Unrestrictive Identification of Multiple Post-translational Modifications from Tandem Mass Spectrometry Using an Error-tolerant Algorithm Based on an Extended Sequence Tag Approach

Identification of post-translational modifications (PTMs) is important to understanding the biological functions of proteins. MS/MS is a useful tool to identify PTMs. Most existing search tools are restricted to take only a few types of PTMs as input. Here we describe a new algorithm, called MODi (p...

Full description

Saved in:
Bibliographic Details
Published in:Molecular & cellular proteomics 2008-12, Vol.7 (12), p.2452-2463
Main Authors: Na, Seungjin, Jeong, Jaeho, Park, Heejin, Lee, Kong-Joo, Paek, Eunok
Format: Article
Language:English
Subjects:
Aged, 80 and over
Algorithms
Amino Acid Sequence
Cataract - metabolism
Databases, Protein
Eye Proteins - analysis
Eye Proteins - chemistry
False Positive Reactions
Glyceraldehyde-3-Phosphate Dehydrogenase (Phosphorylating) - chemistry
Humans
Lens, Crystalline - chemistry
Male
Molecular Sequence Data
Peptides - analysis
Peptides - chemistry
Protein Processing, Post-Translational
Regression Analysis
Software
Tandem Mass Spectrometry - methods
Citations: Items that this one cites
Items that cite this one
Online Access:Get full text
Tags: Add Tag
No Tags, Be the first to tag this record!
Description
Summary:Identification of post-translational modifications (PTMs) is important to understanding the biological functions of proteins. MS/MS is a useful tool to identify PTMs. Most existing search tools are restricted to take only a few types of PTMs as input. Here we describe a new algorithm, called MODi (pronounced “mod eye”), that rapidly searches for all known types of PTMs at once without limiting a multitude of modified sites in a peptide. MODi introduces the notion of a tag chain, a combination structure made from multiple sequence tags, that effectively localizes modified regions within a spectrum and overcomes de novo sequencing errors common in tag-based approaches. MODi showed its performance competence by identifying various types of PTMs in analysis of PTM-rich proteins such as glyceraldehyde-3-phosphate dehydrogenase and lens protein. We demonstrated that MODi innovatively manages the computational complexity of identifying multiple PTMs in a peptide, which may exist in a greater variety than usually expected. In addition, it is suggested that MODi has great potential to discover novel modifications.
ISSN:1535-9476
1535-9484
DOI:10.1074/mcp.M800101-MCP200