MODi : a powerful and convenient web server for identifying multiple post-translational peptide modifications from tandem mass spectra
peer-reviewed · Nucleic Acids Research · 2006
| Date | 2006-07-01 |
| Type | peer-reviewed |
| Venue | Nucleic Acids Research |
| Publisher | Oxford University Press (OUP) |
| Contribution | adjacent |
| DOI | 10.1093/nar/gkl245 |
| Citations (OpenAlex) | 52 |
| Venue 2-year citedness | 16.42 |
Abstract
MOD(i) (http://modi.uos.ac.kr/modi/) is a powerful and convenient web service that facilitates the interpretation of tandem mass spectra for identifying post-translational modifications (PTMs) in a peptide. It is powerful in that it can interpret a tandem mass spectrum even when hundreds of modification types are considered and the number of potential PTMs in a peptide is large, in contrast to most of the methods currently available for spectra interpretation that limit the number of PTM sites and types being used for PTM analysis. For example, using MOD(i), one can consider for analysis both the entire PTM list published on the unimod webpage (http://www.unimod.org) and user-defined PTMs simultaneously, and one can also identify multiple PTM sites in a spectrum. MOD(i) is convenient in that it can take various input file formats such as .mzXML, .dta, .pkl and .mgf files, and it is equipped with a graphical tool called MassPective developed to display MOD(i)’s output in a user-friendly manner and helps users understand MOD(i)’s output quickly. In addition, one can perform manual de novo sequencing using MassPective.
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.
Cites (6)
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- GutenTag: High-Throughput Sequence Tagging via an Empirically Derived Fragmentation Model (2003) semanticscholar
- A Dynamic Programming Approach to De Novo Peptide Sequencing via Tandem Mass Spectrometry (2001) semanticscholar
- Error-Tolerant Identification of Peptides in Sequence Databases by Peptide Sequence Tags (1994) semanticscholar
Cited by (4)
- Open-pNovo: De Novo Peptide Sequencing with Thousands of Protein Modifications (2017) crossref
- Shotgun Protein Sequencing with Meta-contig Assembly (2012) both
- A high-throughput de novo sequencing approach for shotgun proteomics using high-resolution tandem mass spectrometry (2010) both
- Unrestrictive Identification of Multiple Post-translational Modifications from Tandem Mass Spectrometry Using an Error-tolerant Algorithm Based on an Extended Sequence Tag Approach (2008) both