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. 2007 May 3;5:6. doi: 10.1186/1477-5956-5-6

Table 1.

Proteins identified by LC-MS/MS, showing different expression levels in the different cell lines. Detailed information on peptides/proteins identification is reported in Additional File 2.

Spot # Protein identified Symbol Swiss-Prot pI Theor./Exp.b) MW (kD) Theor./Exp.b) #pept. c) Cov% d) Score e)
46 Programmed cell death 6-interacting protein PDCD6IP Q8WUM4 6.13/6 96/95 15 17 93.9
146 Calreticulin CALR P27797 4.3/4.3 48/60 36 62 187.0
206 Aldehyde dehydrogenase 1A3 a ALDH1A3a P47895 6.9/6.4 56/56 20 25 108.6
207 Aldehyde dehydrogenase 1A3 b ALDH1A3b P47895 6.9/7 56/56 19 28 123
349 Elongation factor Tu TUFM P49411 7.3/7.5 49/46 12 30 64.2
431 3-Hydroxyisobutyl Coenzyme A hydrolase HIBCH Q53GA8 8.4/7.4 43/43 16
463 Glyceraldehyde-3-phosphate dehydrogenase GAPDH P04406 8.6/8 36/37 10 27 57.1
479 Annexin A2 ANXA2 P07355 7.6/8.7 38/37 11 33 81.5
680 Transgelin-2 TAGLN2 P37802 8.4/5.8 22/21 3 19 25.1
744 Fatty acid-binding protein FABP4 P15090 6.8/6 14/14 39 73 145.9
801 Lamin-A/C LMNA P02545 6.6/6.2 74/75 35 41 197.6
841 94 kDa glucose-regulated protein GRP94 P14625 4.7/4.7 92/95 15 18 105.2
906 NADH-ubiquinone oxidoreductase 30 kDa subunit NDUFS3 O75489 6.9/5 30/28 10 46 84.3
912 Triosephosphate isomerase TPI P60174 6.5/6 26/27 12 42 77.1

a) Arbitrary label assigned to the different isoforms.

b) Theor.: theoretical, data-based annotations; Exp.: experimental, from 2-D gels.

c) # pept.: number of valid peptide matches found for the given protein

d) Cov%: the percent ratio of all amino acids from valid peptide matches to the total number of amino acids in the protein.

e) Score: the protein score is a function calculated from the individual normalized z-scores of validated peptides. Peptide z-score refers to the distribution of calculated scores compared to that of random peptide sequences in order to find the mean and variance http://www.phenyx-ms.com. Database redundancy is handled and solved by the Phenyx software. If a protein shares all its validated peptides with another one, it is considered a subset and will not appear in the best-scoring protein list. It appears in the protein Details panel under Subset for the principal and better scoring parameters. Therefore the entries reported (Swiss_Prot AC) refer exclusively to the best-scoring protein found by the search engine.