Figure 1

Processing label-free proteomics data. Raw data contains peptide and noise peaks, with each peptide presenting as several peaks due to multiply charged ions and the presence of different isotopes (i.e. the presence of one or more ₁₃C). Ideally, all true peptide peaks are found and combined into a single peak per peptide (though different charge states are often left as multiple features). A common peak detection and de-isotoping technique is to repeatedly determine the most intense peak in the dataset, and determine the charge state and isotopic distribution from the frequency and intensity of the neighboring peaks. The LC retention times and elution order of peptides often shift between runs. The process of correcting these distortions to allow accurate matching across runs is called de-warping. De-warping is either performed on raw profile data, or feature data. After de-warping, peptide features are matched across samples.