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

► Nine different extraction tools tested on 400,000 CID and HCD tandem MS spectra data generated on an Orbitrap Velos. ► Extraction tools differ with regard to assigned charge states of precursors and fragment ion filtering. ► Higher resolution tandem MS data can benefit from charge state deconvolution of fragment ions. ► Charge state deconvolution of fragment ions is favorable for > 2+ peptides. ► Approx. 20% overlap of matches (p > .0.05) when comparing peak lists generated by 9 different tools.