Reanalysis dataset of JPST000208

Quantitative proteome analyses of colorectal cancer cell lines (metastatis: SW620, non-metastatis: SW480) were carried out using SCX-RP-MS/MS with SILAC labeling(SW480: light-label, SW620: heavy-label).
For this reanalysis, MS Datasets were processed for peak picking with MaxQuant v1.6.2.10, and the generated peak lists were searched against human entries of UniProt/Swiss-Prot release 2018_10 using three search engines: MaxQuant v1.6.2.10, X!Tandem v2015.04.01.1, and Comet 2015.02 rev. 0. The decoy database was generated by reversing sequences from the database. Then, the sum of the total number of matched b/y ions and the total number of amino acids comprising the peptide sequence tag were counted to score the reliability of peptide identification independent of these search engines. Finally, the 1% false discovery rate was controlled by the target-decoy approach with this score.