ArticleJournal of proteome research2012
Pepitome: evaluating improved spectral library search for identification complementarity and quality assessment.
Article in Journal of proteome research, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed.
- JUMPlib: Integrative Search Tool Combining Fragment Ion Indexing with Comprehensive TMT Spectral Libraries.Journal of proteome research · 2025Article
- Improving quantitation accuracy in isobaric-labeling mass spectrometry experiments with spectral library searching and feature-based peptide-spectrum match filter.Scientific reports · 2023Article
- MS Ana: Improving Sensitivity in Peptide Identification with Spectral Library Search.Journal of proteome research · 2023Article
- Calibr improves spectral library search for spectrum-centric analysis of data independent acquisition proteomics.Scientific reports · 2022Article
- Deep learning embedder method and tool for mass spectra similarity search.Journal of proteomics · 2021Article
- Review
- Software Options for the Analysis of MS-Proteomic Data.Methods in molecular biology (Clifton, N.J.) · 2021Article
- Methods for Proteogenomics Data Analysis, Challenges, and Scalability Bottlenecks: A Survey.IEEE access : practical innovations, open solutions · 2021Article
- Middle-down approach: a choice to sequence and characterize proteins/proteomes by mass spectrometry.RSC advances · 2018Review
- Spectral Library Search Improves Assignment of TMT Labeled MS/MS Spectra.Journal of proteome research · 2018Article
- Identification of Proteomic Features To Distinguish Benign Pulmonary Nodules from Lung Adenocarcinoma.Journal of proteome research · 2017Article
- Chronic intermittent alcohol disrupts the GluN2B-associated proteome and specifically regulates group I mGlu receptor-dependent long-term depression.Addiction biology · 2017Article
- Recognizing millions of consistently unidentified spectra across hundreds of shotgun proteomics datasets.Nature methods · 2016Article
- Assembly Dynamics and Stoichiometry of the Apoptosis Signal-regulating Kinase (ASK) Signalosome in Response to Electrophile Stress.Molecular & cellular proteomics : MCP · 2016Article
- A Description of the Clinical Proteomic Tumor Analysis Consortium (CPTAC) Common Data Analysis Pipeline.Journal of proteome research · 2016Article
- Quantitative proteomics signature profiling based on network contextualization.Biology direct · 2015Article
- Proteomic analysis of colon and rectal carcinoma using standard and customized databases.Scientific data · 2015Article
- JUMP: a tag-based database search tool for peptide identification with high sensitivity and accuracy.Molecular & cellular proteomics : MCP · 2014Article
- Tracking the sources of blood meals of parasitic arthropods using shotgun proteomics and unidentified tandem mass spectral libraries.Nature protocols · 2014Article
- QC metrics from CPTAC raw LC-MS/MS data interpreted through multivariate statistics.Analytical chemistry · 2014Article
Corrections and comments
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Authors and funding
7 authors.
Funding
Abstract
Spectral libraries have emerged as a viable alternative to protein sequence databases for peptide identification. These libraries contain previously detected peptide sequences and their corresponding tandem mass spectra (MS/MS). Search engines can then identify peptides by comparing experimental MS/MS scans to those in the library. Many of these algorithms employ the dot product score for measuring the quality of a spectrum-spectrum match (SSM). This scoring system does not offer a clear statistical interpretation and ignores fragment ion m/z discrepancies in the scoring. We developed a new spectral library search engine, Pepitome, which employs statistical systems for scoring SSMs. Pepitome outperformed the leading library search tool, SpectraST, when analyzing data sets acquired on three different mass spectrometry platforms. We characterized the reliability of spectral library searches by confirming shotgun proteomics identifications through RNA-Seq data. Applying spectral library and database searches on the same sample revealed their complementary nature. Pepitome identifications enabled the automation of quality analysis and quality control (QA/QC) for shotgun proteomics data acquisition pipelines.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.