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) | 125 |
| Venue 2-year citedness | 3.48 |
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 (3)
Cited by (6)
- De novo sequencing of proteins by mass spectrometry (2020) both
- 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
- Identification of a novel Plasmopara halstedii elicitor protein combining de novo peptide sequencing algorithms and RACE-PCR (2010) semanticscholar
- Lookup Peaks: A Hybrid of de Novo Sequencing and Database Search for Protein Identification by Tandem Mass Spectrometry (2007) crossref