Computational protocol: Nic1 Inactivation Enables Stable Isotope Labeling with 13C615N4-Arginine in Schizosaccharomyces pombe*

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Protocol publication

[…] The MS data were analyzed with the MaxQuant Software Package version () and searched using the Andromeda peptide search engine (). The MS/MS spectra were searched against a database containing the proteome sequence of the S. pombe downloaded from PomBase (03.01.2013). The database contained 5145 entries from the S. pombe proteome, 248 frequently observed contaminants (downloaded from, as well as the reverse version of all sequences. Mass tolerance was set to 6 ppm at the MS and 0.5 Da at the MS/MS level. A minimal length of seven amino acids and full tryptic enzyme specificity were required. Two enzyme missed cleavages were allowed. Oxidation of methionine and protein N-terminal acetylation were defined as variable modifications and carbamidomethylation of cysteines was used as fixed modification. The false discovery rate was set to 1% on the peptide and protein level. In quantitative measurements, SILAC amino acids Lys4, Lys8, Arg6, and/or Arg10 were defined as fixed modifications. Significantly regulated protein groups were defined as those with calculated “Significance B” lower than 0.01. […]

Pipeline specifications

Software tools MaxQuant, Andromeda
Application MS-based untargeted proteomics
Organisms Schizosaccharomyces pombe
Chemicals Ammonia, Quaternary Ammonium Compounds, Guanidine