Computational protocol: Data detailing the platelet acetyl-lysine proteome

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Protocol publication

[…] Tandem mass spectrometry data was collected using a Thermo Orbitrap Fusion Tribrid Mass Spectrometer configured with an EasySpray NanoSource (Thermo Scientific). Survey scans were performed in the Orbitrap mass analyzer, and data-dependent MS2 scans in the linear ion trap following HCD fragmentation in the instrument׳s ion routing multipole, as detailed . Peptides were identified using Protein Discoverer, version 1.4 (Thermo Scientific), using Sequest HT, a human Swiss-Prot database downloaded in April 2013 containing 20,221 protein entries, static modification of +57.021 for C residues, variable modifications of +15.995 and +42.011 for M and K residues, respectively, parent ion tolerance of +/−10 ppm, fragment ion tolerance of 0.6 Da, monoisotopic masses, and trypsin cleavage (max 2 missed cleavages). Searches used a reversed sequence decoy strategy to control peptide false discovery and identifications were validated by Percolator software . Only peptides with q-values <0.01 were accepted, corresponding to a false discovery rate of below 1%. […]

Pipeline specifications

Software tools Comet, Percolator
Databases UniProt
Application MS-based untargeted proteomics
Organisms Homo sapiens