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Chromatographic retention time prediction for posttranslationally modified peptides

Luminita Moruz, An Staes UGent, Joseph M Foster, Maria Hatzou, Evy Timmerman UGent, Lennart Martens UGent and Lukas Käll (2012) PROTEOMICS. 12(8). p.1151-1159
abstract
Retention time prediction of peptides in liquid chromatography has proven to be a valuable tool for mass spectrometry-based proteomics, especially in designing more efficient procedures for state-of-the-art targeted workflows. Additionally, accurate retention time predictions can also be used to increase confidence in identifications in shotgun experiments. Despite these obvious benefits, the use of such methods has so far not been extended to (posttranslationally) modified peptides due to the absence of efficient predictors for such peptides. We here therefore describe a new retention time predictor for modified peptides, built on the foundations of our existing Elude algorithm. We evaluated our software by applying it on five types of commonly encountered modifications. Our results show that Elude now yields equally good prediction performances for modified and unmodified peptides, with correlation coefficients between predicted and observed retention times ranging from 0.93 to 0.98 for all the investigated datasets. Furthermore, we show that our predictor handles peptides carrying multiple modifications as well. This latest version of Elude is fully portable to new chromatographic conditions and can readily be applied to other types of posttranslational modifications. Elude is available under the permissive Apache2 open source License at or can be run via a web-interface at .
Please use this url to cite or link to this publication:
author
organization
year
type
journalArticle (original)
publication status
published
subject
keyword
INFORMATION, PROTEOMICS, MS, ELUTION TIMES, PHOSPHOPROTEOME ANALYSIS, PROTEIN IDENTIFICATION, PHASE LIQUID-CHROMATOGRAPHY, FRACTIONAL DIAGONAL CHROMATOGRAPHY, N-TERMINAL PEPTIDES, TANDEM MASS-SPECTROMETRY, Reversed-phase liquid chromatography, Retention time prediction, Machine learning, Posttranslational modification, Bioinformatics
journal title
PROTEOMICS
Proteomics
volume
12
issue
8
pages
1151 - 1159
Web of Science type
Article
Web of Science id
000303918200009
JCR category
BIOCHEMICAL RESEARCH METHODS
JCR impact factor
4.132 (2012)
JCR rank
14/74 (2012)
JCR quartile
1 (2012)
ISSN
1615-9853
DOI
10.1002/pmic.201100386
project
Bioinformatics: from nucleotids to networks (N2N)
language
English
UGent publication?
yes
classification
A1
copyright statement
I have transferred the copyright for this publication to the publisher
id
2953073
handle
http://hdl.handle.net/1854/LU-2953073
date created
2012-07-03 16:09:46
date last changed
2013-04-05 14:30:10
@article{2953073,
  abstract     = {Retention time prediction of peptides in liquid chromatography has proven to be a valuable tool for mass spectrometry-based proteomics, especially in designing more efficient procedures for state-of-the-art targeted workflows. Additionally, accurate retention time predictions can also be used to increase confidence in identifications in shotgun experiments. Despite these obvious benefits, the use of such methods has so far not been extended to (posttranslationally) modified peptides due to the absence of efficient predictors for such peptides. We here therefore describe a new retention time predictor for modified peptides, built on the foundations of our existing Elude algorithm. We evaluated our software by applying it on five types of commonly encountered modifications. Our results show that Elude now yields equally good prediction performances for modified and unmodified peptides, with correlation coefficients between predicted and observed retention times ranging from 0.93 to 0.98 for all the investigated datasets. Furthermore, we show that our predictor handles peptides carrying multiple modifications as well. This latest version of Elude is fully portable to new chromatographic conditions and can readily be applied to other types of posttranslational modifications. Elude is available under the permissive Apache2 open source License at or can be run via a web-interface at .},
  author       = {Moruz, Luminita and Staes, An and Foster, Joseph M and Hatzou, Maria and Timmerman, Evy and Martens, Lennart and K{\"a}ll, Lukas},
  issn         = {1615-9853},
  journal      = {PROTEOMICS},
  keyword      = {INFORMATION,PROTEOMICS,MS,ELUTION TIMES,PHOSPHOPROTEOME ANALYSIS,PROTEIN IDENTIFICATION,PHASE LIQUID-CHROMATOGRAPHY,FRACTIONAL DIAGONAL CHROMATOGRAPHY,N-TERMINAL PEPTIDES,TANDEM MASS-SPECTROMETRY,Reversed-phase liquid chromatography,Retention time prediction,Machine learning,Posttranslational modification,Bioinformatics},
  language     = {eng},
  number       = {8},
  pages        = {1151--1159},
  title        = {Chromatographic retention time prediction for posttranslationally modified peptides},
  url          = {http://dx.doi.org/10.1002/pmic.201100386},
  volume       = {12},
  year         = {2012},
}

Chicago
Moruz, Luminita, An Staes, Joseph M Foster, Maria Hatzou, Evy Timmerman, Lennart Martens, and Lukas Käll. 2012. “Chromatographic Retention Time Prediction for Posttranslationally Modified Peptides.” Proteomics 12 (8): 1151–1159.
APA
Moruz, L., Staes, A., Foster, J. M., Hatzou, M., Timmerman, E., Martens, L., & Käll, L. (2012). Chromatographic retention time prediction for posttranslationally modified peptides. PROTEOMICS, 12(8), 1151–1159.
Vancouver
1.
Moruz L, Staes A, Foster JM, Hatzou M, Timmerman E, Martens L, et al. Chromatographic retention time prediction for posttranslationally modified peptides. PROTEOMICS. 2012;12(8):1151–9.
MLA
Moruz, Luminita, An Staes, Joseph M Foster, et al. “Chromatographic Retention Time Prediction for Posttranslationally Modified Peptides.” PROTEOMICS 12.8 (2012): 1151–1159. Print.