Introduction

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 http://kyssproject.github.io/.

Publications

  1. KYSS: mass spectrometry data quality assessment for protein analysis and large-scale proteomics.
    Cite this
    Such-Sanmartín G, Sidoli S, Ventura-Espejo E, Jensen ON, 2014-03-01 - Biochemical and biophysical research communications

Credits

  1. Gerard Such-Sanmartín
    Developer

    Department of Biochemistry and Molecular Biology, University of Southern Denmark, Denmark

  2. Simone Sidoli
    Developer

    Department of Biochemistry and Molecular Biology, University of Southern Denmark, Denmark

  3. Estela Ventura-Espejo
    Developer

    Department of Biochemistry and Molecular Biology, University of Southern Denmark, Denmark

  4. Ole N Jensen
    Investigator

    Department of Biochemistry and Molecular Biology, University of Southern Denmark, Denmark

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Summary
AccessionBT006338
Tool TypeApplication
Category
PlatformsLinux/Unix
Technologies
User InterfaceTerminal Command Line
Download Count0
Country/RegionDenmark
Submitted ByOle N Jensen