Gapped Spectral Dictionaries and Their Applications for Database Searches of Tandem Mass Spectra

peer-reviewed · Molecular & Cellular Proteomics · 2011

peer-reviewed · Molecular & Cellular Proteomics · 2011. Kyowon Jeong et al. Generating all plausible de novo interpretations of a peptide tandem mass (MS/MS) spectrum (Spectral…

Date	2011-06-01
Type	peer-reviewed
Venue	Molecular & Cellular Proteomics
Publisher	Elsevier BV
Contribution	adjacent
DOI	10.1074/mcp.m110.002220
Citations (OpenAlex)	22
Venue 2-year citedness	4.69

Abstract

Generating all plausible de novo interpretations of a peptide tandem mass (MS/MS) spectrum (Spectral Dictionary) and quickly matching them against the database represent a recently emerged alternative approach to peptide identification. However, the sizes of the Spectral Dictionaries quickly grow with the peptide length making their generation impractical for long peptides. We introduce Gapped Spectral Dictionaries (all plausible de novo interpretations with gaps) that can be easily generated for any peptide length thus addressing the limitation of the Spectral Dictionary approach. We show that Gapped Spectral Dictionaries are small thus opening a possibility of using them to speed-up MS/MS searches. Our MS-Gapped-Dictionary algorithm (based on Gapped Spectral Dictionaries) enables proteogenomics applications (such as searches in the six-frame translation of the human genome) that are prohibitively time consuming with existing approaches. MS-Gapped-Dictionary generates gapped peptides that occupy a niche between accurate but short peptide sequence tags and long but inaccurate full length peptide reconstructions. We show that, contrary to conventional wisdom, some high-quality spectra do not have good peptide sequence tags and introduce gapped tags that have advantages over the conventional peptide sequence tags in MS/MS database searches.

Authors

1. Kyowon Jeong · University of California San Diego
2. Sangtae Kim · University of California San Diego
3. Nuno Bandeira · University of California San Diego, University of California System
4. Pavel A. Pevzner · Max Planck Institute of Molecular Cell Biology and Genetics, Saint Petersburg Academic University, St Petersburg University, St. Petersburg State University, University of California San Diego, University of Southern California

Methods and tools

• MS-Dictionary: Hybrid method that integrates de novo spectral dictionaries with database search of tandem mass spectra.

Cites (11)

• Spectral Profiles, a Novel Representation of Tandem Mass Spectra and Their Applications for de Novo Peptide Sequencing and Identification (2009) both
• A Ranking-Based Scoring Function for Peptide-Spectrum Matches (2009) both
• Spectral Dictionaries: Integrating de novo Peptide Sequencing with Database Search of Tandem Mass Spectra (2009) both
• Lookup Peaks: A Hybrid of de Novo Sequencing and Database Search for Protein Identification by Tandem Mass Spectrometry (2007) both
• InsPecT: Identification of Posttranslationally Modified Peptides from Tandem Mass Spectra (2005) both
• Identification of Protein Modifications Using MS/MS de Novo Sequencing and the OpenSea Alignment Algorithm (2005) both
• PepNovo: de novo peptide sequencing via probabilistic network modeling (2005) both
• PEAKS: powerful software for peptide de novo sequencing by tandem mass spectrometry (2003) crossref
• Searching Sequence Databases via De Novo Peptide Sequencing by Tandem Mass Spectrometry (2002) both
• De novo peptide sequencing via tandem mass spectrometry (1999) both
• Error-Tolerant Identification of Peptides in Sequence Databases by Peptide Sequence Tags (1994) both

Cited by (2)

• UniNovo: a universal tool for de novo peptide sequencing (2013) both
• De Novo Sequencing and Homology Searching (2012) both

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