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棉 花 学 报 Cotton Science 2008，20(4)：281-288
Mass Spectrum Identification and Bioinformatics Analysis in Proteomic Research Abstract：Using ovules of 6 days postanthesis (DPA) of the upland cotton cultivar TM-1 as the control, we compared 2-dimensional electrophoresis gel profiles of the proteins from the fibers at 6, 10, 14, 18, and 22 DPA, and dug one of the differentially expressed spots of NO37 to digest-in-gel with trypsin, and subjected the recovered peptides to AB4700 Proteomics Analyzer for MALDI-TOF/TOF mass spectrometry (MS) analysis. We obtained a peptide mass fingerprint (PMF) of high quality, according to the peak abundance and quality of this PMF, we selected a peptide peak with mass of \{1517.9\} for tandem MS (MS/MS) analysis, and acquired a fragment fingerprint (FFP) in high quality. The PMF was used to search against NCBInr viridiplantae protein database with MASCOT, ProFound, and MS-Fit engines, and against UniProt viridiplantae protein database with Aldente program, respectively, this PMF was also searched against a local Gossypium EST database downloaded from NCBInr with MASCOT in-house version. Furthermore, the MS/MS data were used to search NCBInr viridiplantae protein database with MASCOT in ion search and sequence query mode respectively, followed by manual MS interpretation for de novo sequencing. The protein in No 37 spot was identified as hydroxmethyltransferase. In this paper we focus our discussion on MS analysis and the application of bioinformatic tools, we also provide our comments on the typical PMF alignment tools in proteomics and their searching results.
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