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

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

Publikation: Bidrag til tidsskriftTidsskriftartikelForskningpeer review

Resumé

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/
OriginalsprogEngelsk
TidsskriftBiochemical and Biophysical Research Communications
Vol/bind445
Udgave nummer4
Sider (fra-til)702–707
ISSN0006-291X
DOI
StatusUdgivet - 2014

Fingeraftryk

Tandem Mass Spectrometry
Mass spectrometry
Peptides
Proteins
Plasmas
Hydrogel
Proteome
Blood
Ions
Experiments
Blood Proteins
Visualization
Proteomics
Data Accuracy
Network protocols
Monitoring

Citer dette

Sanmartín, Gerard Such ; Sidoli, Simone ; Ventura-Espejo, Estela ; Jensen, Ole N. / KYSS : Mass spectrometry data quality assessment for protein analysis and large-scale proteomics. I: Biochemical and Biophysical Research Communications. 2014 ; Bind 445, Nr. 4. s. 702–707.
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abstract = "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/",
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KYSS : Mass spectrometry data quality assessment for protein analysis and large-scale proteomics. / Sanmartín, Gerard Such; Sidoli, Simone; Ventura-Espejo, Estela; Jensen, Ole N.

I: Biochemical and Biophysical Research Communications, Bind 445, Nr. 4, 2014, s. 702–707.

Publikation: Bidrag til tidsskriftTidsskriftartikelForskningpeer review

TY - JOUR

T1 - KYSS

T2 - Mass spectrometry data quality assessment for protein analysis and large-scale proteomics

AU - Sanmartín, Gerard Such

AU - Sidoli, Simone

AU - Ventura-Espejo, Estela

AU - Jensen, Ole N

N1 - Copyright © 2014. Published by Elsevier Inc.

PY - 2014

Y1 - 2014

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/

U2 - 10.1016/j.bbrc.2014.01.066

DO - 10.1016/j.bbrc.2014.01.066

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VL - 445

SP - 702

EP - 707

JO - Biochemical and Biophysical Research Communications

JF - Biochemical and Biophysical Research Communications

SN - 0006-291X

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