Peptide de novo sequencing of mixture tandem mass spectra
peer-reviewed · Proteomics · 2016
| Date | 2016-09-01 |
| Type | peer-reviewed |
| Venue | Proteomics |
| Publisher | Wiley |
| Contribution | algorithm |
| DOI | 10.1002/pmic.201500549 |
| Citations (OpenAlex) | 28 |
| Venue 2-year citedness | 2.58 |
Abstract
The impact of mixture spectra deconvolution on the performance of four popular de novo sequencing programs was tested using artificially constructed mixture spectra as well as experimental proteomics data. Mixture fragmentation spectra are recognized as a limitation in proteomics because they decrease the identification performance using database search engines. De novo sequencing approaches are expected to be even more sensitive to the reduction in mass spectrum quality resulting from peptide precursor co-isolation and thus prone to false identifications. The deconvolution approach matched complementary b-, y-ions to each precursor peptide mass, which allowed the creation of virtual spectra containing sequence specific fragment ions of each co-isolated peptide. Deconvolution processing resulted in equally efficient identification rates but increased the absolute number of correctly sequenced peptides. The improvement was in the range of 20-35% additional peptide identifications for a HeLa lysate sample. Some correct sequences were identified only using unprocessed spectra; however, the number of these was lower than those where improvement was obtained by mass spectral deconvolution. Tight candidate peptide score distribution and high sensitivity to small changes in the mass spectrum introduced by the employed deconvolution method could explain some of the missing peptide identifications.
Methods and tools
- Mixture MS/MS de novo: De novo peptide sequencing method for mixture tandem mass spectra.
Cites (25)
- Novor: Real-Time Peptide de Novo Sequencing Software (2015) both
- pNovo+: De Novo Peptide Sequencing Using Complementary HCD and ETD Tandem Mass Spectra (2013) both
- Mass spectrometry-based protein identification by integrating de novo sequencing with database searching (2013) both
- Antilope—A Lagrangian Relaxation Approach to the de novo Peptide Sequencing Problem (2012) both
- Algorithms for the de novo sequencing of peptides from tandem mass spectra (2011) both
- pNovo: De novo Peptide Sequencing and Identification Using HCD Spectra (2010) both
- A high-throughput de novo sequencing approach for shotgun proteomics using high-resolution tandem mass spectrometry (2010) both
- Spectral Dictionaries: Integrating de novo Peptide Sequencing with Database Search of Tandem Mass Spectra (2009) crossref
- De Novo Peptide Identification via Tandem Mass Spectrometry and Integer Linear Optimization (2007) both
- De Novo Peptide Sequencing and Identification with Precision Mass Spectrometry (2007) both
- Performance Evaluation of Existing De Novo Sequencing Algorithms (2006) both
- De novo peptide sequencing using exhaustive enumeration of peptide composition (2006) both
- Proteomics-Grade de Novo Sequencing Approach (2005) both
- NovoHMM: A Hidden Markov Model for de Novo Peptide Sequencing (2005) both
- AUDENS: A Tool for Automated Peptide de Novo Sequencing (2005) both
- PepNovo: de novo peptide sequencing via probabilistic network modeling (2005) both
- A Hidden Markov Model for de Novo Peptide Sequencing (2004) semanticscholar
- De Novo Peptide Sequencing Based on a Divide-and-Conquer Algorithm and Peptide Tandem Spectrum Simulation (2004) both
- Algorithms for de novo peptide sequencing using tandem mass spectrometry (2004) both
- PEAKS: powerful software for peptide de novo sequencing by tandem mass spectrometry (2003) crossref
- A Suboptimal Algorithm for De Novo Peptide Sequencing via Tandem Mass Spectrometry (2003) both
- A Dynamic Programming Approach to De Novo Peptide Sequencing via Tandem Mass Spectrometry (2001) both
- Implementation and Uses of Automated de Novo Peptide Sequencing by Tandem Mass Spectrometry (2001) both
- De novo peptide sequencing via tandem mass spectrometry (1999) both
- Peptide sequence determination from high-energy collision-induced dissociation spectra using artificial neural networks (1995) both
Cited by (4)
- Extended Snake Venomics by Top-Down In-Source Decay: Investigating the Newly Discovered Anatolian Meadow Viper Subspecies, Vipera anatolica senliki (2020) both
- A potential golden age to come—current tools, recent use cases, and future avenues for de novo sequencing in proteomics (2018) crossref
- Combining De Novo Peptide Sequencing Algorithms, A Synergistic Approach to Boost Both Identifications and Confidence in Bottom-up Proteomics (2017) crossref
- Evaluating de novo sequencing in proteomics: already an accurate alternative to database-driven peptide identification? (2017) crossref