ArticleJournal of proteome research2011
Faster SEQUEST searching for peptide identification from tandem mass spectra.
Article in Journal of proteome research, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 91 papers.
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Who cites it
91 citing papers in PubMed.
- End-to-end deep attention-based multitask pipeline for predicting uncertainty-quantified peptide properties from mass spectrometry data.Scientific reports · 2026Article
- PKA-driven SPP1 activation as a novel mechanism connecting the bone microenvironment to prostate cancer progression.Oncogene · 2025Article
- Immunomics-guided biomarker discovery for human liver fluke infection and infection-associated cholangiocarcinoma.Nature communications · 2025Article
- Assessment of false discovery rate control in tandem mass spectrometry analysis using entrapment.Nature methods · 2025Article
- PyViscount: Validating False Discovery Rate Estimation Methods via Random Search Space Partition.Journal of proteome research · 2025Article
- A transformer-based semi-autoregressive framework for high-speed and accurate de novo peptide sequencing.Communications biology · 2025Article
- A multi-species benchmark for training and validating mass spectrometry proteomics machine learning models.Scientific data · 2024Article
- HMPA: a pioneering framework for the noncanonical peptidome from discovery to functional insights.Briefings in bioinformatics · 2024Article
- Sequence-to-sequence translation from mass spectra to peptides with a transformer model.Nature communications · 2024Article
- Rescoring Peptide Spectrum Matches: Boosting Proteomics Performance by Integrating Peptide Property Predictors Into Peptide Identification.Molecular & cellular proteomics : MCP · 2024Review
- A learned score function improves the power of mass spectrometry database search.Bioinformatics (Oxford, England) · 2024Article
- Bioinformatic Workflows for Metaproteomics.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Making MS Omics Data ML-Ready: SpeCollate Protocols.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Mzion enables deep and precise identification of peptides in data-dependent acquisition proteomics.Scientific reports · 2023Article
- Principles of phosphoproteomics and applications in cancer research.The Biochemical journal · 2023Article
- Peptidomics.Nature reviews. Methods primers · 2023Article
- Progressive search in tandem mass spectrometry.BMC bioinformatics · 2023Article
- The Crux Toolkit for Analysis of Bottom-Up Tandem Mass Spectrometry Proteomics Data.Journal of proteome research · 2023Article
- Integrating Identification and Quantification Uncertainty for Differential Protein Abundance Analysis with Triqler.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Finding haplotypic signatures in proteins.GigaScience · 2022Article
31 more citing papers are in PubMed but not listed here.
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Authors and funding
2 authors.
Funding
Abstract
Computational analysis of mass spectra remains the bottleneck in many proteomics experiments. SEQUEST was one of the earliest software packages to identify peptides from mass spectra by searching a database of known peptides. Though still popular, SEQUEST performs slowly. Crux and TurboSEQUEST have successfully sped up SEQUEST by adding a precomputed index to the search, but the demand for ever-faster peptide identification software continues to grow. Tide, introduced here, is a software program that implements the SEQUEST algorithm for peptide identification and that achieves a dramatic speedup over Crux and SEQUEST. The optimization strategies detailed here employ a combination of algorithmic and software engineering techniques to achieve speeds up to 170 times faster than a recent version of SEQUEST that uses indexing. For example, on a single Xeon CPU, Tide searches 10,000 spectra against a tryptic database of 27,499 Caenorhabditis elegans proteins at a rate of 1550 spectra per second, which compares favorably with a rate of 8.8 spectra per second for a recent version of SEQUEST with index running on the same hardware.
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