MS/MS spectra were searched using MaxQuant (v1.5.1.2) and Andromeda as search engine. Acquired data were searched against an UPS database containing all the spiked-in proteins, and the E. coli SwissProt protein database (November 2015 version). Precursor ion mass tolerance was set to 4.5 ppm at the MS1 level and to 0.5 Da at the fragment ion level. Up to three missed cleavages for trypsin were allowed. Oxidation of methionine and protein N-terminal acetylation were considered as variable modifications, whereas carbamidomethylation on cysteines was set as a fixed modification. False discovery rate (FDR) in peptide and protein identification was evaluated by using a decoy database and it was set to a maximum of 1%. All identified peptides were quantified with MaxQuant's LFQ algorithm, with the 'match between runs' option activated using a matching time window of 0.7 min and an alignment time window of 20 min. PSM areas were extracted with the intensity extraction algorithm of MaxQuant. The differential abundance analysis was performed by MSstats (v3.13.5) R package. description.pdf including details for data processing and statistical analysis and R script are available in the ‘methods’ folder.
**Publication : Choi et al. (Under revision) MSstats increases the reproducibility of detecting differentially abundant proteins across tools that process raw mass spectra.
[doi:10.25345/C5014C]
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results attachment job
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Keywords: MassIVE.quant reviewed - Platinum
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