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.