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. 2010 May 13;9(9):1920–1936. doi: 10.1074/mcp.M900345-MCP200

Table I. Cytoplasmic proteins identified by LC-MS/MS demonstrating ≥2-fold change in abundance in response to IBV infection.

Notes on protein function were obtained from annotations in the UniProt database. ssDNA, single-stranded DNA; dsDNA, double-stranded DNA.

Protein ID Name Ratio Peptides Sequence coverage PEP Function
%
Proteins present in increased abundance in IBV-infected cells
    IPI00299554 KIF14 121.5 13 0.7 0.030844 Essential for cytokinesis
    IPI00910009 cDNA FLJ53554 119.4 15 6.6 0.017233 Unknown
    IPI00152881 Shroom3 21.8 7 0.5 0.021639 Cell morphology
    IPI00289501 VGF 4.4 5 10.4 3.51 × 10−11 Regulation of cell-cell interactions
    IPI00902514 Histone H2A 4.3 3 11.2 0.013631 DNA binding, nucleosome component
    IPI00876941 Caveolin 1 variant 4.1 3 13.4 6.75 × 10−11 A scaffolding protein within caveolar membranes
    IPI00418471 Vimentin 3.6 137 63.7 9.49 × 10−297 Cytoskeleton
    IPI00004669 pp-GaNTase 2 3.4 2 4.4 0.001276 O-Linked glycosylation
    IPI00220739 mPR 3.2 3 14.9 2.37 × 10−17 Progesterone receptor
    IPI00218466 SEC61A1 3.0 2 6 0.001145 Insertion of membrane or secretory proteins into the ER
    IPI00102069 eIF 3 3.0 3 10.2 6.86 × 10−9 Protein synthesis
    IPI00910513 cDNA FLJ78119 3.0 3 4.4 0.004264 Highly similar to Homo sapiens G1 to S phase transition 1
    IPI00855785 Fibronectin 2.9 8 3.7 2.07 × 10−34 Cell adhesion, cell morphology
    IPI00166293 Histone H2B type 3-B 2.9 10 35.7 7.54 × 10−36 DNA binding, nucleosome component
    IPI00296190 C10orf58 2.8 2 10 0.003213 Unknown
    IPI00010951 Epiplakin 2.8 2 3.7 1.51 × 10−21 Cytoskeleton
    IPI00328319 RBBP4 2.7 2 9.4 5.23 × 10−20 Chromatin remodeling
    IPI00019353 Acylglycerol kinase 2.7 2 11.1 0.008944 Lipid kinase
    IPI00232533 eIF 1A 2.6 3 11.8 0.001923 Protein biosynthesis
    IPI00017726 Type II HADH 2.6 2 12.3 0.000319 Mitochondrial tRNA maturation
    IPI00398002 Plectin-1 2.6 216 30.5 0 Structural/regulatory component of cytoskeleton
    IPI00030847 TM9SF3 2.5 3 6.3 7.02 × 10−29 Unknown
    IPI00025831 CYP3A5 2.5 4 8.6 7.24 × 10−28 Oxidation of a variety of compounds
    IPI00013122 p50Cdc37 2.5 2 5.6 8.13 × 10−8 Promotes kinase interaction with the HSP90 complex
    IPI00847322 Superoxide dismutase 2.5 8 42.8 4.65 × 10−60 Removal of oxygen radicals
    IPI00554788 Keratin 2.4 16 21.4 9.04 × 10−84 Filament reorganization
    IPI00642584 KIAA0090 2.4 2 2.9 0.001148 Unknown
    IPI00294840 AIM1 2.3 3 2.7 2.50 × 10−8 Interacts with cytoskeleton
    IPI00024976 hTom22 2.3 3 31 3.03E-06 Import of cytoplasmic mitochondrial proteins
    IPI00759493 cDNA FLJ76284 2.3 2 9 0.004796 Unknown
    IPI00237884 AKAP 250 2.3 3 0.8 2.69 × 10−7 Anchoring protein for protein kinases A and C
    IPI00021695 PMCA1 2.3 3 3.7 9.83 × 10−17 Calcium export
    IPI00465432 Nodal modulator 2 2.2 4 4.3 0.000351 Nodal signaling
    IPI00026970 hSPT16 2.2 5 4.8 6.53 × 10−5 Nucleosome reorganization
    IPI00027175 Sorcin 2.2 2 11.1 0.000415 Calcium ion binding
    IPI00220487 ATP5H 2.2 11 44.1 6.23 × 10−15 ATP synthesis
    IPI00873223 cDNA FLJ56155 2.2 2 4.6 6.81 × 10−12 Nucleotidyltransferase activity
    IPI00020557 LRP 2.1 2 0.6 6.32 × 10−6 Involved in endocytosis, phagocytosis, cell growth
    IPI00003269 κ-Actin 2.1 6 14.1 1.00 × 10−19 Cytoskeleton, cell motility
    IPI00005537 L12mt 2.1 4 18.2 3.92 × 10−9 Mitochondrial ribosome component
    IPI00156689 VAT1 2.1 6 14.8 1.04 × 10−22 Zinc ion binding, oxidoreductase activity
    IPI00017283 IleRS 2.1 5 4.5 0.000219 Isoleucine-tRNA ligase
    IPI00018783 ITPase 2.1 2 19.1 0.000154 Nucleotide metabolism
    IPI00334190 SLP-2 2.1 6 33.7 4.23 × 10−73 Associated with the cytoskeleton
    IPI00008982 P5CS 2.1 4 3 9.05 × 10−19 Proline biosynthesis
    IPI00219097 HMG-2 2.1 2 7.2 0.00367 Binds ssDNA and unwinds dsDNA
    IPI00215719 RPL18 2.1 2 12.8 3.42 × 10−7 Large ribosome subunit
    IPI00386271 SLC25A12 2.1 5 11.1 2.05 × 10−18 Calcium-dependent mitochondrial aspartate and glutamate carrier
    IPI00014424 eEF1A-2 2.1 8 50.5 5.11 × 10−90 Protein biosynthesis
    IPI00010845 CI-23kD 2.1 2 4.3 0.004255 Core subunit of the mitochondrial membrane respiratory chain
    IPI00554481 4F2hc 2.1 4 4.8 2.29 × 10−13 Amino acid transport, required for cell growth
    IPI00015476 ASCT1 2.0 3 4.9 0.001305 Sodium-dependent amino acid transport
    IPI00296337 DNPK1 2.0 18 5.8 1.01 × 10−53 Sensor for DNA damage and functions in DNA repair
    IPI00003925 PDHE1-B 2.0 6 17.3 3.61 × 10−14 Conversion of pyruvate to acetyl-CoA and CO2
    IPI00022793 TP-β 2.0 4 8.6 1.50 × 10−12 Fatty acid oxidation
    IPI00419258 HMG-1 2.0 8 21.9 1.19 × 10−7 Binds ssDNA and unwinds dsDNA
    IPI00029264 Cytochrome c1 2.0 2 8.9 4.24 × 10−6 Mitochondrial respiratory chain
    IPI00299571 PDIA6 2.0 13 20.7 1.72 × 10−65 Catalyzes the rearrangement of disulfide bonds
    IPI00011253 40 S ribosomal protein S3 2.0 15 50.6 1.30 × 10−18 Ribosomal protein
    IPI00029737 LACS 4 2.0 15 23.5 9.19 × 10−33 Synthesis of cellular lipids and degradation via β-oxidation
    IPI00021338 PDC-E2 2.0 5 6.2 0.000723 Catalyzes the conversion of pyruvate to acetyl-CoA and CO2
    IPI00328415 B5R 2.0 5 14.6 2.29 × 10−15 Desaturation and elongation of fatty acids, cholesterol biosynthesis
    IPI00014230 gC1qBP 2.0 3 12.4 2.44 × 10−20 Immune response, complement activation
    IPI00021048 Myoferlin 2.0 12 5.4 2.37 × 10−42 Plasma membrane repair
    IPI00871843 TGM2 2.0 3 4.9 2.12 × 10−8 Catalyzes protein cross-linking, polyamine-protein conjugation
    IPI00513768 ATAD3C 2.0 13 3.9 0.003615 Nucleoside triphosphatase activity
Proteins present in decreased abundance in IBV-infected cells
    IPI00873829 ACAA2 5.2 2 7.8 9.51 × 10−9 Acyltransferase