Error-Tolerant Identification of Peptides in Sequence Databases by Peptide Sequence Tags
peer-reviewed · Analytical Chemistry · 1994
| Date | 1994-12-15 |
| Type | peer-reviewed |
| Venue | Analytical Chemistry |
| Publisher | American Chemical Society (ACS) |
| Contribution | adjacent |
| DOI | 10.1021/ac00096a002 |
| Citations (OpenAlex) | 1477 |
| Venue 2-year citedness | 6.29 |
Abstract
We demonstrate a new approach to the identification of mass spectrometrically fragmented peptides. A fragmentation spectrum usually contains a short, easily identifiable series of sequence ions, which yields a partial sequence. This partial sequence divides the peptide into three parts-regions 1, 2, and 3-characterized by the added mass m1 of region 1, the partial sequence of region 2, and the added mass m3 of region 3. We call the construct, m1 partial sequence m3, a “peptide sequence tag” and show that it is a highly specific identifier of the peptide. An algorithm developed here that uses the sequence tag to find the peptide in a sequence database is up to 1 million-fold more discriminating than the partial sequence information alone. Peptides can be identified even in the presence of an unknown posttranslational modification or an amino acid substitution between an entry in the sequence database and the measured peptide. These concepts are demonstrated with model and practical examples of electrospray mass spectrometry/mass spectrometry of tryptic peptides. Just two to three amino acid residues derived by fragmentation are enough to identify these peptides. In peptide mapping applications, even less information is necessary.
Methods and tools
- Peptide sequence tags: Error-tolerant peptide identification using short de novo sequence tags and flanking masses.
Cited by (40)
- MARS an improved de novo peptide candidate selection method for non-canonical antigen target discovery in cancer (2024) both
- Accurate de novo peptide sequencing using fully convolutional neural networks (2023) both
- Uncovering Hidden Members and Functions of the Soil Microbiome Using De Novo Metaproteomics (2022) semanticscholar
- Flying blind, or just flying under the radar? The underappreciated power of de novo methods of mass spectrometric peptide identification (2020) crossref
- Uncovering Thousands of New Peptides with Sequence-Mask-Search Hybrid De Novo Peptide Sequencing Framework (2019) both
- A potential golden age to come—current tools, recent use cases, and future avenues for de novo sequencing in proteomics (2018) crossref
- Open-pNovo: De Novo Peptide Sequencing with Thousands of Protein Modifications (2017) crossref
- Lessons in de novo peptide sequencing by tandem mass spectrometry (2015) both
- Shotgun Protein Sequencing with Meta-contig Assembly (2012) both
- Constrained De Novo Sequencing of Conotoxins (2012) both
- De Novo Sequencing and Homology Searching (2012) both
- pNovo: De novo Peptide Sequencing and Identification Using HCD Spectra (2010) crossref
- A high-throughput de novo sequencing approach for shotgun proteomics using high-resolution tandem mass spectrometry (2010) both
- De novo sequencing of peptides by MS/MS (2010) crossref
- Spectral Profiles, a Novel Representation of Tandem Mass Spectra and Their Applications for de Novo Peptide Sequencing and Identification (2009) both
- Spectral Dictionaries: Integrating de novo Peptide Sequencing with Database Search of Tandem Mass Spectra (2009) both
- DirecTag: Accurate Sequence Tags from Peptide MS/MS through Statistical Scoring (2008) both
- Assessing peptide de novo sequencing algorithms performance on large and diverse data sets (2007) crossref
- MSNovo: A Dynamic Programming Algorithm for de Novo Peptide Sequencing via Tandem Mass Spectrometry (2007) crossref
- Lookup Peaks: A Hybrid of de Novo Sequencing and Database Search for Protein Identification by Tandem Mass Spectrometry (2007) crossref
- De Novo Peptide Identification via Tandem Mass Spectrometry and Integer Linear Optimization (2007) crossref
- De Novo Peptide Sequencing and Identification with Precision Mass Spectrometry (2007) crossref
- A mixed-integer optimization framework for de novo peptide identification (2007) crossref
- De Novo Analysis of Peptide Tandem Mass Spectra by Spectral Graph Partitioning (2006) crossref
- SPIDER: software for protein identification from sequence tags with de novo sequencing error (2005) crossref
- An effective algorithm for peptide de novo sequencing from MS/MS spectra (2005) both
- Identification of Protein Modifications Using MS/MS de Novo Sequencing and the OpenSea Alignment Algorithm (2005) crossref
- PepNovo: de novo peptide sequencing via probabilistic network modeling (2005) crossref
- Sequit: software for de novo peptide sequencing by matrix-assisted laser desorption/ionization post-source decay mass spectrometry (2004) crossref
- Algorithms for de novo peptide sequencing using tandem mass spectrometry (2004) crossref
- GutenTag: High-Throughput Sequence Tagging via an Empirically Derived Fragmentation Model (2003) crossref
- PEAKS: powerful software for peptide de novo sequencing by tandem mass spectrometry (2003) crossref
- De novo sequencing of peptides using MALDI/TOF-TOF (2002) both
- De Novo Peptide Sequencing via Manual Interpretation of MS/MS Spectra (2002) crossref
- De novo peptide sequencing and quantitative profiling of complex protein mixtures using mass-coded abundance tagging (2002) crossref
- Implementation and Uses of Automated de Novo Peptide Sequencing by Tandem Mass Spectrometry (2001) crossref
- Derivatization procedures to facilitate de novo sequencing of lysine-terminated tryptic peptides using postsource decay matrix-assisted laser desorption/ionization mass spectrometry (2000) crossref
- Quantitation and Facilitated de Novo Sequencing of Proteins by Isotopic N-Terminal Labeling of Peptides with a Fragmentation-Directing Moiety (2000) crossref
- Automated interpretation of low-energy collision-induced dissociation spectra by SeqMS, a software aid for de novo sequencing by tandem mass spectrometry (2000) crossref
- De novo peptide sequencing via tandem mass spectrometry (1999) crossref