TY - JOUR
T1 - KYSS
T2 - Mass spectrometry data quality assessment for protein analysis and large-scale proteomics
AU - Such-Sanmartín, Gerard
AU - Sidoli, Simone
AU - Ventura-Espejo, Estela
AU - Jensen, Ole N.
N1 - Funding Information:
We thank our colleagues in the Protein Research Group for discussions and comments. Work in the ONJ laboratory was supported by Grants from the Danish Ministry of Science and Innovation .
PY - 2014/3/21
Y1 - 2014/3/21
N2 - 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/.
AB - 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/.
KW - Bioinformatics
KW - Data quality control
KW - Quantitative proteome analysis
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U2 - 10.1016/j.bbrc.2014.01.066
DO - 10.1016/j.bbrc.2014.01.066
M3 - Article
C2 - 24480439
AN - SCOPUS:84897129577
SN - 0006-291X
VL - 445
SP - 702
EP - 707
JO - Biochemical and Biophysical Research Communications
JF - Biochemical and Biophysical Research Communications
IS - 4
ER -