Unrestrictive Identification of Multiple Post-translational Modifications from Tandem Mass Spectrometry Using an Error-tolerant Algorithm Based on an Extended Sequence Tag Approach
peer-reviewed · Molecular & Cellular Proteomics · 2008
| Date | 2008-12-01 |
| Type | peer-reviewed |
| Venue | Molecular & Cellular Proteomics |
| Publisher | Elsevier BV |
| Contribution | adjacent |
| DOI | 10.1074/mcp.m800101-mcp200 |
| Citations (OpenAlex) | 54 |
| Venue 2-year citedness | 4.69 |
Abstract
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 MOD(i) (pronounced “mod eye”), that rapidly searches for all known types of PTMs at once without limiting a multitude of modified sites in a peptide. MOD(i) 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. MOD(i) 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 MOD(i) 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 MOD(i) has great potential to discover novel modifications.
Methods and tools
- MODi: Error-tolerant search for multiple unrestricted PTMs that chains de novo sequence tags into tag chains to localise modified regions, also offered as a web server.