KYSS: Mass spectrometry data quality assessment for protein analysis and large-scale proteomics

Gerard Such-Sanmartín, Simone Sidoli, Estela Ventura-Espejo, Ole N. Jensen

Research output: Contribution to journalArticlepeer-review

3 Scopus citations


We introduce the computer tool "Know Your Samples" (KYSS) for assessment and visualisation of large scale proteomics datasets, obtained by mass spectrometry (MS) experiments. KYSS facilitates the evaluation of sample preparation protocols, LC peptide separation, and MS and MS/MS performance by monitoring the number of missed cleavages, precursor ion charge states, number of protein identifications and peptide mass error in experiments. KYSS generates several different protein profiles based on protein abundances, and allows for comparative analysis of multiple experiments. KYSS was adapted for blood plasma proteomics and provides concentrations of identified plasma proteins. We demonstrate the utility of the KYSS tool for MS based proteome analysis of blood plasma and for assessment of hydrogel particles for depletion of abundant proteins in plasma. The KYSS software is open source and is freely available at

Original languageEnglish (US)
Pages (from-to)702-707
Number of pages6
JournalBiochemical and Biophysical Research Communications
Issue number4
StatePublished - Mar 21 2014
Externally publishedYes


  • Bioinformatics
  • Data quality control
  • Quantitative proteome analysis

ASJC Scopus subject areas

  • Biophysics
  • Biochemistry
  • Molecular Biology
  • Cell Biology


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