CFdb: chromatograms

This upload contains processed chromatogram matrices for 411 CF-MS experiments. Database search and protein quantitation was performed with MaxQuant (version 1.6.5.0), and potential contaminants, reverse hits, and proteins identified only by modified peptides were filtered out. 

Multiple chromatograms are provided for each experiment, corresponding to different protein quantitation strategies. These include iBAQ, MaxLFQ, MS1 intensity, and spectral counts, for label-free datasets, and the isotopologue ratio for SILAC or dimethyl labelling datasets. Each directory also contains a metadata file, which contains further information about each row in the corresponding chromatogram matrices output by MaxQuant.

Chromatograms are also provided for phosphorylation sites detected in a separate MaxQuant search including STY phosphorylation as a variable modification (in the "Phosphorylation" directory). 

Separate chromatograms are provided for raw phosphosite intensities and the ratio between modified and unmodified phosphosite intensities (phosphorylation stoichiometries). For datasets collected with SILAC or dimethyl labelling, isotopologue ratio chromatograms are also provided. For TMT datasets, reporter intensities for phosphosites were not output by MaxQuant, meaning that only aggregate measurements of phosphosite intensity and stoichiometry over all experiments in the TMT plex could be obtained.

In addition to processed chromatograms, which are provided in the "Chromatograms" directory, the upload also contains the raw output files ('proteinGroups.txt' and 'Phospho(STY) sites.txt') from each MaxQuant search. These files are provided within the "Protein groups" directory. 

Complete MaxQuant outputs for each experiment are available from the PRIDE repository (see the manuscript for accession).