Data extraction from proteomics raw data: an evaluation of nine tandem MS tools using a large Orbitrap data set

In shot-gun proteomics raw tandem MS data are processed with extraction tools to produce condensed peak lists that can be uploaded to database search engines. Many extraction tools are available but to our knowledge, a systematic comparison of such tools has not yet been carried out. Using raw data containing more than 400,000 tandem MS spectra acquired using an Orbitrap Velos we compared 9 tandem MS extraction tools, freely available as well as commercial. We compared the tools with respect to number of extracted MS/MS events, fragment ion information, number of matches, precursor mass accuracies and agreement in-between tools. Processing a primary data set with 9 different tandem MS extraction tools resulted in a low overlap of identified peptides. The tools differ by assigned charge states of precursors, precursor and fragment ion masses, and we show that peptides identified very confidently using one extraction tool might not be matched when using another tool. We also found a bias towards peptides of lower charge state when extracting fragment ion data from higher resolution raw data without deconvolution. Collecting and comparing the extracted data from the same raw data allow adjusting parameters and expectations and selecting the right tool for extraction of tandem MS data.