Identification of Protein Modifications Using MS/MS de Novo Sequencing and the OpenSea Alignment Algorithm
peer-reviewed · Journal of Proteome Research · 2005
| Date | 2005-04-01 |
| Type | peer-reviewed |
| Venue | Journal of Proteome Research |
| Publisher | American Chemical Society (ACS) |
| Contribution | adjacent |
| DOI | 10.1021/pr049781j |
| Citations (OpenAlex) | 123 |
| Venue 2-year citedness | 3.83 |
Abstract
Algorithms that can robustly identify post-translational protein modifications from mass spectrometry data are needed for data-mining and furthering biological interpretations. In this study, we determined that a mass-based alignment algorithm (OpenSea) for de novo sequencing results could identify post-translationally modified peptides in a high-throughput environment. A complex digest of proteins from human cataractous lens, a tissue containing a high abundance of modified proteins, was analyzed using two-dimensional liquid chromatography, and data was collected on both high and low mass accuracy instruments. The data were analyzed using automated de novo sequencing followed by OpenSea mass-based sequence alignment. A total of 80 modifications were detected, 36 of which were previously unreported in the lens. This demonstrates the potential to identify large numbers of known and previously unknown protein modifications in a given tissue using automated data processing algorithms such as OpenSea.
Methods and tools
- OpenSea: Alignment algorithm using MS/MS de novo sequencing to identify protein modifications.
Cites (6)
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Cited by (12)
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- Mass spectrometry-based protein identification by integrating de novo sequencing with database searching (2013) both
- Shotgun Protein Sequencing with Meta-contig Assembly (2012) both
- Algorithms for the de novo sequencing of peptides from tandem mass spectra (2011) crossref
- Gapped Spectral Dictionaries and Their Applications for Database Searches of Tandem Mass Spectra (2011) both
- Template Proteogenomics: Sequencing Whole Proteins Using an Imperfect Database (2010) both
- Identification of a novel Plasmopara halstedii elicitor protein combining de novo peptide sequencing algorithms and RACE-PCR (2010) semanticscholar
- 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
- A Hybrid Method for Peptide Identification Using Integer Linear Optimization, Local Database Search, and Quadrupole Time-of-Flight or OrbiTrap Tandem Mass Spectrometry (2008) crossref
- A robust algorithm for identification of proteins in a database (2007) crossref
- Protein identification by spectral networks analysis (2007) crossref
- Lookup Peaks: A Hybrid of de Novo Sequencing and Database Search for Protein Identification by Tandem Mass Spectrometry (2007) crossref