Published in OMICS on July 17, 2012
MS-GF+ makes progress towards a universal database search tool for proteomics. Nat Commun (2014) 2.22
The mzQuantML data standard for mass spectrometry-based quantitative studies in proteomics. Mol Cell Proteomics (2013) 1.28
A software toolkit and interface for performing stable isotope labeling and top3 quantification using Progenesis LC-MS. OMICS (2012) 1.09
Open source libraries and frameworks for mass spectrometry based proteomics: a developer's perspective. Biochim Biophys Acta (2013) 1.00
Development of data representation standards by the human proteome organization proteomics standards initiative. J Am Med Inform Assoc (2015) 0.96
The jmzQuantML programming interface and validator for the mzQuantML data standard. Proteomics (2014) 0.90
The mzqLibrary--An open source Java library supporting the HUPO-PSI quantitative proteomics standard. Proteomics (2015) 0.84
A tutorial for software development in quantitative proteomics using PSI standard formats. Biochim Biophys Acta (2013) 0.83
Galaxy Integrated Omics: Web-based Standards-Compliant Workflows for Proteomics Informed by Transcriptomics. Mol Cell Proteomics (2015) 0.81
Quantitation of endogenous peptides using mass spectrometry based methods. Curr Opin Chem Biol (2013) 0.80
The application of Gaussian mixture models for signal quantification in MALDI-TOF mass spectrometry of peptides. PLoS One (2014) 0.80
A Quantitative Glycomics and Proteomics Combined Purification Strategy. J Vis Exp (2016) 0.79
Development of a 45kpsi ultrahigh pressure liquid chromatography instrument for gradient separations of peptides using long microcapillary columns and sub-2μm particles. J Chromatogr A (2016) 0.78
Proteomic approaches to uncovering virus-host protein interactions during the progression of viral infection. Expert Rev Proteomics (2016) 0.77
Perturbational Profiling of Metabolites in Patient Fibroblasts Implicates α-Aminoadipate as a Potential Biomarker for Bipolar Disorder. Mol Neuropsychiatry (2016) 0.75
Bioinformatics challenges and solutions in proteomics as quantitative methods mature. OMICS (2012) 0.75
An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database. J Am Soc Mass Spectrom (1994) 45.51
MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification. Nat Biotechnol (2008) 38.00
Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search. Anal Chem (2002) 35.30
Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics. Mol Cell Proteomics (2002) 30.58
A statistical model for identifying proteins by tandem mass spectrometry. Anal Chem (2003) 29.58
Mass spectrometry-based proteomics. Nature (2003) 28.94
Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry. Nat Methods (2007) 25.29
Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nat Biotechnol (1999) 21.92
A model for random sampling and estimation of relative protein abundance in shotgun proteomics. Anal Chem (2004) 19.20
TANDEM: matching proteins with tandem mass spectra. Bioinformatics (2004) 17.41
Open mass spectrometry search algorithm. J Proteome Res (2004) 15.25
Skyline: an open source document editor for creating and analyzing targeted proteomics experiments. Bioinformatics (2010) 13.35
A common open representation of mass spectrometry data and its application to proteomics research. Nat Biotechnol (2004) 11.42
Absolute quantification of proteins and phosphoproteins from cell lysates by tandem MS. Proc Natl Acad Sci U S A (2003) 10.82
Exponentially modified protein abundance index (emPAI) for estimation of absolute protein amount in proteomics by the number of sequenced peptides per protein. Mol Cell Proteomics (2005) 10.67
Absolute protein expression profiling estimates the relative contributions of transcriptional and translational regulation. Nat Biotechnol (2006) 9.95
A uniform proteomics MS/MS analysis platform utilizing open XML file formats. Mol Syst Biol (2005) 9.81
ProteoWizard: open source software for rapid proteomics tools development. Bioinformatics (2008) 9.47
Mass spectrometry and protein analysis. Science (2006) 8.05
Mass spectrometry-based proteomics turns quantitative. Nat Chem Biol (2005) 7.52
Quantitative mass spectrometry in proteomics: a critical review. Anal Bioanal Chem (2007) 6.80
InsPecT: identification of posttranslationally modified peptides from tandem mass spectra. Anal Chem (2005) 6.65
Tandem mass tags: a novel quantification strategy for comparative analysis of complex protein mixtures by MS/MS. Anal Chem (2003) 6.63
Selected reaction monitoring for quantitative proteomics: a tutorial. Mol Syst Biol (2008) 6.38
Large-scale proteomic analysis of the human spliceosome. Genome Res (2002) 5.75
Quantitative profiling of differentiation-induced microsomal proteins using isotope-coded affinity tags and mass spectrometry. Nat Biotechnol (2001) 5.69
Mass spectrometric quantitation of peptides and proteins using Stable Isotope Standards and Capture by Anti-Peptide Antibodies (SISCAPA). J Proteome Res (2004) 5.57
A guided tour of the Trans-Proteomic Pipeline. Proteomics (2010) 5.09
A practical guide to the MaxQuant computational platform for SILAC-based quantitative proteomics. Nat Protoc (2009) 4.84
mzML--a community standard for mass spectrometry data. Mol Cell Proteomics (2010) 4.81
MS1, MS2, and SQT-three unified, compact, and easily parsed file formats for the storage of shotgun proteomic spectra and identifications. Rapid Commun Mass Spectrom (2004) 4.76
Automated approach for quantitative analysis of complex peptide mixtures from tandem mass spectra. Nat Methods (2004) 4.62
TOPP--the OpenMS proteomics pipeline. Bioinformatics (2007) 4.37
The proteomics standards initiative. Proteomics (2003) 3.78
A survey of computational methods and error rate estimation procedures for peptide and protein identification in shotgun proteomics. J Proteomics (2010) 3.78
Development and validation of a spectral library searching method for peptide identification from MS/MS. Proteomics (2007) 3.74
The absolute quantification strategy: a general procedure for the quantification of proteins and post-translational modifications. Methods (2005) 3.71
SuperHirn - a novel tool for high resolution LC-MS-based peptide/protein profiling. Proteomics (2007) 3.60
Systems biology, proteomics, and the future of health care: toward predictive, preventative, and personalized medicine. J Proteome Res (2004) 3.46
An assessment of software solutions for the analysis of mass spectrometry based quantitative proteomics data. J Proteome Res (2008) 3.36
A quantitative analysis software tool for mass spectrometry-based proteomics. Nat Methods (2008) 3.35
Automated statistical analysis of protein abundance ratios from data generated by stable-isotope dilution and tandem mass spectrometry. Anal Chem (2003) 3.33
VIPER: an advanced software package to support high-throughput LC-MS peptide identification. Bioinformatics (2007) 3.15
mProphet: automated data processing and statistical validation for large-scale SRM experiments. Nat Methods (2011) 3.10
Quantitative proteomic analysis by accurate mass retention time pairs. Anal Chem (2005) 3.05
Using annotated peptide mass spectrum libraries for protein identification. J Proteome Res (2006) 3.03
ProbID: a probabilistic algorithm to identify peptides through sequence database searching using tandem mass spectral data. Proteomics (2002) 3.01
Protein labeling by iTRAQ: a new tool for quantitative mass spectrometry in proteome research. Proteomics (2007) 2.97
The mzIdentML data standard for mass spectrometry-based proteomics results. Mol Cell Proteomics (2012) 2.82
Multiplexed absolute quantification in proteomics using artificial QCAT proteins of concatenated signature peptides. Nat Methods (2005) 2.81
OLAV: towards high-throughput tandem mass spectrometry data identification. Proteomics (2003) 2.73
Platform-independent and label-free quantitation of proteomic data using MS1 extracted ion chromatograms in skyline: application to protein acetylation and phosphorylation. Mol Cell Proteomics (2012) 2.66
Charting the proteomes of organisms with unsequenced genomes by MALDI-quadrupole time-of-flight mass spectrometry and BLAST homology searching. Anal Chem (2001) 2.65
MSQuant, an open source platform for mass spectrometry-based quantitative proteomics. J Proteome Res (2010) 2.40
Multiplexed absolute quantification for proteomics using concatenated signature peptides encoded by QconCAT genes. Nat Protoc (2006) 2.37
i-Tracker: for quantitative proteomics using iTRAQ. BMC Genomics (2005) 2.22
A software suite for the generation and comparison of peptide arrays from sets of data collected by liquid chromatography-mass spectrometry. Mol Cell Proteomics (2005) 2.08
Role of spectral counting in quantitative proteomics. Expert Rev Proteomics (2010) 2.00
jmzML, an open-source Java API for mzML, the PSI standard for MS data. Proteomics (2010) 1.96
A novel strategy for quantitative proteomics using isotope-coded protein labels. Proteomics (2005) 1.91
PEPPeR, a platform for experimental proteomic pattern recognition. Mol Cell Proteomics (2006) 1.90
Critical assessment of alignment procedures for LC-MS proteomics and metabolomics measurements. BMC Bioinformatics (2008) 1.80
The proteios software environment: an extensible multiuser platform for management and analysis of proteomics data. J Proteome Res (2009) 1.76
MapQuant: open-source software for large-scale protein quantification. Proteomics (2006) 1.66
TraML--a standard format for exchange of selected reaction monitoring transition lists. Mol Cell Proteomics (2011) 1.65
The APEX Quantitative Proteomics Tool: generating protein quantitation estimates from LC-MS/MS proteomics results. BMC Bioinformatics (2008) 1.54
Isotope dilution strategies for absolute quantitative proteomics. J Proteomics (2009) 1.54
jmzIdentML API: A Java interface to the mzIdentML standard for peptide and protein identification data. Proteomics (2012) 1.44
A geometric approach for the alignment of liquid chromatography-mass spectrometry data. Bioinformatics (2007) 1.44
ZoomQuant: an application for the quantitation of stable isotope labeled peptides. J Am Soc Mass Spectrom (2005) 1.41
Multi-Q: a fully automated tool for multiplexed protein quantitation. J Proteome Res (2006) 1.38
Mascot file parsing and quantification (MFPaQ), a new software to parse, validate, and quantify proteomics data generated by ICAT and SILAC mass spectrometric analyses: application to the proteomics study of membrane proteins from primary human endothelial cells. Mol Cell Proteomics (2007) 1.27
Peptide mass fingerprinting. Methods (2005) 1.24
Automated quantification tool for high-throughput proteomics using stable isotope labeling and LC-MSn. Anal Chem (2006) 1.20
Semi-supervised LC/MS alignment for differential proteomics. Bioinformatics (2006) 1.19
Free computational resources for designing selected reaction monitoring transitions. Proteomics (2010) 1.17
Global absolute quantification of a proteome: Challenges in the deployment of a QconCAT strategy. Proteomics (2011) 1.16
ProRata: A quantitative proteomics program for accurate protein abundance ratio estimation with confidence interval evaluation. Anal Chem (2006) 1.16
CONSeQuence: prediction of reference peptides for absolute quantitative proteomics using consensus machine learning approaches. Mol Cell Proteomics (2011) 1.12
Computational methods for protein identification from mass spectrometry data. PLoS Comput Biol (2008) 1.10
Biomarker discovery and clinical proteomics. Trends Analyt Chem (2010) 1.06
Protein identification: the origins of peptide mass fingerprinting. J Am Soc Mass Spectrom (2003) 1.03
STEM: a software tool for large-scale proteomic data analyses. J Proteome Res (2005) 1.00
Capture and analysis of quantitative proteomic data. Proteomics (2007) 0.96
Software for computational peptide identification from MS-MS data. Drug Discov Today (2006) 0.96
Toward objective evaluation of proteomic algorithms. Nat Methods (2012) 0.96
LC-MS for protein characterization: current capabilities and future trends. Expert Rev Proteomics (2008) 0.94
The Multi-Q web server for multiplexed protein quantitation. Nucleic Acids Res (2007) 0.92
Qupe--a Rich Internet Application to take a step forward in the analysis of mass spectrometry-based quantitative proteomics experiments. Bioinformatics (2009) 0.86
MaXIC-Q Web: a fully automated web service using statistical and computational methods for protein quantitation based on stable isotope labeling and LC-MS. Nucleic Acids Res (2009) 0.79
The minimum information about a genome sequence (MIGS) specification. Nat Biotechnol (2008) 31.04
Reactome knowledgebase of human biological pathways and processes. Nucleic Acids Res (2008) 15.69
The PRoteomics IDEntifications (PRIDE) database and associated tools: status in 2013. Nucleic Acids Res (2012) 13.14
Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project. Nat Biotechnol (2008) 12.96
A common open representation of mass spectrometry data and its application to proteomics research. Nat Biotechnol (2004) 11.42
Reactome: a database of reactions, pathways and biological processes. Nucleic Acids Res (2010) 11.23
The minimum information about a proteomics experiment (MIAPE). Nat Biotechnol (2007) 10.24
The Ontology Lookup Service, a lightweight cross-platform tool for controlled vocabulary queries. BMC Bioinformatics (2006) 8.68
The Reactome pathway knowledgebase. Nucleic Acids Res (2013) 8.56
The minimum information required for reporting a molecular interaction experiment (MIMIx). Nat Biotechnol (2007) 8.24
Broadening the horizon--level 2.5 of the HUPO-PSI format for molecular interactions. BMC Biol (2007) 8.03
PRIDE: the proteomics identifications database. Proteomics (2005) 7.52
The IntAct molecular interaction database in 2012. Nucleic Acids Res (2011) 7.49
Calling on a million minds for community annotation in WikiProteins. Genome Biol (2008) 7.11
Integrating biological data--the Distributed Annotation System. BMC Bioinformatics (2008) 6.56
A guide to the Proteomics Identifications Database proteomics data repository. Proteomics (2009) 5.63
A genetic variation map for chicken with 2.8 million single-nucleotide polymorphisms. Nature (2004) 5.24
PSICQUIC and PSISCORE: accessing and scoring molecular interactions. Nat Methods (2011) 5.01
mzML--a community standard for mass spectrometry data. Mol Cell Proteomics (2010) 4.81
The Ontology Lookup Service: more data and better tools for controlled vocabulary queries. Nucleic Acids Res (2008) 4.73
Toward interoperable bioscience data. Nat Genet (2012) 4.72
Allele frequency net: a database and online repository for immune gene frequencies in worldwide populations. Nucleic Acids Res (2010) 4.62
The Proteomics Identifications database: 2010 update. Nucleic Acids Res (2009) 4.47
PRIDE: new developments and new datasets. Nucleic Acids Res (2007) 4.42
The MIntAct project--IntAct as a common curation platform for 11 molecular interaction databases. Nucleic Acids Res (2013) 4.39
PRIDE: a public repository of protein and peptide identifications for the proteomics community. Nucleic Acids Res (2006) 4.19
The Protein Identifier Cross-Referencing (PICR) service: reconciling protein identifiers across multiple source databases. BMC Bioinformatics (2007) 3.97
The implications of alternative splicing in the ENCODE protein complement. Proc Natl Acad Sci U S A (2007) 3.93
The proteomics standards initiative. Proteomics (2003) 3.78
Recommendations from the 2008 International Summit on Proteomics Data Release and Sharing Policy: the Amsterdam principles. J Proteome Res (2009) 3.77
The Proteomics Identifications Database (PRIDE) and the ProteomExchange Consortium: making proteomics data accessible. Expert Rev Proteomics (2006) 3.74
Five years of progress in the Standardization of Proteomics Data 4th Annual Spring Workshop of the HUPO-Proteomics Standards Initiative April 23-25, 2007 Ecole Nationale Supérieure (ENS), Lyon, France. Proteomics (2007) 3.69
A systematic approach to modeling, capturing, and disseminating proteomics experimental data. Nat Biotechnol (2003) 3.57
The Functional Genomics Experiment model (FuGE): an extensible framework for standards in functional genomics. Nat Biotechnol (2007) 3.55
A strategy capitalizing on synergies: the Reporting Structure for Biological Investigation (RSBI) working group. OMICS (2006) 3.51
H7N9 influenza viruses are transmissible in ferrets by respiratory droplet. Science (2013) 3.33
Dasty2, an Ajax protein DAS client. Bioinformatics (2008) 3.26
Protein interaction data curation: the International Molecular Exchange (IMEx) consortium. Nat Methods (2012) 3.17
Mapping the Arabidopsis organelle proteome. Proc Natl Acad Sci U S A (2006) 3.03
Clinical proteomics: A need to define the field and to begin to set adequate standards. Proteomics Clin Appl (2007) 2.84
The mzIdentML data standard for mass spectrometry-based proteomics results. Mol Cell Proteomics (2012) 2.82
Protein-folding location can regulate manganese-binding versus copper- or zinc-binding. Nature (2008) 2.81
Submit your interaction data the IMEx way: a step by step guide to trouble-free deposition. Proteomics (2007) 2.74
Dasty and UniProt DAS: a perfect pair for protein feature visualization. Bioinformatics (2005) 2.74
Global translational responses to oxidative stress impact upon multiple levels of protein synthesis. J Biol Chem (2006) 2.66
InterPro: an integrated documentation resource for protein families, domains and functional sites. Brief Bioinform (2002) 2.66
Tyrosine phosphorylation of mitochondrial pyruvate dehydrogenase kinase 1 is important for cancer metabolism. Mol Cell (2011) 2.61
BioJS: an open source JavaScript framework for biological data visualization. Bioinformatics (2013) 2.53
A comprehensive collection of chicken cDNAs. Curr Biol (2002) 2.47
Phosphoglycerate mutase 1 coordinates glycolysis and biosynthesis to promote tumor growth. Cancer Cell (2012) 2.39
The work of the Human Proteome Organisation's Proteomics Standards Initiative (HUPO PSI). OMICS (2006) 2.38
Annotating cancer variants and anti-cancer therapeutics in reactome. Cancers (Basel) (2012) 2.35
The Protein Feature Ontology: a tool for the unification of protein feature annotations. Bioinformatics (2008) 2.33
Pituitary homeobox 2 (PITX2) promotes thyroid carcinogenesis by activation of cyclin D2. Cell Cycle (2010) 2.29
The use of common ontologies and controlled vocabularies to enable data exchange and deposition for complex proteomic experiments. Pac Symp Biocomput (2005) 2.29
The Ontology Lookup Service: bigger and better. Nucleic Acids Res (2010) 2.27
i-Tracker: for quantitative proteomics using iTRAQ. BMC Genomics (2005) 2.22
Differential expression of ion channel transcripts in atrial muscle and sinoatrial node in rabbit. Circ Res (2006) 2.17
Global gene expression profiling reveals widespread yet distinctive translational responses to different eukaryotic translation initiation factor 2B-targeting stress pathways. Mol Cell Biol (2005) 2.13
The PRoteomics IDEntification (PRIDE) Converter 2 framework: an improved suite of tools to facilitate data submission to the PRIDE database and the ProteomeXchange consortium. Mol Cell Proteomics (2012) 2.10
PRIDE Inspector: a tool to visualize and validate MS proteomics data. Nat Biotechnol (2012) 2.10
ProteomeBinders: planning a European resource of affinity reagents for analysis of the human proteome. Nat Methods (2007) 2.04
UKPMC: a full text article resource for the life sciences. Nucleic Acids Res (2010) 1.92
MINT and IntAct contribute to the Second BioCreative challenge: serving the text-mining community with high quality molecular interaction data. Genome Biol (2008) 1.76
Recent developments in public proteomic MS repositories and pipelines. Proteomics (2009) 1.72
Common interchange standards for proteomics data: Public availability of tools and schema. Proteomics (2004) 1.68
Comparative genome analysis of filamentous fungi reveals gene family expansions associated with fungal pathogenesis. PLoS One (2008) 1.68
Dasty3, a WEB framework for DAS. Bioinformatics (2011) 1.67
The Reactome BioMart. Database (Oxford) (2011) 1.66
PRIDE: quality control in a proteomics data repository. Database (Oxford) (2012) 1.63
The PSI semantic validator: a framework to check MIAPE compliance of proteomics data. Proteomics (2009) 1.62
A reagent resource to identify proteins and peptides of interest for the cancer community: a workshop report. Mol Cell Proteomics (2006) 1.60
The chicken as a model for large-scale analysis of vertebrate gene function. Nat Rev Genet (2003) 1.57
Guidelines for reporting the use of gel electrophoresis in proteomics. Nat Biotechnol (2008) 1.54
Further steps towards data standardisation: the Proteomic Standards Initiative HUPO 3(rd) annual congress, Beijing 25-27(th) October, 2004. Proteomics (2005) 1.54
jmzReader: A Java parser library to process and visualize multiple text and XML-based mass spectrometry data formats. Proteomics (2012) 1.49
implementing data standards: a report on the HUPOPSI workshop September 2009, Toronto, Canada. Proteomics (2010) 1.46
From Peptidome to PRIDE: public proteomics data migration at a large scale. Proteomics (2013) 1.46
Minimum information about a bioactive entity (MIABE). Nat Rev Drug Discov (2011) 1.44
jmzIdentML API: A Java interface to the mzIdentML standard for peptide and protein identification data. Proteomics (2012) 1.44
Making proteomics data accessible and reusable: current state of proteomics databases and repositories. Proteomics (2015) 1.44
Recurated protein interaction datasets. Nat Methods (2009) 1.43
Identifying the important HIV-1 recombination breakpoints. PLoS Comput Biol (2008) 1.42
Upstream sequence elements direct post-transcriptional regulation of gene expression under stress conditions in yeast. BMC Genomics (2009) 1.42
MRMaid, the web-based tool for designing multiple reaction monitoring (MRM) transitions. Mol Cell Proteomics (2008) 1.41
trans-Diaqua-bis-(1H-imidazole-4-carboxyl-ato-κN,O)nickel(II). Acta Crystallogr Sect E Struct Rep Online (2011) 1.40
Intraventricular craniopharyngioma: morphological analysis and outcome evaluation of 17 cases. Acta Neurochir (Wien) (2011) 1.40
Analyzing large-scale proteomics projects with latent semantic indexing. J Proteome Res (2007) 1.39
Improving sensitivity in proteome studies by analysis of false discovery rates for multiple search engines. Proteomics (2009) 1.37
Data management and preliminary data analysis in the pilot phase of the HUPO Plasma Proteome Project. Proteomics (2005) 1.37
The proteome of Toxoplasma gondii: integration with the genome provides novel insights into gene expression and annotation. Genome Biol (2008) 1.35
Meeting Report from the Second "Minimum Information for Biological and Biomedical Investigations" (MIBBI) workshop. Stand Genomic Sci (2010) 1.35
Di-μ-chlorido-bis-{[2-(8-quinol-yloxy)-acetato-κN,O,O]copper(II)}. Acta Crystallogr Sect E Struct Rep Online (2008) 1.35