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Pipeline publication

[…] al dissociation fragmentation. Lock mass option was enabled to ensure high mass accuracy during many following runs (). The full MS scan range was 300–2000 m/z with resolution of 70,000 and an automatic gain control (AGC) value of 3 × 106 total ion counts with a maximal ion-injection time of 160 ms. MS/MS scans were recorded with a resolution of 17,500, an isolation window of 2 m/z, and an AGC value set to 105 ions with a maximal ion-injection time of 150 ms. Selected ions were excluded in a time frame of 20 s following the fragmentation event. Full-scan data were acquired in profile, and fragments were analyzed in centroid mode by Xcalibur software. The LC unit was controlled by Chromeleon Xpress software., For data analysis, MaxQuant 1.5.3.30 (), Perseus 1.5.4.1 (), and Excel (Microsoft Office 2013) were used. The enzyme specificity was set to trypsin, and missed cleavages were limited to 2. N-terminal acetylation (+42.01) and oxidation of methionine (+15.99) were selected as variable modifications, and carbamidomethylation (+57.02) on cysteines was selected as a fixed modification. The S. cerevisiae reference proteome set (Uniprot, March 2016) was used to identify peptides and proteins with a false discovery rate (FDR) less than 1%. The minimal ratio count for label-free quantification (LFQ) was 1. Reverse identifications and common contaminants were removed, and the data set was reduced to proteins that were identified in at least […]

Pipeline specifications

Software tools XPRESS, MaxQuant, Perseus
Organisms Saccharomyces cerevisiae