| Training, selection, and robust calibration of retention time models for targeted proteomics. | |
| | |
MedLine Citation:
|
PMID: 20735070 Owner: NLM Status: MEDLINE |
Abstract/OtherAbstract:
|
Accurate predictions of peptide retention times (RT) in liquid chromatography have many applications in mass spectrometry-based proteomics. Most notably such predictions are used to weed out incorrect peptide-spectrum matches, and to design targeted proteomics experiments. In this study, we describe a RT predictor, ELUDE, which can be employed in both applications. ELUDE's predictions are based on 60 features derived from the peptide's amino acid composition and optimally combined using kernel regression. When sufficient data is available, ELUDE derives a retention time index for the condition at hand making it fully portable to new chromatographic conditions. In cases when little training data is available, as often is the case in targeted proteomics experiments, ELUDE selects and calibrates a model from a library of pretrained predictors. Both model selection and calibration are carried out via robust statistical methods and thus ELUDE can handle situations where the calibration data contains erroneous data points. We benchmarked our method against two state-of-the-art predictors and showed that ELUDE outperforms these methods and tracked up to 34% more peptides in a theoretical SRM method creation experiment. ELUDE is freely available under Apache License from http://per-colator.com. |
| | |
Authors:
|
Luminita Moruz; Daniela Tomazela; Lukas Käll |
Publication Detail:
|
Type: Journal Article; Research Support, Non-U.S. Gov't |
Journal Detail:
|
Title: Journal of proteome research Volume: 9 ISSN: 1535-3907 ISO Abbreviation: J. Proteome Res. Publication Date: 2010 Oct |
Date Detail:
|
Created Date: 2010-10-04 Completed Date: 2010-10-29 Revised Date: - |
Medline Journal Info:
|
Nlm Unique ID: 101128775 Medline TA: J Proteome Res Country: United States |
Other Details:
|
Languages: eng Pagination: 5209-16 Citation Subset: IM |
Affiliation:
|
Center for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden. |
Export Citation:
|
APA/MLA Format Download EndNote Download BibTex |
| MeSH Terms | |
Descriptor/Qualifier:
|
Algorithms Animals Caenorhabditis elegans / metabolism Caenorhabditis elegans Proteins / analysis* Calibration Chromatography, Liquid / methods* Internet Mass Spectrometry / methods* Models, Theoretical Proteomics / methods* Reproducibility of Results Software Time Factors |
| Chemical | |
Reg. No./Substance:
|
0/Caenorhabditis elegans Proteins |
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine
Previous Document: Fabrication of free-standing, electrochemically active, and biocompatible graphene oxide-polyaniline...
Next Document: Defining a stem length-dependent binding mechanism for the cocaine-binding aptamer. A combined NMR a...