Large-Scale Reanalysis of Publicly Available HeLa Cell Proteomics Data in the Context of the Human Proteome Project

The practice of data sharing in the proteomics field took off and quickly spread in recent years as a result of collective effort. Nowadays, most journal editors mandate the submission of the original raw mass spectra to one of the databases of the ProteomeXchange consortium. With the exception of large institutional initiatives such as PeptideAtlas or the GPMDB, few new studies are however based on the reanalysis of mass spectrometry data. A wealth of information is thus left unexploited in public databases and repositories. Here, we present the large-scale reanalysis of 41 publicly available data sets corresponding to experiments carried out on the HeLa cancer cell line using a custom workflow. In addition to the search of new post-translational modification sites and “missing proteins”, our main goal is to identify single amino acid variants and evaluate their impact on protein expression and stability through the spectral counting quantification approach. The X!Tandem software was selected to perform ...