Computational protocol: Characterization of Mug33 reveals complementary roles for actin cable-dependent transport and exocyst regulators in fission yeast exocytosis

Similar protocols

Protocol publication

[…] As each step was executed, its spectra were recorded to a RAW file and converted into.ms2 format using RawXtract (Version 1.9). Poor quality spectra were removed from the.ms2 dataset using an automated spectral quality assessment algorithm (). Remaining spectra remaining were searched with the SEQUEST algorithm () against the SGD_S.Pombe (October 2006) protein database concatenated to a decoy database in which the sequence for each entry in the original database was reversed (). All searches were parallelized and performed on a Beowulf computer cluster consisting of 100 1.2 GHz Athlon CPUs (). SEQUEST results were assembled and filtered using the DTASelect (version 2.0) program (; ) to dynamically set XCorr and DeltaCN thresholds for the entire dataset to achieve a user-specified false positive rate. The complete list of proteins identified by mass spectrometric analysis following two-step purification of Tea1–TAPS is given in supplementary material Table S1. […]

Pipeline specifications

Software tools RawConverter, Comet, DTASelect
Application MS-based untargeted proteomics
Organisms Schizosaccharomyces pombe, Saccharomyces cerevisiae