Published in Proteomics on March 01, 2010
mzML--a community standard for mass spectrometry data. Mol Cell Proteomics (2010) 4.81
The CRAPome: a contaminant repository for affinity purification-mass spectrometry data. Nat Methods (2013) 4.34
A survey of computational methods and error rate estimation procedures for peptide and protein identification in shotgun proteomics. J Proteomics (2010) 3.78
Quantitative analysis of fission yeast transcriptomes and proteomes in proliferating and quiescent cells. Cell (2012) 3.26
PASSEL: the PeptideAtlas SRMexperiment library. Proteomics (2012) 3.14
Survey of tyrosine kinase signaling reveals ROS kinase fusions in human cholangiocarcinoma. PLoS One (2011) 3.10
iProphet: multi-level integrative analysis of shotgun proteomic data improves peptide and protein identification rates and error estimates. Mol Cell Proteomics (2011) 2.88
Mass spectrometry-based proteomics in cell biology. J Cell Biol (2010) 2.66
A complete mass-spectrometric map of the yeast proteome applied to quantitative trait analysis. Nature (2013) 2.61
MS-GF+ makes progress towards a universal database search tool for proteomics. Nat Commun (2014) 2.22
COMPASS: a suite of pre- and post-search proteomics software tools for OMSSA. Proteomics (2011) 2.19
Protein analysis by shotgun/bottom-up proteomics. Chem Rev (2013) 2.13
Analysis of high accuracy, quantitative proteomics data in the MaxQB database. Mol Cell Proteomics (2012) 1.81
DIA-Umpire: comprehensive computational framework for data-independent acquisition proteomics. Nat Methods (2015) 1.77
The state of the human proteome in 2012 as viewed through PeptideAtlas. J Proteome Res (2012) 1.72
The complete structure of the large subunit of the mammalian mitochondrial ribosome. Nature (2014) 1.67
Vinculin network-mediated cytoskeletal remodeling regulates contractile function in the aging heart. Sci Transl Med (2015) 1.59
State of the human proteome in 2013 as viewed through PeptideAtlas: comparing the kidney, urine, and plasma proteomes for the biology- and disease-driven Human Proteome Project. J Proteome Res (2013) 1.52
LC-MS data processing with MAVEN: a metabolomic analysis and visualization engine. Curr Protoc Bioinformatics (2012) 1.52
Estimation of absolute protein quantities of unlabeled samples by selected reaction monitoring mass spectrometry. Mol Cell Proteomics (2011) 1.51
Comparative Analysis of Label-Free and 8-Plex iTRAQ Approach for Quantitative Tissue Proteomic Analysis. PLoS One (2015) 1.50
Multiplex N-terminome analysis of MMP-2 and MMP-9 substrate degradomes by iTRAQ-TAILS quantitative proteomics. Mol Cell Proteomics (2010) 1.48
Making proteomics data accessible and reusable: current state of proteomics databases and repositories. Proteomics (2015) 1.44
The neXtProt knowledgebase on human proteins: current status. Nucleic Acids Res (2015) 1.42
Comparative analysis of different label-free mass spectrometry based protein abundance estimates and their correlation with RNA-Seq gene expression data. J Proteome Res (2012) 1.39
Gasdermin D is an executor of pyroptosis and required for interleukin-1β secretion. Cell Res (2015) 1.37
The protein expression landscape of the Arabidopsis root. Proc Natl Acad Sci U S A (2012) 1.36
Proteomics data repositories: providing a safe haven for your data and acting as a springboard for further research. J Proteomics (2010) 1.35
GProX, a user-friendly platform for bioinformatics analysis and visualization of quantitative proteomics data. Mol Cell Proteomics (2011) 1.30
Meta-omic characterization of the marine invertebrate microbial consortium that produces the chemotherapeutic natural product ET-743. ACS Chem Biol (2011) 1.26
A critical appraisal of techniques, software packages, and standards for quantitative proteomic analysis. OMICS (2012) 1.25
Abacus: a computational tool for extracting and pre-processing spectral count data for label-free quantitative proteomic analysis. Proteomics (2011) 1.24
Rapid mass spectrometric conversion of tissue biopsy samples into permanent quantitative digital proteome maps. Nat Med (2015) 1.22
Computational and informatics strategies for identification of specific protein interaction partners in affinity purification mass spectrometry experiments. Proteomics (2012) 1.21
Analyzing protein-protein interactions from affinity purification-mass spectrometry data with SAINT. Curr Protoc Bioinformatics (2012) 1.20
Combining results of multiple search engines in proteomics. Mol Cell Proteomics (2013) 1.20
Proteomic analyses reveal an acidic prime side specificity for the astacin metalloprotease family reflected by physiological substrates. Mol Cell Proteomics (2011) 1.20
Trans-Proteomic Pipeline, a standardized data processing pipeline for large-scale reproducible proteomics informatics. Proteomics Clin Appl (2015) 1.19
Total and putative surface proteomics of malaria parasite salivary gland sporozoites. Mol Cell Proteomics (2013) 1.19
Computational mass spectrometry-based proteomics. PLoS Comput Biol (2011) 1.18
mz5: space- and time-efficient storage of mass spectrometry data sets. Mol Cell Proteomics (2011) 1.16
Analysis of protein mixtures from whole-cell extracts by single-run nanoLC-MS/MS using ultralong gradients. Nat Protoc (2012) 1.10
Maintenance of gene silencing by the coordinate action of the H3K9 methyltransferase G9a/KMT1C and the H3K4 demethylase Jarid1a/KDM5A. Proc Natl Acad Sci U S A (2012) 1.10
Interaction proteome of human Hippo signaling: modular control of the co-activator YAP1. Mol Syst Biol (2013) 1.10
Stable-isotope-labeled histone peptide library for histone post-translational modification and variant quantification by mass spectrometry. Mol Cell Proteomics (2014) 1.08
Quantitative proteomics analysis of signalosome dynamics in primary T cells identifies the surface receptor CD6 as a Lat adaptor-independent TCR signaling hub. Nat Immunol (2014) 1.07
A face in the crowd: recognizing peptides through database search. Mol Cell Proteomics (2011) 1.07
Crux: rapid open source protein tandem mass spectrometry analysis. J Proteome Res (2014) 1.06
Deep coverage of the Escherichia coli proteome enables the assessment of false discovery rates in simple proteogenomic experiments. Mol Cell Proteomics (2013) 1.05
A statistics-based platform for quantitative N-terminome analysis and identification of protease cleavage products. Mol Cell Proteomics (2010) 1.05
The substrate degradome of meprin metalloproteases reveals an unexpected proteolytic link between meprin β and ADAM10. Cell Mol Life Sci (2012) 1.05
A mass spectrometric-derived cell surface protein atlas. PLoS One (2015) 1.04
VAPs and ACBD5 tether peroxisomes to the ER for peroxisome maintenance and lipid homeostasis. J Cell Biol (2017) 1.04
File formats commonly used in mass spectrometry proteomics. Mol Cell Proteomics (2012) 1.01
Quantitative proteomic analysis of HIV-1 infected CD4+ T cells reveals an early host response in important biological pathways: protein synthesis, cell proliferation, and T-cell activation. Virology (2012) 1.01
Open source libraries and frameworks for mass spectrometry based proteomics: a developer's perspective. Biochim Biophys Acta (2013) 1.00
Proximity biotinylation and affinity purification are complementary approaches for the interactome mapping of chromatin-associated protein complexes. J Proteomics (2014) 1.00
Cross-linking measurements of the Potato leafroll virus reveal protein interaction topologies required for virion stability, aphid transmission, and virus-plant interactions. J Proteome Res (2012) 1.00
Computational approaches to protein inference in shotgun proteomics. BMC Bioinformatics (2012) 0.99
A fast workflow for identification and quantification of proteomes. Mol Cell Proteomics (2013) 0.98
Personal genomes, quantitative dynamic omics and personalized medicine. Quant Biol (2013) 0.98
Tools (Viewer, Library and Validator) that facilitate use of the peptide and protein identification standard format, termed mzIdentML. Mol Cell Proteomics (2013) 0.97
Using PeptideAtlas, SRMAtlas, and PASSEL: Comprehensive Resources for Discovery and Targeted Proteomics. Curr Protoc Bioinformatics (2014) 0.96
Lapatinib-binding protein kinases in the African trypanosome: identification of cellular targets for kinase-directed chemical scaffolds. PLoS One (2013) 0.96
Sites of ubiquitin attachment in Saccharomyces cerevisiae. Proteomics (2011) 0.95
Structure and regulation of the cellulose degradome in Clostridium cellulolyticum. Biotechnol Biofuels (2013) 0.95
Big biomedical data as the key resource for discovery science. J Am Med Inform Assoc (2015) 0.95
Surrogate genetics and metabolic profiling for characterization of human disease alleles. Genetics (2012) 0.94
Investigating neoplastic progression of ulcerative colitis with label-free comparative proteomics. J Proteome Res (2010) 0.94
Divide and conquer: the application of organelle proteomics to heart failure. Circ Res (2011) 0.94
TolC-dependent secretion of an ankyrin repeat-containing protein of Rickettsia typhi. J Bacteriol (2012) 0.94
HDXFinder: automated analysis and data reporting of deuterium/hydrogen exchange mass spectrometry. J Am Soc Mass Spectrom (2011) 0.93
Proteomics portrait of archival lesions of chronic pancreatitis. PLoS One (2011) 0.93
A statistical model-building perspective to identification of MS/MS spectra with PeptideProphet. BMC Bioinformatics (2012) 0.93
Visualize: a free and open source multifunction tool for proteomics data analysis. Proteomics (2011) 0.93
Using ProHits to store, annotate, and analyze affinity purification-mass spectrometry (AP-MS) data. Curr Protoc Bioinformatics (2012) 0.92
Molecular networking and pattern-based genome mining improves discovery of biosynthetic gene clusters and their products from Salinispora species. Chem Biol (2015) 0.92
Simulation Analysis Platform (SnAP): a tool for evaluation of public health surveillance and disease control strategies. AMIA Annu Symp Proc (2011) 0.92
Nanospray FAIMS fractionation provides significant increases in proteome coverage of unfractionated complex protein digests. Mol Cell Proteomics (2011) 0.92
Extensive mass spectrometry-based analysis of the fission yeast proteome: the Schizosaccharomyces pombe PeptideAtlas. Mol Cell Proteomics (2013) 0.92
Utility of RNA-seq and GPMDB protein observation frequency for improving the sensitivity of protein identification by tandem MS. J Proteome Res (2014) 0.91
A mass spectrometry proteomics data management platform. Mol Cell Proteomics (2012) 0.90
A honey bee (Apis mellifera L.) PeptideAtlas crossing castes and tissues. BMC Genomics (2011) 0.89
Evaluation of proteomic search engines for the analysis of histone modifications. J Proteome Res (2014) 0.89
Analysis of mass spectrometry data from the secretome of an explant model of articular cartilage exposed to pro-inflammatory and anti-inflammatory stimuli using machine learning. BMC Musculoskelet Disord (2013) 0.89
Mycobacterium tuberculosis supports protein tyrosine phosphorylation. Proc Natl Acad Sci U S A (2014) 0.89
LuciPHOr: algorithm for phosphorylation site localization with false localization rate estimation using modified target-decoy approach. Mol Cell Proteomics (2013) 0.88
A RanGTP-independent mechanism allows ribosomal protein nuclear import for ribosome assembly. Elife (2014) 0.88
Integrated phosphoproteomics analysis of a signaling network governing nutrient response and peroxisome induction. Mol Cell Proteomics (2010) 0.88
Survey of activated FLT3 signaling in leukemia. PLoS One (2011) 0.88
Building and searching tandem mass spectral libraries for peptide identification. Mol Cell Proteomics (2011) 0.88
Quantitative proteomic and interaction network analysis of cisplatin resistance in HeLa cells. PLoS One (2011) 0.87
The interaction of the von Hippel-Lindau tumor suppressor and heterochromatin protein 1. Arch Biochem Biophys (2012) 0.86
Assessing the translational landscape of myogenic differentiation by ribosome profiling. Nucleic Acids Res (2015) 0.86
Numerical compression schemes for proteomics mass spectrometry data. Mol Cell Proteomics (2014) 0.85
VESPA: software to facilitate genomic annotation of prokaryotic organisms through integration of proteomic and transcriptomic data. BMC Genomics (2012) 0.85
Proteomic dissection of the von Hippel-Lindau (VHL) interactome. J Proteome Res (2011) 0.85
Current approaches on viral infection: proteomics and functional validations. Front Microbiol (2012) 0.85
Proteomic amino-termini profiling reveals targeting information for protein import into complex plastids. PLoS One (2013) 0.85
Major histocompatibility complex class II+ invariant chain negative breast cancer cells present unique peptides that activate tumor-specific T cells from breast cancer patients. Mol Cell Proteomics (2012) 0.85
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
Probability-based protein identification by searching sequence databases using mass spectrometry data. Electrophoresis (1999) 45.01
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
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
TANDEM: matching proteins with tandem mass spectra. Bioinformatics (2004) 17.41
Open mass spectrometry search algorithm. J Proteome Res (2004) 15.25
A common open representation of mass spectrometry data and its application to proteomics research. Nat Biotechnol (2004) 11.42
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
PRIDE: the proteomics identifications database. Proteomics (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
PeptideAtlas: a resource for target selection for emerging targeted proteomics workflows. EMBO Rep (2008) 6.10
MyriMatch: highly accurate tandem mass spectral peptide identification by multivariate hypergeometric analysis. J Proteome Res (2007) 5.85
Quantitative profiling of differentiation-induced microsomal proteins using isotope-coded affinity tags and mass spectrometry. Nat Biotechnol (2001) 5.69
TOPP--the OpenMS proteomics pipeline. Bioinformatics (2007) 4.37
Computational Proteomics Analysis System (CPAS): an extensible, open-source analytic system for evaluating and publishing proteomic data and high throughput biological experiments. J Proteome Res (2006) 4.32
Development and validation of a spectral library searching method for peptide identification from MS/MS. Proteomics (2007) 3.74
Reporting protein identification data: the next generation of guidelines. Mol Cell Proteomics (2006) 3.50
mzML: a single, unifying data format for mass spectrometer output. Proteomics (2008) 3.45
General framework for developing and evaluating database scoring algorithms using the TANDEM search engine. Bioinformatics (2006) 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
Targeted quantitative analysis of Streptococcus pyogenes virulence factors by multiple reaction monitoring. Mol Cell Proteomics (2008) 3.29
ProbID: a probabilistic algorithm to identify peptides through sequence database searching using tandem mass spectral data. Proteomics (2002) 3.01
MRMer, an interactive open source and cross-platform system for data extraction and visualization of multiple reaction monitoring experiments. Mol Cell Proteomics (2008) 2.89
Analysis, statistical validation and dissemination of large-scale proteomics datasets generated by tandem MS. Drug Discov Today (2004) 2.82
The standard protein mix database: a diverse data set to assist in the production of improved Peptide and protein identification software tools. J Proteome Res (2007) 2.77
A perspective on the use of iTRAQ reagent technology for protein complex and profiling studies. J Exp Bot (2006) 2.50
DeconMSn: a software tool for accurate parent ion monoisotopic mass determination for tandem mass spectra. Bioinformatics (2008) 2.38
False discovery rates and related statistical concepts in mass spectrometry-based proteomics. J Proteome Res (2007) 2.36
Semisupervised model-based validation of peptide identifications in mass spectrometry-based proteomics. J Proteome Res (2007) 2.33
Data analysis and bioinformatics tools for tandem mass spectrometry in proteomics. Physiol Genomics (2008) 2.23
Statistical validation of peptide identifications in large-scale proteomics using the target-decoy database search strategy and flexible mixture modeling. J Proteome Res (2007) 2.09
Stable isotope labeling by amino acids in cell culture for quantitative proteomics. Methods Mol Biol (2007) 1.96
SBEAMS-Microarray: database software supporting genomic expression analyses for systems biology. BMC Bioinformatics (2006) 1.94
The protein information and property explorer: an easy-to-use, rich-client web application for the management and functional analysis of proteomic data. Bioinformatics (2008) 1.81
A tool to visualize and evaluate data obtained by liquid chromatography-electrospray ionization-mass spectrometry. Anal Chem (2004) 1.74
Automated identification of SUMOylation sites using mass spectrometry and SUMmOn pattern recognition software. Nat Methods (2006) 1.68
YPED: a web-accessible database system for protein expression analysis. J Proteome Res (2007) 1.28
Revised draft guidelines for proteomic data publication. Mol Cell Proteomics (2005) 1.21
Trans-Proteomic Pipeline supports and improves analysis of electron transfer dissociation data sets. Proteomics (2010) 1.11
MaRiMba: a software application for spectral library-based MRM transition list assembly. J Proteome Res (2009) 0.99
High-performance peptide identification by tandem mass spectrometry allows reliable automatic data processing in proteomics. Proteomics (2004) 0.98
Getting started in computational mass spectrometry-based proteomics. PLoS Comput Biol (2009) 0.98
Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search. Anal Chem (2002) 35.30
Circulating microRNAs as stable blood-based markers for cancer detection. Proc Natl Acad Sci U S A (2008) 33.65
A statistical model for identifying proteins by tandem mass spectrometry. Anal Chem (2003) 29.58
Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature (2004) 24.40
A common open representation of mass spectrometry data and its application to proteomics research. Nat Biotechnol (2004) 11.42
The minimum information about a proteomics experiment (MIAPE). Nat Biotechnol (2007) 10.24
A uniform proteomics MS/MS analysis platform utilizing open XML file formats. Mol Syst Biol (2005) 9.81
Mass spectrometry and protein analysis. Science (2006) 8.05
The PeptideAtlas project. Nucleic Acids Res (2006) 7.87
Computational prediction of proteotypic peptides for quantitative proteomics. Nat Biotechnol (2006) 7.56
Identification and quantification of N-linked glycoproteins using hydrazide chemistry, stable isotope labeling and mass spectrometry. Nat Biotechnol (2003) 6.86
Full dynamic range proteome analysis of S. cerevisiae by targeted proteomics. Cell (2009) 6.54
Selected reaction monitoring for quantitative proteomics: a tutorial. Mol Syst Biol (2008) 6.38
Interpretation of shotgun proteomic data: the protein inference problem. Mol Cell Proteomics (2005) 6.28
PeptideAtlas: a resource for target selection for emerging targeted proteomics workflows. EMBO Rep (2008) 6.10
A global protein kinase and phosphatase interaction network in yeast. Science (2010) 5.95
Targeted data extraction of the MS/MS spectra generated by data-independent acquisition: a new concept for consistent and accurate proteome analysis. Mol Cell Proteomics (2012) 5.95
Comprehensive, Integrative Genomic Analysis of Diffuse Lower-Grade Gliomas. N Engl J Med (2015) 5.71
Crucial step in cholesterol homeostasis: sterols promote binding of SCAP to INSIG-1, a membrane protein that facilitates retention of SREBPs in ER. Cell (2002) 5.70
An essential switch in subunit composition of a chromatin remodeling complex during neural development. Neuron (2007) 5.35
Analysis and validation of proteomic data generated by tandem mass spectrometry. Nat Methods (2007) 5.10
Coordinate regulation of energy transduction modules in Halobacterium sp. analyzed by a global systems approach. Proc Natl Acad Sci U S A (2002) 4.96
Selected reaction monitoring-based proteomics: workflows, potential, pitfalls and future directions. Nat Methods (2012) 4.93
Integration with the human genome of peptide sequences obtained by high-throughput mass spectrometry. Genome Biol (2004) 4.91
CTCF physically links cohesin to chromatin. Proc Natl Acad Sci U S A (2008) 4.89
mzML--a community standard for mass spectrometry data. Mol Cell Proteomics (2010) 4.81
High sensitivity detection of plasma proteins by multiple reaction monitoring of N-glycosites. Mol Cell Proteomics (2007) 4.72
Analysis of protein complexes using mass spectrometry. Nat Rev Mol Cell Biol (2007) 4.70
Scoring proteomes with proteotypic peptide probes. Nat Rev Mol Cell Biol (2005) 4.63
The quantitative proteome of a human cell line. Mol Syst Biol (2011) 4.57
Human Plasma PeptideAtlas. Proteomics (2005) 4.52
A cross-platform toolkit for mass spectrometry and proteomics. Nat Biotechnol (2012) 4.48
The CRAPome: a contaminant repository for affinity purification-mass spectrometry data. Nat Methods (2013) 4.34
High-throughput generation of selected reaction-monitoring assays for proteins and proteomes. Nat Methods (2009) 4.17
The need for guidelines in publication of peptide and protein identification data: Working Group on Publication Guidelines for Peptide and Protein Identification Data. Mol Cell Proteomics (2004) 4.15
Integrated genomic and proteomic analyses of gene expression in Mammalian cells. Mol Cell Proteomics (2004) 4.09
Proteome-wide cellular protein concentrations of the human pathogen Leptospira interrogans. Nature (2009) 4.07
Rewiring of genetic networks in response to DNA damage. Science (2010) 4.03
Identification of cross-linked peptides from large sequence databases. Nat Methods (2008) 4.03
Proteome organization in a genome-reduced bacterium. Science (2009) 3.97
Complementary profiling of gene expression at the transcriptome and proteome levels in Saccharomyces cerevisiae. Mol Cell Proteomics (2002) 3.89
An embryonic stem cell chromatin remodeling complex, esBAF, is essential for embryonic stem cell self-renewal and pluripotency. Proc Natl Acad Sci U S A (2009) 3.82
Development and validation of a spectral library searching method for peptide identification from MS/MS. Proteomics (2007) 3.74
SuperHirn - a novel tool for high resolution LC-MS-based peptide/protein profiling. Proteomics (2007) 3.60
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
Options and considerations when selecting a quantitative proteomics strategy. Nat Biotechnol (2010) 3.51
An evaluation, comparison, and accurate benchmarking of several publicly available MS/MS search algorithms: sensitivity and specificity analysis. Proteomics (2005) 3.51
SAINT: probabilistic scoring of affinity purification-mass spectrometry data. Nat Methods (2010) 3.50
Reporting protein identification data: the next generation of guidelines. Mol Cell Proteomics (2006) 3.50
Integrated pipeline for mass spectrometry-based discovery and confirmation of biomarkers demonstrated in a mouse model of breast cancer. J Proteome Res (2007) 3.48
Reproducible isolation of distinct, overlapping segments of the phosphoproteome. Nat Methods (2007) 3.46
Probing native protein structures by chemical cross-linking, mass spectrometry, and bioinformatics. Mol Cell Proteomics (2010) 3.44
Molecular architecture of the 26S proteasome holocomplex determined by an integrative approach. Proc Natl Acad Sci U S A (2012) 3.42
A high-confidence human plasma proteome reference set with estimated concentrations in PeptideAtlas. Mol Cell Proteomics (2011) 3.37
An assessment of software solutions for the analysis of mass spectrometry based quantitative proteomics data. J Proteome Res (2008) 3.36
General framework for developing and evaluating database scoring algorithms using the TANDEM search engine. Bioinformatics (2006) 3.35
A high-quality catalog of the Drosophila melanogaster proteome. Nat Biotechnol (2007) 3.34
Automated statistical analysis of protein abundance ratios from data generated by stable-isotope dilution and tandem mass spectrometry. Anal Chem (2003) 3.33
Characterization of the rapamycin-sensitive phosphoproteome reveals that Sch9 is a central coordinator of protein synthesis. Genes Dev (2009) 3.31
Targeted quantitative analysis of Streptococcus pyogenes virulence factors by multiple reaction monitoring. Mol Cell Proteomics (2008) 3.29
Orm family proteins mediate sphingolipid homeostasis. Nature (2010) 3.29
Quantitative analysis of fission yeast transcriptomes and proteomes in proliferating and quiescent cells. Cell (2012) 3.26
A database of mass spectrometric assays for the yeast proteome. Nat Methods (2008) 3.19
PASSEL: the PeptideAtlas SRMexperiment library. Proteomics (2012) 3.14
Significance analysis of spectral count data in label-free shotgun proteomics. Mol Cell Proteomics (2008) 3.12
mProphet: automated data processing and statistical validation for large-scale SRM experiments. Nat Methods (2011) 3.10
Comparative functional analysis of the Caenorhabditis elegans and Drosophila melanogaster proteomes. PLoS Biol (2009) 3.09
ProbID: a probabilistic algorithm to identify peptides through sequence database searching using tandem mass spectral data. Proteomics (2002) 3.01
Protein identification false discovery rates for very large proteomics data sets generated by tandem mass spectrometry. Mol Cell Proteomics (2009) 2.96
An integrated workflow for charting the human interaction proteome: insights into the PP2A system. Mol Syst Biol (2009) 2.92
Quantitative phosphoproteomic analysis of T cell receptor signaling reveals system-wide modulation of protein-protein interactions. Sci Signal (2009) 2.92
Mass spectrometry in high-throughput proteomics: ready for the big time. Nat Methods (2010) 2.91
iProphet: multi-level integrative analysis of shotgun proteomic data improves peptide and protein identification rates and error estimates. Mol Cell Proteomics (2011) 2.88