Table 1.
SSAT RNA binding proteins identified by Gel-LCMSa
| UniProt accession no. | Description (gene name) | Theoretical mass (Da) | Identified peptide(s) | Protein score |
|---|---|---|---|---|
| Q08211 | ATP-dependent RNA helicase A (DHX9) | 140,869 | AAECNIVVTQPR | 135 |
| YQILPLHSQIPR | ||||
| LQISHEAAACITGLR | ||||
| ELDALDANDELTPLGR | ||||
| AENNSEVGASGYGVPGPTWDR | ||||
| LSMSQLNEK | ||||
| DVVQAYPEVR | ||||
| SSVNCPFSSQDMK | ||||
| QPAIISQLDPVNER | ||||
| P67809 | Nuclease-sensitive element binding protein 1 (YBX1) | 35,903 | GAEAANVTGPGGVPVQGSK | 248 |
| SVGDGETVEFDVVEGEK | ||||
| AADPPAENSSAPEAEQGGAE | ||||
| EDGNEEDKENQGDETQGQQPPQR | ||||
| P19338 | Nucleolin (NCL) | 76,568 | NDLAVVDVR | 231 |
| EVFEDAAEIR | ||||
| GLSEDTTEETLK | ||||
| EAMEDGEIDGNK | ||||
| TGISDVFAK | ||||
| SISLYYTGEK | ||||
| P05455 | Lupus La protein (SSB) | 46,808 | QKLEEDAEMK | 170 |
| FSGDLDDQTCR | ||||
| IIEDQQESLNK | ||||
| LTTDFNVIVEALSK | ||||
| P16989 | DNA binding protein A (CSDA) | 40,066 | AGEAPTENPAPPTQQSSAE | 49 |
| GAEAANVTGPDGVPVEGSR | ||||
| P06733 | Alpha enolase (ENO1) | 47,139 | VNQIGSVTESLQACK | 110 |
Mass spectrum processing was performed using the Mascot Distiller software program (version 2.3.0.0) with search and quantitation toolbox options. The generated deisotoped peak list was submitted to an in-house Mascot 2.2 server for searching against the Swiss-Prot database (version 56.6). Mascot search parameters were set as follows: species, Homo sapiens; enzyme, trypsin with maximal 1 missed cleavage; fixed modification, cysteine carbamidomethylation; variable modification, methionine oxidation; 0.50-Da mass tolerance for precursor peptide ions; and 0.6 Da for MS/MS fragment ions. All peptides matches were filtered using an ion score cutoff of 30. The following two criteria were used to evaluate protein identification: one peptide with ion score of ≥50, two or more peptides with at least one ion score of ≥32 (P < 0.05 threshold) and cumulative Mascot scores of ≥50; for all the proteins with cumulative MOWSE scores of ≥50 and ≤80, the theoretical and experimental gel molecular weights had to be consistent. When these criteria were used to search against a reversed decoy Swiss-Prot database, there was no false-positive match (false discovery < 0.5%).