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Spectral archives: extending spectral libraries to analyze both identified and unidentified spectra

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1002/pmic.200300511openalex-snapshot

Proteogenomic mapping as a complementary method to perform genome annotation

inferredcites →https://doi.org/10.1002/pmic.200300652openalex-snapshot

Improving large‐scale proteomics by clustering of mass spectrometry data

inferredcites →https://doi.org/10.1002/pmic.200500309openalex-snapshot

Improving the reliability and throughput of mass spectrometry‐based proteomics by spectrum quality filtering

inferredcites →https://doi.org/10.1002/pmic.200600625openalex-snapshot

Development and validation of a spectral library searching method for peptide identification from MS/MS

inferredcites →https://doi.org/10.1002/pmic.200700003openalex-snapshot

Sequence similarity‐driven proteomics in organisms with unknown genomes by LC‐MS/MS and automated de novo sequencing

inferredcites →https://doi.org/10.1002/pmic.200700160openalex-snapshot

Implementation and application of a versatile clustering tool for tandem mass spectrometry data

inferredcites →https://doi.org/10.1002/rcm.1196openalex-snapshot

PEAKS: powerful software for peptide de novo sequencing by tandem mass spectrometry

inferredcites →https://doi.org/10.1016/1044-0305(94)87009-8openalex-snapshot

Optimization and testing of mass spectral library search algorithms for compound identification

inferredcites →https://doi.org/10.1016/j.jasms.2005.04.010openalex-snapshot

MS2Grouper: Group assessment and synthetic replacement of duplicate proteomic tandem mass spectra

inferredcites →https://doi.org/10.1016/s0167-7799(01)01795-4openalex-snapshot

Matching peptide mass spectra to EST and genomic DNA databases

inferredcites →https://doi.org/10.1016/s1044-0305(01)00327-0openalex-snapshot

Comparing similar spectra: From similarity index to spectral contrast angle

inferredcites →https://doi.org/10.1021/ac0013709openalex-snapshot

Charting the Proteomes of Organisms with Unsequenced Genomes by MALDI-Quadrupole Time-of-Flight Mass Spectrometry and BLAST Homology Searching

inferredcites →https://doi.org/10.1021/ac026424oopenalex-snapshot

Similarity among Tandem Mass Spectra from Proteomic Experiments: Detection, Significance, and Utility

inferredcites →https://doi.org/10.1021/ac048788hopenalex-snapshot

PepNovo: De Novo Peptide Sequencing via Probabilistic Network Modeling

inferredcites →https://doi.org/10.1021/ac049043eopenalex-snapshot

Targeted Comparative Proteomics by Liquid Chromatography-Tandem Fourier Ion Cyclotron Resonance Mass Spectrometry

inferredcites →https://doi.org/10.1021/ac050102dopenalex-snapshot

InsPecT: Identification of Posttranslationally Modified Peptides from Tandem Mass Spectra

inferredcites →https://doi.org/10.1021/ac052197popenalex-snapshot

Robust Algorithm for Alignment of Liquid Chromatography−Mass Spectrometry Analyses in an Accurate Mass and Time Tag Data Analysis Pipeline

inferredcites →https://doi.org/10.1021/ac060279nopenalex-snapshot

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

inferredcites →https://doi.org/10.1021/ac801123popenalex-snapshot

De Novo Sequencing of Unique Sequence Tags for Discovery of Post-Translational Modifications of Proteins

inferredcites →https://doi.org/10.1021/ac980122yopenalex-snapshot

Method To Compare Collision-Induced Dissociation Spectra of Peptides: Potential for Library Searching and Subtractive Analysis

inferredcites →https://doi.org/10.1021/pr050288xopenalex-snapshot

Proteomics-Grade de Novo Sequencing Approach

inferredcites →https://doi.org/10.1021/pr0602085openalex-snapshot

Using Annotated Peptide Mass Spectrum Libraries for Protein Identification

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Algorithm for Identification of Fusion Proteins via Mass Spectrometry

inferredcites →https://doi.org/10.1021/pr070361eopenalex-snapshot

Clustering Millions of Tandem Mass Spectra

inferredcites →https://doi.org/10.1021/pr070540wopenalex-snapshot

Improving Sensitivity by Probabilistically Combining Results from Multiple MS/MS Search Methodologies

inferredcites →https://doi.org/10.1021/pr800140vopenalex-snapshot

Separating the Wheat from the Chaff: Unbiased Filtering of Background Tandem Mass Spectra Improves Protein Identification

inferredcites →https://doi.org/10.1021/pr9004794openalex-snapshot

False Discovery Rates of Protein Identifications: A Strike against the Two-Peptide Rule

inferredcites →https://doi.org/10.1038/nbt1168openalex-snapshot

Identification of post-translational modifications by blind search of mass spectra

inferredcites →https://doi.org/10.1038/nmeth1019openalex-snapshot

Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry

inferredcites →https://doi.org/10.1073/pnas.0701130104openalex-snapshot

Protein identification by spectral networks analysis

inferredcites →https://doi.org/10.1074/mcp.m500319-mcp200openalex-snapshot

Dynamic Spectrum Quality Assessment and Iterative Computational Analysis of Shotgun Proteomic Data

inferredcites →https://doi.org/10.1074/mcp.m800103-mcp200openalex-snapshot

Spectral Dictionaries

inferredcites →https://doi.org/10.1074/mcp.m800345-mcp200openalex-snapshot

Identification of Early Intestinal Neoplasia Protein Biomarkers Using Laser Capture Microdissection and MALDI MS

inferredcites →https://doi.org/10.1093/bioinformatics/bth947openalex-snapshot

Automatic Quality Assessment of Peptide Tandem Mass Spectra

inferredcites →https://doi.org/10.1093/bioinformatics/bti829openalex-snapshot

Quality classification of tandem mass spectrometry data

inferredcites →https://doi.org/10.1093/bioinformatics/btl118openalex-snapshot

A fast coarse filtering method for peptide identification by mass spectrometry

inferredcites →https://doi.org/10.1101/gr.5646507openalex-snapshot

Improving gene annotation using peptide mass spectrometry

inferredcites →https://doi.org/10.1101/gr.6427907openalex-snapshot

Whole proteome analysis of post-translational modifications: Applications of mass-spectrometry for proteogenomic annotation

inferredcites →https://doi.org/10.1101/gr.7128207openalex-snapshot

Targeted discovery of novel human exons by comparative genomics

inferredcites →https://doi.org/10.1109/csb.2005.34openalex-snapshot

Identification of post-translational modifications via blind search of mass-spectra

inferredcites →https://doi.org/10.1142/s0219720005001247openalex-snapshot

SPIDER: SOFTWARE FOR PROTEIN IDENTIFICATION FROM SEQUENCE TAGS WITH DE NOVO SEQUENCING ERROR

inferredcites →https://doi.org/10.1145/1327452.1327494openalex-snapshot

Near-optimal hashing algorithms for approximate nearest neighbor in high dimensions

inferredcites →https://doi.org/10.1186/1471-2105-8-51openalex-snapshot

msmsEval: tandem mass spectral quality assignment for high-throughput proteomics

inferredcites →https://doi.org/10.1186/1477-5956-5-3openalex-snapshot

Methods for peptide identification by spectral comparison

inferredcites →https://doi.org/10.1186/gb-2004-6-1-r9openalex-snapshot

Integration with the human genome of peptide sequences obtained by high-throughput mass spectrometry

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Computational Proteomics

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