Sequence Protein Identification by Randomized Sequence Database and Transcriptome Mass Spectrometry (SPIDER-TMS): From Manual to Automatic Application of a ‘ de Novo Sequencing’ Approach
peer-reviewed · European Journal of Mass Spectrometry · 2016
| Date | 2016-08-01 |
| Type | peer-reviewed |
| Venue | European Journal of Mass Spectrometry |
| Publisher | SAGE Publications |
| Contribution | adjacent |
| DOI | 10.1255/ejms.1434 |
| Citations (OpenAlex) | 2 |
Abstract
Sequence protein identification by a randomized sequence database and transcriptome mass spectrometry software package has been developed at the University of Basilicata in Potenza (Italy) and designed to facilitate the determination of the amino acid sequence of a peptide as well as an unequivocal identification of proteins in a high-throughput manner with enormous advantages of time, economical resource and expertise. The software package is a valid tool for the automation of a de novo sequencing approach, overcoming the main limits and a versatile platform useful in the proteomic field for an unequivocal identification of proteins, starting from tandem mass spectrometry data. The strength of this software is that it is a user-friendly and non-statistical approach, so protein identification can be considered unambiguous.
Methods and tools
- SPIDER-TMS: A software package automating de novo sequencing by matching spectra to a randomized sequence database and transcriptome data for protein identification.
Cites (8)
- De novo sequencing of peptides by MS/MS (2010) crossref
- Peptide Fragment Ion Analyser (PFIA): a simple and versatile tool for the interpretation of tandem mass spectrometric data and de novo sequencing of peptides (2007) crossref
- De Novo Peptide Sequencing and Identification with Precision Mass Spectrometry (2007) crossref
- InsPecT: Identification of Posttranslationally Modified Peptides from Tandem Mass Spectra (2005) crossref
- De novo sequencing, peptide composition analysis, and composition-based sequencing: A new strategy employing accurate mass determination by Fourier transform ion cyclotron resonance mass spectrometry (2004) crossref
- High-Throughput Identification of Proteins and Unanticipated Sequence Modifications Using a Mass-Based Alignment Algorithm for MS/MS de Novo Sequencing Results (2004) crossref
- PEAKS: powerful software for peptide de novo sequencing by tandem mass spectrometry (2003) crossref
- Error-Tolerant Identification of Peptides in Sequence Databases by Peptide Sequence Tags (1994) crossref