A tool to evaluate correspondence between extraction ion chromatographic peaks and peptide-spectrum matches in shotgun proteomics experiments

Ruse, C. I., Peacock, S., Ghiban, C., Rivera, K., Pappin, D. J., Leopold, P. (June 2013) A tool to evaluate correspondence between extraction ion chromatographic peaks and peptide-spectrum matches in shotgun proteomics experiments. Proteomics, 13 (16). pp. 2386-2397. ISSN 1615-9861 (Electronic)1615-9853 (Linking)

URL: http://www.ncbi.nlm.nih.gov/pubmed/23733317
DOI: 10.1002/pmic.201300022

Abstract

Chromatographed peptide signals form the basis of further data processing that eventually results in functional information derived from data-dependent bottom-up proteomics assays. We seek to rank LC/MS parent ions by the quality of their extracted ion chromatograms (ExICs.) Ranked extracted ion chromatograms (RExICs) act as an intuitive physical/chemical preselection filter to improve the quality of MS/MS fragment scans submitted for database search. We identify more than 4,900 proteins when considering detector shifts of less than 7ppm. High quality parent ions for which the database search yields no hits become candidates for subsequent unrestricted analysis for post-translational modifications. Following this rational approach, we prioritize identification of more than 5,000 spectrum matches from modified peptides and confirmed the presence of acetylaldehyde modified His/Lys. We present a logical workflow that scores data-dependent selected ion chromatograms and leverage information about semi-analytical LC/LC dimension prior to mass spectrometry. Our method can be successfully used to identify unexpected modifications in peptides with excellent chromatography characteristics, independent of fragmentation pattern and activation methods. We illustrate analysis of ion chromatograms detected in two different modes by RF linear ion trap and electrostatic field orbitrap. This article is protected by copyright. All rights reserved.

Item Type: Paper
Subjects: bioinformatics > genomics and proteomics
biotechnology > chromatography
CSHL Authors:
Communities: CSHL Cancer Center Program > Signal Transduction
CSHL Cancer Center Shared Resources > Proteomics Service
CSHL labs > Pappin lab
CSHL Cancer Center Shared Resources > Mass Spectrometry Service
Depositing User: Matt Covey
Date: 3 June 2013
Date Deposited: 24 Jun 2013 19:14
Last Modified: 30 Oct 2015 14:43
Related URLs:
URI: http://repository.cshl.edu/id/eprint/28372

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