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Analysis of Peptide MS/MS Spectra from Large-Scale Proteomics Experiments Using Spectrum Libraries

https://doi.org/10.1021/ac060279n
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Outgoing claims: the papers this work cites, builds on, or argues with.

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Probability-based protein identification by searching sequence databases using mass spectrometry data
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MS1, MS2, and SQT—three unified, compact, and easily parsed file formats for the storage of shotgun proteomic spectra and identifications
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The use of proteotypic peptide libraries for protein identification
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Qscore: An algorithm for evaluating SEQUEST database search results
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An Automated Multidimensional Protein Identification Technology for Shotgun Proteomics
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Method To Compare Collision-Induced Dissociation Spectra of Peptides: Potential for Library Searching and Subtractive Analysis
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Code Developments to Improve the Efficiency of Automated MS/MS Spectra Interpretation
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Evaluation of Multidimensional Chromatography Coupled with Tandem Mass Spectrometry (LC/LC−MS/MS) for Large-Scale Protein Analysis: The Yeast Proteome
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A New Algorithm for the Evaluation of Shotgun Peptide Sequencing in Proteomics: Support Vector Machine Classification of Peptide MS/MS Spectra and SEQUEST Scores
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Parallel Tandem: A Program for Parallel Processing of Tandem Mass Spectra Using PVM or MPI and X!Tandem
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Large-scale analysis of the yeast proteome by multidimensional protein identification technology
inferredcites →https://doi.org/10.1038/nmeth705openalex-snapshot
Automated approach for quantitative analysis of complex peptide mixtures from tandem mass spectra

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Incoming claims: where this work appears in other papers’ reference lists and arguments.

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Identification of Related Peptides through the Analysis of Fragment Ion Mass Shifts
inferred← citeshttps://doi.org/10.1021/pr500500dopenalex-snapshot
Expediting SRM Assay Development for Large-Scale Targeted Proteomics Experiments
inferred← citeshttps://doi.org/10.1021/pr5007697openalex-snapshot
Kinetic Analysis of BCL11B Multisite Phosphorylation–Dephosphorylation and Coupled Sumoylation in Primary Thymocytes by Multiple Reaction Monitoring Mass Spectroscopy
inferred← citeshttps://doi.org/10.1021/pr700836qopenalex-snapshot
Evaluation of Data-Dependent versus Targeted Shotgun Proteomic Approaches for Monitoring Transcription Factor Expression in Breast Cancer
inferred← citeshttps://doi.org/10.1021/pr800226wopenalex-snapshot
A Spectral Clustering Approach to MS/MS Identification of Post-Translational Modifications
inferred← citeshttps://doi.org/10.1021/pr800955nopenalex-snapshot
Increased Confidence in Large-Scale Phosphoproteomics Data by Complementary Mass Spectrometric Techniques and Matching of Phosphopeptide Data Sets
inferred← citeshttps://doi.org/10.1021/pr801028bopenalex-snapshot
Expediting the Development of Targeted SRM Assays: Using Data from Shotgun Proteomics to Automate Method Development
inferred← citeshttps://doi.org/10.1021/pr900298bopenalex-snapshot
Correlation between y-Type Ions Observed in Ion Trap and Triple Quadrupole Mass Spectrometers
inferred← citeshttps://doi.org/10.1021/pr900947uopenalex-snapshot
Artificial Decoy Spectral Libraries for False Discovery Rate Estimation in Spectral Library Searching in Proteomics
inferred← citeshttps://doi.org/10.1038/nature11835openalex-snapshot
A complete mass-spectrometric map of the yeast proteome applied to quantitative trait analysis
inferred← citeshttps://doi.org/10.1038/ncomms2730openalex-snapshot
Identifying sources of tick blood meals using unidentified tandem mass spectral libraries
inferred← citeshttps://doi.org/10.1038/nmeth.1254openalex-snapshot
Building consensus spectral libraries for peptide identification in proteomics
inferred← citeshttps://doi.org/10.1038/nmeth.1609openalex-snapshot
Spectral archives: extending spectral libraries to analyze both identified and unidentified spectra
inferred← citeshttps://doi.org/10.1038/nmeth.1633openalex-snapshot
Spectral archives: a vision for future proteomics data repositories
inferred← citeshttps://doi.org/10.1038/nmeth.1770openalex-snapshot
Rapid empirical discovery of optimal peptides for targeted proteomics
inferred← citeshttps://doi.org/10.1038/nmeth.2528openalex-snapshot
Multiplexed MS/MS for improved data-independent acquisition
inferred← citeshttps://doi.org/10.1038/nmeth.4643openalex-snapshot
Specter: linear deconvolution for targeted analysis of data-independent acquisition mass spectrometry proteomics
inferred← citeshttps://doi.org/10.1038/nmeth1088openalex-snapshot
Analysis and validation of proteomic data generated by tandem mass spectrometry
inferred← citeshttps://doi.org/10.1038/nmeth1113openalex-snapshot
Semi-supervised learning for peptide identification from shotgun proteomics datasets
inferred← citeshttps://doi.org/10.1038/nprot.2014.048openalex-snapshot
Tracking the sources of blood meals of parasitic arthropods using shotgun proteomics and unidentified tandem mass spectral libraries
inferred← citeshttps://doi.org/10.1038/nprot.2015.015openalex-snapshot
Building high-quality assay libraries for targeted analysis of SWATH MS data
inferred← citeshttps://doi.org/10.1038/s41467-018-07454-wopenalex-snapshot
Chromatogram libraries improve peptide detection and quantification by data independent acquisition mass spectrometry
inferred← citeshttps://doi.org/10.1038/s41467-020-15346-1openalex-snapshot
Generating high quality libraries for DIA MS with empirically corrected peptide predictions
inferred← citeshttps://doi.org/10.1038/s41467-023-40129-9openalex-snapshot
MSBooster: improving peptide identification rates using deep learning-based features
inferred← citeshttps://doi.org/10.1038/s41587-026-03003-9openalex-snapshot
Sensitive detection of cancer antigens enabled by user-defined peptide libraries
inferred← citeshttps://doi.org/10.1038/s41592-019-0498-4openalex-snapshot
Thesaurus: quantifying phosphopeptide positional isomers
inferred← citeshttps://doi.org/10.1038/s41596-022-00714-6openalex-snapshot
Utilizing Skyline to analyze lipidomics data containing liquid chromatography, ion mobility spectrometry and mass spectrometry dimensions
inferred← citeshttps://doi.org/10.1038/s41597-022-01259-9openalex-snapshot
The PeptideAtlas of a widely cultivated fish Labeo rohita: A resource for the Aquaculture Community
inferred← citeshttps://doi.org/10.1039/c2mb25085copenalex-snapshot
The spectral networks paradigm in high throughput mass spectrometry
inferred← citeshttps://doi.org/10.1039/c7cp04738jopenalex-snapshot
Sodium-cationized carbohydrate gas-phase fragmentation chemistry: influence of glycosidic linkage position
inferred← citeshttps://doi.org/10.1039/c8ra07200kopenalex-snapshot
Middle-down approach: a choice to sequence and characterize proteins/proteomes by mass spectrometry
inferred← citeshttps://doi.org/10.1039/d4sc03519dopenalex-snapshot
High density information storage through isotope ratio encoding
inferred← citeshttps://doi.org/10.1039/d6an00268dopenalex-snapshot
Differentiation of disaccharide isomers via diagnostic-ion-weighted spectral library searching using data from tandem MS analysis of chloride adducts
inferred← citeshttps://doi.org/10.1074/mcp.m000136-mcp201openalex-snapshot
Peptide Identification from Mixture Tandem Mass Spectra
inferred← citeshttps://doi.org/10.1074/mcp.m111.007666openalex-snapshot
Spectrum-to-Spectrum Searching Using a Proteome-wide Spectral Library
inferred← citeshttps://doi.org/10.1074/mcp.m111.016493openalex-snapshot
Development of a Pharmaceutical Hepatotoxicity Biomarker Panel Using a Discovery to Targeted Proteomics Approach
inferred← citeshttps://doi.org/10.1074/mcp.m112.026500openalex-snapshot
Maximizing Peptide Identification Events in Proteomic Workflows Using Data-Dependent Acquisition (DDA)
inferred← citeshttps://doi.org/10.1074/mcp.m115.051300openalex-snapshot
Using Data Independent Acquisition (DIA) to Model High-responding Peptides for Targeted Proteomics Experiments
inferred← citeshttps://doi.org/10.1074/mcp.m600320-mcp200openalex-snapshot
Improved Validation of Peptide MS/MS Assignments Using Spectral Intensity Prediction
inferred← citeshttps://doi.org/10.1074/mcp.m800384-mcp200openalex-snapshot
A Simulated MS/MS Library for Spectrum-to-spectrum Searching in Large Scale Identification of Proteins
inferred← citeshttps://doi.org/10.1074/mcp.o111.016717openalex-snapshot
Targeted Data Extraction of the MS/MS Spectra Generated by Data-independent Acquisition: A New Concept for Consistent and Accurate Proteome Analysis
inferred← citeshttps://doi.org/10.1074/mcp.o113.036475openalex-snapshot
Conserved Peptide Fragmentation as a Benchmarking Tool for Mass Spectrometers and a Discriminating Feature for Targeted Proteomics
inferred← citeshttps://doi.org/10.1074/mcp.o113.037135openalex-snapshot
Tandem Mass Spectral Libraries of Peptides in Digests of Individual Proteins: Human Serum Albumin (HSA)
inferred← citeshttps://doi.org/10.1074/mcp.o114.047035openalex-snapshot
Peptide-Centric Proteome Analysis: An Alternative Strategy for the Analysis of Tandem Mass Spectrometry Data
inferred← citeshttps://doi.org/10.1074/mcp.r111.008565openalex-snapshot
Building and Searching Tandem Mass Spectral Libraries for Peptide Identification
inferred← citeshttps://doi.org/10.1074/mcp.r112.019695openalex-snapshot
File Formats Commonly Used in Mass Spectrometry Proteomics
inferred← citeshttps://doi.org/10.1074/mcp.r113.027797openalex-snapshot
Combining Results of Multiple Search Engines in Proteomics
inferred← citeshttps://doi.org/10.1080/14789450.2023.2265062openalex-snapshot
A Galaxy of informatics resources for MS-based proteomics
inferred← citeshttps://doi.org/10.1089/cmb.2007.0071openalex-snapshot
HMMatch: Peptide Identification by Spectral Matching of Tandem Mass Spectra Using Hidden Markov Models
inferred← citeshttps://doi.org/10.1093/bioinformatics/btq054openalex-snapshot
Skyline: an open source document editor for creating and analyzing targeted proteomics experiments
inferred← citeshttps://doi.org/10.1093/bioinformatics/btq185openalex-snapshot
Open MS/MS spectral library search to identify unanticipated post-translational modifications and increase spectral identification rate
inferred← citeshttps://doi.org/10.1093/bioinformatics/btr445openalex-snapshot
NeuroPedia: neuropeptide database and spectral library
inferred← citeshttps://doi.org/10.1093/bioinformatics/bts083openalex-snapshot
A method of finding optimal weight factors for compound identification in gas chromatography–mass spectrometry
inferred← citeshttps://doi.org/10.1093/femsyr/foz088openalex-snapshot
Shot-gun proteomics: why thousands of unidentified signals matter
inferred← citeshttps://doi.org/10.1101/2021.08.02.454768openalex-snapshot
IntroSpect: motif-guided immunopeptidome database building tool to improve the sensitivity of HLA binding peptide identification
inferred← citeshttps://doi.org/10.1101/2022.10.19.512904openalex-snapshot
MSBooster: Improving Peptide Identification Rates using Deep Learning-Based Features
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