Computational protocol: p38- and MK2-dependent signalling promotes stress-induced centriolar satellite remodelling via 14-3-3-dependent sequestration of CEP131/AZI1

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Protocol publication

[…] Raw data files were analysed using MaxQuant. Parent ion and MS2 spectra were searched against a database containing 88,473 human protein sequences obtained from the UniProtKB released in December 2013 using the Andromeda search engine. Spectra were searched with a mass tolerance of 6 p.p.m. in the MS mode, 20 p.p.m. in the higher-energy C-trap dissociation MS2 mode, strict trypsin specificity and allowing up to three miscleavages. Cysteine carbamidomethylation was searched as a fixed modification, whereas protein N-terminal acetylation, methionine oxidation and phosphorylation of serine, threonine and tyrosine were searched as variable modifications. Site localization probabilities were determined by MaxQuant using the PTM scoring algorithm. The data set was filtered based on posterior error probability to arrive at a false discovery rate of below 1% estimated using a target-decoy approach. […]

Pipeline specifications

Software tools MaxQuant, Andromeda
Databases UniProtKB
Application MS-based untargeted proteomics