NDLI: Fast multi-blind modification search through tandem mass spectrometry.

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Fast multi-blind modification search through tandem mass spectrometry.

Content Provider	World Health Organization (WHO)-Global Index Medicus
Author	Na, Seungjin Bandeira, Nuno Paek, Eunok
Description	Author Affiliation: Na S ( Division of Computer Science and Engineering, Hanyang University, Seoul 133-791, Korea.)
Abstract	With great biological interest in post-translational modifications (PTMs), various approaches have been introduced to identify PTMs using MS/MS. Recent developments for PTM identification have focused on an unrestrictive approach that searches MS/MS spectra for all known and possibly even unknown types of PTMs at once. However, the resulting expanded search space requires much longer search time and also increases the number of false positives (incorrect identifications) and false negatives (missed true identifications), thus creating a bottleneck in high throughput analysis. Here we introduce MODa, a novel 'multi-blind' spectral alignment algorithm that allows for fast unrestrictive PTM searches with no limitation on the number of modifications per peptide while featuring over an order of magnitude speedup in relation to existing approaches. We demonstrate the sensitivity of MODa on human shotgun proteomics data where it reveals multiple mutations, a wide range of modifications (including glycosylation), and evidence for several putative novel modifications. Based on the reported findings, we argue that the efficiency and sensitivity of MODa make it the first unrestrictive search tool with the potential to fully replace conventional restrictive identification of proteomics mass spectrometry data.
File Format	HTM / HTML
ISSN	15359476
e-ISSN	15359484
DOI	10.1074/mcp.M111.010199
Journal	Molecular & Cellular Proteomics
Issue Number	4
Volume Number	11
Language	English
Publisher	American Society for Biochemistry and Molecular Biology
Publisher Date	2012-04-01
Publisher Place	United States
Access Restriction	Open
Subject Keyword	Discipline Proteomics Algorithms Protein Processing, Post-translational Proteins Metabolism Proteomics Databases, Protein Hek293 Cells Lens, Crystalline Mutation Genetics Proteome Tandem Mass Spectrometry Research Support, N.i.h., Extramural Research Support, Non-u.s. Gov't
Content Type	Text
Resource Type	Article
Subject	Medicine Analytical Chemistry Molecular Biology Biochemistry

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2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
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9	IDR Setup or Support	Queries related to establishment and support of Institutional Digital Repository (IDR) and IDR workshops	idr@ndl.gov.in

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Fast Multi-blind Modification Search through Tandem Mass Spectrometry*

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Fast multi-blind modification search through tandem mass spectrometry.

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