Anatomy and evolution of database search engines-a central component of mass spectrometry based proteomic workflows

Systematic Errors in Peptide and Protein Identification and Quantification by Modified Peptides

(2016) Boris Bogdanow et al.   MOLECULAR & CELLULAR PROTEOMICS

A Human Interactome in Three Quantitative Dimensions Organized by Stoichiometries and Abundances

(2015) Marco Y. Hein et al.   CELL

Pladipus Enables Universal Distributed Computing in Proteomics Bioinformatics

(2015) Kenneth Verheggen et al.   JOURNAL OF PROTEOME RESEARCH

Tandem Mass Spectrum Identification via Cascaded Search

(2015) Attila Kertesz-Farkas et al.   JOURNAL OF PROTEOME RESEARCH

A Decoy-Free Approach to the Identification of Peptides

(2015) Giulia Gonnelli et al.   JOURNAL OF PROTEOME RESEARCH

Why phosphoproteomics is still a challenge

(2015) Fiorella A. Solari et al.   Molecular BioSystems

Multi-omic data analysis using Galaxy

(2015) Jorrit Boekel et al.   NATURE BIOTECHNOLOGY

PeptideShaker enables reanalysis of MS-derived proteomics data sets

(2015) Marc Vaudel et al.   NATURE BIOTECHNOLOGY

A mass-tolerant database search identifies a large proportion of unassigned spectra in shotgun proteomics as modified peptides

(2015) Joel M Chick et al.   NATURE BIOTECHNOLOGY

Mass spectrometrists should search only for peptides they care about

(2015) William Stafford Noble   NATURE METHODS

DIA mass spectrometry

(2015) Allison Doerr   NATURE METHODS

The neXtProt knowledgebase on human proteins: current status

(2015) Pascale Gaudet et al.   NUCLEIC ACIDS RESEARCH

DNA data bank of Japan (DDBJ) progress report

(2015) Jun Mashima et al.   NUCLEIC ACIDS RESEARCH

sORFs.org: a repository of small ORFs identified by ribosome profiling

(2015) Volodimir Olexiouk et al.   NUCLEIC ACIDS RESEARCH

An update on LNCipedia: a database for annotated human lncRNA sequences

(2015) P.J. Volders et al.   NUCLEIC ACIDS RESEARCH

2016 update of the PRIDE database and its related tools

(2015) Juan Antonio Vizcaíno et al.   NUCLEIC ACIDS RESEARCH

Exploring the potential of public proteomics data

(2015) Marc Vaudel et al.   PROTEOMICS

In-depth evaluation of software tools for data-independent acquisition based label-free quantification

(2015) Jörg Kuharev et al.   PROTEOMICS

Navigating through metaproteomics data: A logbook of database searching

(2015) Thilo Muth et al.   PROTEOMICS

Making proteomics data accessible and reusable: Current state of proteomics databases and repositories

(2015) Yasset Perez-Riverol et al.   PROTEOMICS

Identification of Regulatory Networks in HSCs and Their Immediate Progeny via Integrated Proteome, Transcriptome, and DNA Methylome Analysis

(2014) Nina Cabezas-Wallscheid et al.   Cell Stem Cell

MS Amanda, a Universal Identification Algorithm Optimized for High Accuracy Tandem Mass Spectra

(2014) Viktoria Dorfer et al.   JOURNAL OF PROTEOME RESEARCH

Wavelet-Based Peak Detection and a New Charge Inference Procedure for MS/MS Implemented in ProteoWizard’s msConvert

(2014) William R. French et al.   JOURNAL OF PROTEOME RESEARCH

Processing Shotgun Proteomics Data on the Amazon Cloud with the Trans-Proteomic Pipeline

(2014) Joseph Slagel et al.   MOLECULAR & CELLULAR PROTEOMICS

Preprocessing Significantly Improves the Peptide/Protein Identification Sensitivity of High-resolution Isobarically Labeled Tandem Mass Spectrometry Data

(2014) Quanhu Sheng et al.   MOLECULAR & CELLULAR PROTEOMICS

A draft map of the human proteome

(2014) Min-Sik Kim et al.   NATURE

Mass-spectrometry-based draft of the human proteome

(2014) Mathias Wilhelm et al.   NATURE

Proteogenomics: concepts, applications and computational strategies

(2014) Alexey I Nesvizhskii   NATURE METHODS

The Pathogen-Host Interactions database (PHI-base): additions and future developments

(2014) Martin Urban et al.   NUCLEIC ACIDS RESEARCH

UniProt: a hub for protein information

(2014)   NUCLEIC ACIDS RESEARCH

Shedding light on black boxes in protein identification

(2014) Marc Vaudel et al.   PROTEOMICS

Performance of super-SILAC based quantitative proteomics for comparison of different acute myeloid leukemia (AML) cell lines

(2014) Elise Aasebø et al.   PROTEOMICS

MS-GF+ makes progress towards a universal database search tool for proteomics

(2014) Sangtae Kim et al.   Nature Communications

In-Vivo Quantitative Proteomics Reveals a Key Contribution of Post-Transcriptional Mechanisms to the Circadian Regulation of Liver Metabolism

(2014) Maria S. Robles et al.   PLoS Genetics

Crowdsourcing in proteomics: public resources lead to better experiments

(2013) Harald Barsnes et al.   AMINO ACIDS

Introduction to opportunities and pitfalls in functional mass spectrometry based proteomics

(2013) Marc Vaudel et al.   BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS

Effectively addressing complex proteomic search spaces with peptide spectrum matching

(2013) Diogo Borges et al.   BIOINFORMATICS

Phosphoproteomics-More than meets the eye

(2013) Stefan Loroch et al.   ELECTROPHORESIS

A Proteomics Search Algorithm Specifically Designed for High-Resolution Tandem Mass Spectra

(2013) Craig D. Wenger et al.   JOURNAL OF PROTEOME RESEARCH

ProteoCloud: A full-featured open source proteomics cloud computing pipeline

(2013) Thilo Muth et al.   Journal of Proteomics

Lessons inde novopeptide sequencing by tandem mass spectrometry

(2013) Katalin F. Medzihradszky et al.   MASS SPECTROMETRY REVIEWS

Western BlotsversusSelected Reaction Monitoring Assays: Time to Turn the Tables?

(2013) Ruedi Aebersold et al.   MOLECULAR & CELLULAR PROTEOMICS

Combining Results of Multiple Search Engines in Proteomics

(2013) David Shteynberg et al.   MOLECULAR & CELLULAR PROTEOMICS

WormBase 2014: new views of curated biology

(2013) Todd W. Harris et al.   NUCLEIC ACIDS RESEARCH

Distributed computing and data storage in proteomics: Many hands make light work, and a stronger memory

(2013) Kenneth Verheggen et al.   PROTEOMICS

Machine learning applications in proteomics research: How the past can boost the future

(2013) Pieter Kelchtermans et al.   PROTEOMICS

False discovery rates in spectral identification

(2012) Kyowon Jeong et al.   BMC BIOINFORMATICS

Current methods for global proteome identification

(2012) Marc Vaudel et al.   Expert Review of Proteomics

Tempest: GPU-CPU Computing for High-Throughput Database Spectral Matching

(2012) Jeffrey A. Milloy et al.   JOURNAL OF PROTEOME RESEARCH

Re-Fraction: A Machine Learning Approach for Deterministic Identification of Protein Homologues and Splice Variants in Large-scale MS-based Proteomics

(2012) Pengyi Yang et al.   JOURNAL OF PROTEOME RESEARCH

Expert System for Computer-assisted Annotation of MS/MS Spectra

(2012) Nadin Neuhauser et al.   MOLECULAR & CELLULAR PROTEOMICS

Analysis of High Accuracy, Quantitative Proteomics Data in the MaxQB Database

(2012) Christoph Schaab et al.   MOLECULAR & CELLULAR PROTEOMICS

File Formats Commonly Used in Mass Spectrometry Proteomics

(2012) Eric W. Deutsch   MOLECULAR & CELLULAR PROTEOMICS

The mzIdentML Data Standard for Mass Spectrometry-Based Proteomics Results

(2012) Andrew R. Jones et al.   MOLECULAR & CELLULAR PROTEOMICS

Targeted Data Extraction of the MS/MS Spectra Generated by Data-independent Acquisition: A New Concept for Consistent and Accurate Proteome Analysis

(2012) Ludovic C. Gillet et al.   MOLECULAR & CELLULAR PROTEOMICS

Searching for a needle in a stack of needles: challenges in metaproteomics data analysis

(2012) Thilo Muth et al.   Molecular BioSystems

A cross-platform toolkit for mass spectrometry and proteomics

(2012) Matthew C Chambers et al.   NATURE BIOTECHNOLOGY

ZFIN, the Zebrafish Model Organism Database: increased support for mutants and transgenics

(2012) Douglas G. Howe et al.   NUCLEIC ACIDS RESEARCH

Comet: An open-source MS/MS sequence database search tool

(2012) Jimmy K. Eng et al.   PROTEOMICS

MapReduce implementation of a hybrid spectral library-database search method for large-scale peptide identification

(2011) Ananth Kalyanaraman et al.   BIOINFORMATICS

Algorithms for thede novosequencing of peptides from tandem mass spectra

(2011) Jens Allmer   Expert Review of Proteomics

Analysis of the Resolution Limitations of Peptide Identification Algorithms

(2011) Niklaas Colaert et al.   JOURNAL OF PROTEOME RESEARCH

MassWiz: A Novel Scoring Algorithm with Target-Decoy Based Analysis Pipeline for Tandem Mass Spectrometry

(2011) Amit Kumar Yadav et al.   JOURNAL OF PROTEOME RESEARCH

SQID: An Intensity-Incorporated Protein Identification Algorithm for Tandem Mass Spectrometry

(2011) Wenzhou Li et al.   JOURNAL OF PROTEOME RESEARCH

Comment on “Unbiased Statistical Analysis for Multi-Stage Proteomic Search Strategies”

(2011) Marshall Bern et al.   JOURNAL OF PROTEOME RESEARCH

Faster SEQUEST Searching for Peptide Identification from Tandem Mass Spectra

(2011) Benjamin J. Diament et al.   JOURNAL OF PROTEOME RESEARCH

More than 100,000 Detectable Peptide Species Elute in Single Shotgun Proteomics Runs but the Majority is Inaccessible to Data-Dependent LC−MS/MS

(2011) Annette Michalski et al.   JOURNAL OF PROTEOME RESEARCH

Andromeda: A Peptide Search Engine Integrated into the MaxQuant Environment

(2011) Jürgen Cox et al.   JOURNAL OF PROTEOME RESEARCH

Fast Multi-blind Modification Search through Tandem Mass Spectrometry

(2011) Seungjin Na et al.   MOLECULAR & CELLULAR PROTEOMICS

Interpretation of Data Underlying the Link Between Colony Collapse Disorder (CCD) and an Invertebrate Iridescent Virus

(2011) Leonard J. Foster   MOLECULAR & CELLULAR PROTEOMICS

PEAKS DB:De NovoSequencing Assisted Database Search for Sensitive and Accurate Peptide Identification

(2011) Jing Zhang et al.   MOLECULAR & CELLULAR PROTEOMICS

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

(2011) Ari M Frank et al.   NATURE METHODS

FlyBase 101 - the basics of navigating FlyBase

(2011) P. McQuilton et al.   NUCLEIC ACIDS RESEARCH

The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools

(2011) Philippe Lamesch et al.   NUCLEIC ACIDS RESEARCH

High Abundance Proteins Depletion vs Low Abundance Proteins Enrichment: Comparison of Methods to Reduce the Plasma Proteome Complexity

(2011) Renato Millioni et al.   PLoS One

The Effect of Using an Inappropriate Protein Database for Proteomic Data Analysis

(2011) Giselle M. Knudsen et al.   PLoS One

A stringent approach to improve the quality of nitrotyrosine peptide identifications

(2011) Bart Ghesquière et al.   PROTEOMICS

Peptide identification quality control

(2011) Marc Vaudel et al.   PROTEOMICS

SearchGUI: An open-source graphical user interface for simultaneous OMSSA and X!Tandem searches

(2011) Marc Vaudel et al.   PROTEOMICS

MacroSEQUEST: Efficient Candidate-Centric Searching and High-Resolution Correlation Analysis for Large-Scale Proteomics Data Sets

(2010) Brendan K. Faherty et al.   ANALYTICAL CHEMISTRY

Accurate peak list extraction from proteomic mass spectra for identification and profiling studies

(2010) Nicola Barbarini et al.   BMC BIOINFORMATICS

TagRecon: High-Throughput Mutation Identification through Sequence Tagging

(2010) Surendra Dasari et al.   JOURNAL OF PROTEOME RESEARCH

Quantifying the Impact of Chimera MS/MS Spectra on Peptide Identification in Large-Scale Proteomics Studies

(2010) Stephane Houel et al.   JOURNAL OF PROTEOME RESEARCH

A survey of computational methods and error rate estimation procedures for peptide and protein identification in shotgun proteomics

(2010) Alexey I. Nesvizhskii   Journal of Proteomics

mzML—a Community Standard for Mass Spectrometry Data

(2010) Lennart Martens et al.   MOLECULAR & CELLULAR PROTEOMICS

Maximizing the sensitivity and reliability of peptide identification in large-scale proteomic experiments by harnessing multiple search engines

(2010) Wen Yu et al.   PROTEOMICS

A guided tour of the Trans-Proteomic Pipeline

(2010) Eric W. Deutsch et al.   PROTEOMICS

Effect of Gas Pressure and Gas Type on the Fragmentation of Peptide and Oligosaccharide Ions Generated in an Elevated Pressure UV/IR-MALDI Ion Source Coupled to an Orthogonal Time-of-Flight Mass Spectrometer

(2009) Jens Soltwisch et al.   ANALYTICAL CHEMISTRY

Databases of homologous gene families for comparative genomics

(2009) Simon Penel et al.   BMC BIOINFORMATICS

Reanalysis ofTyrannosaurus rexMass Spectra

(2009) Marshall Bern et al.   JOURNAL OF PROTEOME RESEARCH

Low Cost, Scalable Proteomics Data Analysis Using Amazon’s Cloud Computing Services and Open Source Search Algorithms

(2009) Brian D. Halligan et al.   JOURNAL OF PROTEOME RESEARCH

A New Probabilistic Database Search Algorithm for ETD Spectra

(2009) Rovshan G. Sadygov et al.   JOURNAL OF PROTEOME RESEARCH

IDPicker 2.0: Improved Protein Assembly with High Discrimination Peptide Identification Filtering

(2009) Ze-Qiang Ma et al.   JOURNAL OF PROTEOME RESEARCH

Unbiased Statistical Analysis for Multi-Stage Proteomic Search Strategies

(2009) Logan J. Everett et al.   JOURNAL OF PROTEOME RESEARCH

Comparison of Database Search Strategies for High Precursor Mass Accuracy MS/MS Data

(2009) Edward J. Hsieh et al.   JOURNAL OF PROTEOME RESEARCH

Finding Chimeras: a Bioinformatics Strategy for Identification of Cross-linked Peptides

(2009) Feixia Chu et al.   MOLECULAR & CELLULAR PROTEOMICS

When less can yield more - Computational preprocessing of MS/MS spectra for peptide identification

(2009) Bernhard Y. Renard et al.   PROTEOMICS

MassMatrix: A database search program for rapid characterization of proteins and peptides from tandem mass spectrometry data

(2009) Hua Xu et al.   PROTEOMICS

De novosequencing of peptides by MS/MS

(2009) Joerg Seidler et al.   PROTEOMICS

A noise model for mass spectrometry based proteomics

(2008) P. Du et al.   BIOINFORMATICS

Modeling peptide fragmentation with dynamic Bayesian networks for peptide identification

(2008) A. A. Klammer et al.   BIOINFORMATICS

OpenMS – An open-source software framework for mass spectrometry

(2008) Marc Sturm et al.   BMC BIOINFORMATICS

RAId_DbS: mass-spectrometry based peptide identification web server with knowledge integration

(2008) Gelio Alves et al.   BMC GENOMICS

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

(2008) Brian C. Searle et al.   JOURNAL OF PROTEOME RESEARCH

A Fast SEQUEST Cross Correlation Algorithm

(2008) Jimmy K. Eng et al.   JOURNAL OF PROTEOME RESEARCH

Rapid and Accurate Peptide Identification from Tandem Mass Spectra

(2008) Christopher Y. Park et al.   JOURNAL OF PROTEOME RESEARCH

MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification

(2008) Jürgen Cox et al.   NATURE BIOTECHNOLOGY

TB database: an integrated platform for tuberculosis research

(2008) T. B. K. Reddy et al.   NUCLEIC ACIDS RESEARCH

Computational Methods for Protein Identification from Mass Spectrometry Data

(2008) Leo McHugh et al.   PLoS Computational Biology