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Chromatographic retention time prediction for posttranslationally modified peptides

(2012) PROTEOMICS. 12(8). p.1151-1159
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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 .
Keywords
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

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Citation

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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.
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.
Chicago author-date
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.
Chicago author-date (all authors)
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.
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.
IEEE
[1]
L. Moruz et al., “Chromatographic retention time prediction for posttranslationally modified peptides,” PROTEOMICS, vol. 12, no. 8, pp. 1151–1159, 2012.
@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 Käll, Lukas},
  issn         = {1615-9853},
  journal      = {PROTEOMICS},
  keywords     = {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},
}

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