;7 | Aquaporin | 29742 | 5 | 1 | 0.37 | 15 | LR |
| AT3G26520 | TIP1;2 | Aquaporin | 25889 | 7 | 1 | 0.70 | 20 | LR |
| AT1G59870 | ABCG36 | ABC transporter | 165831 | 15 | 3 | 0.16 (0.14) | 14 | Lr |
| AT3G47960 | Oligopeptide transporter, H+ symport | 67778 | 12 | 1 | 0.84 | 23 | L | |
| AT2G18960 | AHA1 | Plasma membrane H+-ATPase | 104614 | 10 | 1 | 0.44 | 1 | LR |
| Membrane trafficking | ||||||||
| AT3G09740 | SYP71* | Syntaxin, Qc-SNARE | 30135 | 1 | 2 | 0.45 (0.04) | 9 | LR |
| ATG09740 | SYP71* | Syntaxin, Qc-SNARE | 30135 | 1 | 2 | 0.73 (0.00) | 7 | LR |
| AT3G09740 | SYP71* | Syntaxin, Qc-SNARE | 30135 | 1 | 2 | 0.00 (0.00) | 4 | LR |
| AT3G11820 | SYP121 | Syntaxin, Qa-SNARE | 38105 | 1 | 2 | 0.39 (0.02) | 6 | LR |
| AT5G08080 | SYP132 | Syntaxin, Qa-SNARE | 34225 | 1 | 3 | 0.57 (0.01) | 7 | lR |
| AT2G20990 | SYT1 | Synaptotagmin | 61933 | 1 | 1 | 0.51 | 4 | LR |
| AT1G61250 | SC3 | Secretory carrier | 32763 | 4 | 2 | 0.49 (0.01) | 6 | LR |
| Cell-wall related proteins | ||||||||
| AT2G04780 | FLA7 | Fasciclin-like arabinogalactan-protein | 26845 | 1 | 1 | 0.53 | 15 | lR |
| AT2G45470 | FLA8 | Fasciclin-like arabinogalactan-protein | 43162 | 1 | 2 | 0.00 (0.00) | 20 | LR |
| AT4G12420 | SKU5 | Cu2+ binding, root tip growth | 65767 | 1 | 2 | 0.30 (0.01) | 6 | LR |
| AT2G44790 | UCC2 | Uclacyanin, blue copper protein | 20512 | 1 | 2 | 1.00 (0.00) | 43 | R |
| AT4G26690 | SHV3 | Glycerophosphoryldiester phosphodiesterase | 82967 | 1 | 1 | 1.00 | 1 | LR |
| AT5G55480 | SVL1 | Glycerophosphoryldiester phosphodiesterase | 84511 | 1 | 2 | 0.47 (0.08) | 2 | lR |
| AT1G66970 | SVL2 | Glycerophosphoryldiester phosphodiesterase | 84192 | 1 | 1 | 0.00 | 8 | L |
| AT3G04010 | O-Glycosyl hydrolase, family 17 | 54482 | 1 | 1 | 0.49 | 5 | R | |
| Signal transduction and stress responses | ||||||||
| AT3G08510 | PLC2 | Phosphoinositide-spec phospholipase C | 66122 | 2 | 10 | 0.42 (0.15) | 53 | Lr |
| AT3G19820 | DWF1 | Brassinosteroid biosynthesis | 65394 | 1 | 2 | 0.70 (0.00) | 4 | lR |
| AT3G48890 | MSBP2 | Progesterone binding protein | 25367 | 1 | 1 | 0.40 | 3 | LR |
| AT5G06320 | NHL3 | Similar to hairpin-induced (tobacco) | 26444 | 1 | 1 | 0.00 | 1 | Lr |
| AT1G30360 | ERD4 | Early responsive to dehydration | 82282 | 11 | 9 | 0.37 (0.03) | 49 | LR |
| AT1G63500 | Protein kinase | 55504 | 1 | 3 | 0.59 (0.11) | 7 | LR | |
| AT3G51330 | Aspartyl protease | 58625 | 1 | 1 | 0.82 | 1 | lR | |
| AT4G04720 | CPK21 | Ca2+-dependant protein kinase | 60199 | 1 | 1 | 0.60 | 3 | Lr |
| AT5G53560 | B5-A | Cytochrome b5 | 15132 | 1 | 2 | 0.51 (0.00) | 12 | lR |
| AT2G37710 | LRK1 | L-Lectin (LEC) RLK | 75779 | 1 | 1 | 1.00 | 6 | Lr |
| AT3G02880 | LRR III (5) RLK | 68167 | 2 | 2 | 0.63 (0.01) | 2 | LR | |
| Unknown | ||||||||
| AT1G58270 | ZW9 | Unknown molecular functions | 45235 | 1 | 1 | 1.00 | 2 | lR |
| AT2G39530 | Unknown molecular functions | 19191 | 3 | 1 | 1.00 | 13 | R | |
| AT4G15610 | Unknown molecular functions | 20796 | 4 | 1 | 0.81 | 12 | lR | |
| AT5G44550 | Unknown molecular functions | 21019 | 4 | 1 | 1.00 | 7 | R | |
Proteins are grouped according to function and all annotation is via the database TAIR.
Predicted transmembrane domains determined by Phobius (Kall et al., 2004).
Number of unique peptides first identified by MS/MS and then detected in reliable 14N/15N spectra used for determination of the q-value for that specific protein. All these spectra have fulfilled all criteria for that specific peptide/protein, including correct position of the protein on the SDS-gel, consistent elution of the peptide in the nano-LC gradient, and correct peptide molecular mass as well as isotopic pattern.
The q-value is a measure of the distribution of the peptide between root and leaf plasma membranes: A q-value of 1 means that the peptide is found in roots only; 0, in leaves only. SD is the standard deviation for the q-value of the protein based on all unique peptides for that specific protein.
Number of MS spectra containing reliable data for the 14N/15N peptide pair(s) used to determine the q-value.
Genevestigator data for mRNA distribution between Arabidopsis leaf rosettes and roots converted to a simple letter code: L, mRNA found in leaves only, R, in roots only; LR, about equally distributed between leaves and roots; Lr, mainly in leaves; lR, mainly in roots.
The three q-values for SYP71 were obtained with two unique peptides found in three neighboring segments of the SDS gel (see text for discussion).