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Protocol publication

[…] Raw data was imported into the Expressionist software (Genedata, San Francisco, CA) and processed as described previously (). The software was used for retention time alignment and peak detection of precursor peptides. A master peak list was generated from all MS/MS events and sent for database searching using Mascot v2.5 (Matrix Sciences) and MSGF+ (Integrative Omics, https://omics.pnl.gov/software/ms-gf). Data was searched against the Saccharomyces cerevisiae (strain ATCC 204508/S288c) protein database as downloaded from UniprotKB (http://www.uniprot.org/), and appended with 125 common laboratory contaminant proteins as well as the mCherry protein sequence (Uniprot accession X5DSL3). Fixed modification was set to carbamidomethylation of cysteines and variable modifications were set to oxidation of methionines and deamidation of N or Q. Search results were then filtered using the PeptideProphet algorithm () to achieve maximum false discovery rate of 1% at the protein level. Peptide identifications were imported back to Expressionist to annotate identified peaks. Quantification of proteins from the peptide data was performed using an in-house script (). Data was normalized based on the total ion current. Protein abundance was obtained by summing the three most intense, unique peptides per protein. A Student’s t-Test, after logarithmic transformation, was used to identify significant differences across the biological replica. If not annotated differently in the figure caption, the analysis was based on the median of three biological repeats. […]

Pipeline specifications

Software tools MS-GF, PeptideProphet
Databases UniProtKB
Application MS-based untargeted proteomics
Organisms Saccharomyces cerevisiae