Computational protocol: Coi1 is a novel assembly factor of the yeast complex III–complex IV supercomplex

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Protocol publication

[…] For data analysis, MaxQuant (), Perseus (), and Excel (Microsoft Office 2013) were used. The enzyme specificity was set to trypsin, and missed cleavages were limited to 2. N-terminal acetylation (+42.01) and oxidation of methionine (+15.99) were selected as variable modifications, and carbamidomethylation (+57.02) on cysteines was selected as a fixed modification. The S. cerevisiae reference proteome set (Uniprot, March 2016) was used to identify peptides and proteins with a false discovery rate (FDR) less than 1%. The minimal ratio count for label-free quantification (LFQ) was 1. Reverse identifications and common contaminants were removed, and the data set was reduced to proteins that were identified in at least four of six samples in one experimental group. LFQ values were normalized to median, and missing values were replaced by random background values. Significantly interacting proteins were determined by permutation-based FDR calculation. Proteins were plotted in a volcano plot, setting threshold for proteins of interest at FDR <0.03. For complexome profiling, intensity-based absolute quantification (IBAQ) values were used to generate abundance profiles of proteins as described in . […]

Pipeline specifications

Software tools MaxQuant, Perseus
Application MS-based untargeted proteomics
Organisms Saccharomyces cerevisiae