Published in Nat Methods on March 20, 2011
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
Selected reaction monitoring-based proteomics: workflows, potential, pitfalls and future directions. Nat Methods (2012) 4.93
PASSEL: the PeptideAtlas SRMexperiment library. Proteomics (2012) 3.14
Parallel reaction monitoring for high resolution and high mass accuracy quantitative, targeted proteomics. Mol Cell Proteomics (2012) 3.05
A complete mass-spectrometric map of the yeast proteome applied to quantitative trait analysis. Nature (2013) 2.61
Targeted peptide measurements in biology and medicine: best practices for mass spectrometry-based assay development using a fit-for-purpose approach. Mol Cell Proteomics (2014) 2.37
Using iRT, a normalized retention time for more targeted measurement of peptides. Proteomics (2012) 2.29
OpenSWATH enables automated, targeted analysis of data-independent acquisition MS data. Nat Biotechnol (2014) 2.20
Reproducible quantification of cancer-associated proteins in body fluids using targeted proteomics. Sci Transl Med (2012) 2.06
Quantitative analysis of peptides and proteins in biomedicine by targeted mass spectrometry. Nat Methods (2013) 2.04
DIA-Umpire: comprehensive computational framework for data-independent acquisition proteomics. Nat Methods (2015) 1.77
A blood-based proteomic classifier for the molecular characterization of pulmonary nodules. Sci Transl Med (2013) 1.69
Quantifying protein interaction dynamics by SWATH mass spectrometry: application to the 14-3-3 system. Nat Methods (2013) 1.56
Demonstrating the feasibility of large-scale development of standardized assays to quantify human proteins. Nat Methods (2013) 1.54
Estimation of absolute protein quantities of unlabeled samples by selected reaction monitoring mass spectrometry. Mol Cell Proteomics (2011) 1.51
Development of a highly automated and multiplexed targeted proteome pipeline and assay for 112 rat brain synaptic proteins. Proteomics (2015) 1.46
A computational tool to detect and avoid redundancy in selected reaction monitoring. Mol Cell Proteomics (2012) 1.46
Protein significance analysis in selected reaction monitoring (SRM) measurements. Mol Cell Proteomics (2011) 1.45
The Mtb proteome library: a resource of assays to quantify the complete proteome of Mycobacterium tuberculosis. Cell Host Microbe (2013) 1.44
Making proteomics data accessible and reusable: current state of proteomics databases and repositories. Proteomics (2015) 1.44
Mapping differential interactomes by affinity purification coupled with data-independent mass spectrometry acquisition. Nat Methods (2013) 1.41
Glycoproteomic analysis of prostate cancer tissues by SWATH mass spectrometry discovers N-acylethanolamine acid amidase and protein tyrosine kinase 7 as signatures for tumor aggressiveness. Mol Cell Proteomics (2014) 1.33
A repository of assays to quantify 10,000 human proteins by SWATH-MS. Sci Data (2014) 1.32
ATAQS: A computational software tool for high throughput transition optimization and validation for selected reaction monitoring mass spectrometry. BMC Bioinformatics (2011) 1.28
A critical appraisal of techniques, software packages, and standards for quantitative proteomic analysis. OMICS (2012) 1.25
Extending the limits of quantitative proteome profiling with data-independent acquisition and application to acetaminophen-treated three-dimensional liver microtissues. Mol Cell Proteomics (2015) 1.24
Recent advances in quantitative neuroproteomics. Methods (2013) 1.23
MS-DIAL: data-independent MS/MS deconvolution for comprehensive metabolome analysis. Nat Methods (2015) 1.22
Trans-Proteomic Pipeline, a standardized data processing pipeline for large-scale reproducible proteomics informatics. Proteomics Clin Appl (2015) 1.19
Computational mass spectrometry-based proteomics. PLoS Comput Biol (2011) 1.18
Statistical characterization of multiple-reaction monitoring mass spectrometry (MRM-MS) assays for quantitative proteomics. BMC Bioinformatics (2012) 1.18
PTMScan direct: identification and quantification of peptides from critical signaling proteins by immunoaffinity enrichment coupled with LC-MS/MS. Mol Cell Proteomics (2012) 1.18
The development of selected reaction monitoring methods for targeted proteomics via empirical refinement. Proteomics (2012) 1.10
Recommendations for the Generation, Quantification, Storage, and Handling of Peptides Used for Mass Spectrometry-Based Assays. Clin Chem (2016) 1.10
Sequential Window Acquisition of all Theoretical Mass Spectra (SWATH) Analysis for Characterization and Quantification of Histone Post-translational Modifications. Mol Cell Proteomics (2015) 1.06
Multiplex targeted proteomic assay for biomarker detection in plasma: a pancreatic cancer biomarker case study. J Proteome Res (2012) 1.06
Analysis of Major Histocompatibility Complex (MHC) Immunopeptidomes Using Mass Spectrometry. Mol Cell Proteomics (2015) 1.05
Global Phosphoproteomic Analysis of Human Skeletal Muscle Reveals a Network of Exercise-Regulated Kinases and AMPK Substrates. Cell Metab (2015) 1.04
The rice immune receptor XA21 recognizes a tyrosine-sulfated protein from a Gram-negative bacterium. Sci Adv (2015) 1.02
Quantitative profiling of caspase-cleaved substrates reveals different drug-induced and cell-type patterns in apoptosis. Proc Natl Acad Sci U S A (2012) 1.02
File formats commonly used in mass spectrometry proteomics. Mol Cell Proteomics (2012) 1.01
Open source libraries and frameworks for mass spectrometry based proteomics: a developer's perspective. Biochim Biophys Acta (2013) 1.00
Automated selected reaction monitoring software for accurate label-free protein quantification. J Proteome Res (2012) 0.99
Using PeptideAtlas, SRMAtlas, and PASSEL: Comprehensive Resources for Discovery and Targeted Proteomics. Curr Protoc Bioinformatics (2014) 0.96
Reproducible and consistent quantification of the Saccharomyces cerevisiae proteome by SWATH-mass spectrometry. Mol Cell Proteomics (2015) 0.96
Mass spectrometric protein maps for biomarker discovery and clinical research. Expert Rev Mol Diagn (2013) 0.96
Automated selected reaction monitoring data analysis workflow for large-scale targeted proteomic studies. Nat Protoc (2013) 0.96
Quantitative measurement of intact alpha-synuclein proteoforms from post-mortem control and Parkinson's disease brain tissue by intact protein mass spectrometry. Sci Rep (2014) 0.95
Peptide-Centric Proteome Analysis: An Alternative Strategy for the Analysis of Tandem Mass Spectrometry Data. Mol Cell Proteomics (2015) 0.94
xTract: software for characterizing conformational changes of protein complexes by quantitative cross-linking mass spectrometry. Nat Methods (2015) 0.94
Recommendations for mass spectrometry data quality metrics for open access data (corollary to the Amsterdam Principles). Mol Cell Proteomics (2011) 0.94
Applications of selected reaction monitoring (SRM)-mass spectrometry (MS) for quantitative measurement of signaling pathways. Methods (2013) 0.94
An assessment of current bioinformatic solutions for analyzing LC-MS data acquired by selected reaction monitoring technology. Proteomics (2012) 0.92
jTraML: an open source Java API for TraML, the PSI standard for sharing SRM transitions. J Proteome Res (2011) 0.92
Recommendations for mass spectrometry data quality metrics for open access data (corollary to the Amsterdam Principles). J Proteome Res (2011) 0.91
Quantification of SAHA-Dependent Changes in Histone Modifications Using Data-Independent Acquisition Mass Spectrometry. J Proteome Res (2015) 0.91
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Multiplexed Targeted Mass Spectrometry-Based Assays for the Quantification of N-Linked Glycosite-Containing Peptides in Serum. Anal Chem (2015) 0.88
Biochemical fractionation and stable isotope dilution liquid chromatography-mass spectrometry for targeted and microdomain-specific protein quantification in human postmortem brain tissue. Mol Cell Proteomics (2012) 0.87
Automated Validation of Results and Removal of Fragment Ion Interferences in Targeted Analysis of Data-independent Acquisition Mass Spectrometry (MS) using SWATHProphet. Mol Cell Proteomics (2015) 0.85
Quantitative analysis of chaperone network throughput in budding yeast. Proteomics (2013) 0.85
RIP-chip-SRM--a new combinatorial large-scale approach identifies a set of translationally regulated bantam/miR-58 targets in C. elegans. Genome Res (2012) 0.85
SWATH Mass Spectrometry Performance Using Extended Peptide MS/MS Assay Libraries. Mol Cell Proteomics (2016) 0.85
Conserved peptide fragmentation as a benchmarking tool for mass spectrometers and a discriminating feature for targeted proteomics. Mol Cell Proteomics (2014) 0.84
Systematic measurement of transcription factor-DNA interactions by targeted mass spectrometry identifies candidate gene regulatory proteins. Proc Natl Acad Sci U S A (2013) 0.83
Direct and Absolute Quantification of over 1800 Yeast Proteins via Selected Reaction Monitoring. Mol Cell Proteomics (2016) 0.82
Protein sets define disease states and predict in vivo effects of drug treatment. Mol Cell Proteomics (2013) 0.82
TRIC: an automated alignment strategy for reproducible protein quantification in targeted proteomics. Nat Methods (2016) 0.81
SWATH2stats: An R/Bioconductor Package to Process and Convert Quantitative SWATH-MS Proteomics Data for Downstream Analysis Tools. PLoS One (2016) 0.81
Quantitative protein topography analysis and high-resolution structure prediction using hydroxyl radical labeling and tandem-ion mass spectrometry (MS). Mol Cell Proteomics (2015) 0.79
Proteomics and the analysis of proteomic data: 2013 overview of current protein-profiling technologies. Curr Protoc Bioinformatics (2013) 0.79
Advances in Proteomic Technologies and Its Contribution to the Field of Cancer. Adv Med (2014) 0.79
Advances in targeted proteomics and applications to biomedical research. Proteomics (2016) 0.79
Untargeted, spectral library-free analysis of data-independent acquisition proteomics data generated using Orbitrap mass spectrometers. Proteomics (2016) 0.78
Targeted proteomics for multiplexed verification of markers of colorectal tumorigenesis. Mol Cell Proteomics (2017) 0.78
High-precision iRT prediction in the targeted analysis of data-independent acquisition and its impact on identification and quantitation. Proteomics (2016) 0.77
A multicenter study benchmarks software tools for label-free proteome quantification. Nat Biotechnol (2016) 0.77
Plasma preparation to measure FDA-approved protein markers by selected reaction monitoring. Clin Transl Med (2015) 0.77
Statistical control of peptide and protein error rates in large-scale targeted data-independent acquisition analyses. Nat Methods (2017) 0.76
Multi-laboratory assessment of reproducibility, qualitative and quantitative performance of SWATH-mass spectrometry. Nat Commun (2017) 0.76
Absolute protein quantification of the yeast chaperome under conditions of heat shock. Proteomics (2016) 0.76
Development of a pharmaceutical hepatotoxicity biomarker panel using a discovery to targeted proteomics approach. Mol Cell Proteomics (2012) 0.76
Proteomic analysis of host brain components that bind to infectious particles in Creutzfeldt-Jakob disease. Proteomics (2015) 0.76
Fast and Efficient XML Data Access for Next-Generation Mass Spectrometry. PLoS One (2015) 0.76
Data-independent MS/MS quantification of neuropeptides for determination of putative feeding-related neurohormones in microdialysate. ACS Chem Neurosci (2015) 0.76
Targeted proteomics: Current status and future perspectives for quantification of food allergens. J Proteomics (2016) 0.76
Systems-level Proteomics of Two Ubiquitous Leaf Commensals Reveals Complementary Adaptive Traits for Phyllosphere Colonization. Mol Cell Proteomics (2016) 0.75
Natural Genetic Variation Influences Protein Abundances in C. elegans Developmental Signalling Pathways. PLoS One (2016) 0.75
Quantitative LC-MS/MS Analysis of Proteins Involved in Metastasis of Breast Cancer. PLoS One (2015) 0.75
Differential proteomics analysis of mononuclear cells in cerebrospinal fluid of Parkinson's disease. Int J Clin Exp Pathol (2015) 0.75
Mass Spectrometry Analysis of Lysine Posttranslational Modifications of Tau Protein from Alzheimer's Disease Brain. Methods Mol Biol (2017) 0.75
Data Pre-Processing for Label-Free Multiple Reaction Monitoring (MRM) Experiments. Biology (Basel) (2014) 0.75
Expression of Aspergillus niger CAZymes is determined by compositional changes in wheat straw generated by hydrothermal or ionic liquid pretreatments. Biotechnol Biofuels (2017) 0.75
Combining Untargeted and Targeted Proteomic Strategies for Discrimination and Quantification of Cashmere Fibers. PLoS One (2016) 0.75
Locus-specific Retention Predictor (LsRP): A Peptide Retention Time Predictor Developed for Precision Proteomics. Sci Rep (2017) 0.75
mzDB: a file format using multiple indexing strategies for the efficient analysis of large LC-MS/MS and SWATH-MS data sets. Mol Cell Proteomics (2014) 0.75
Differential quantification of isobaric phosphopeptides using data-independent acquisition mass spectrometry. Mol Biosyst (2016) 0.75
Targeted feature detection for data-dependent shotgun proteomics. J Proteome Res (2017) 0.75
pyQms enables universal and accurate quantification of mass spectrometry data. Mol Cell Proteomics (2017) 0.75
Application of wide selected-ion monitoring data-independent acquisition to identify tomato fruit proteins regulated by the CUTIN DEFICIENT2 transcription factor. Proteomics (2016) 0.75
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
Femoroacetabular impingement: a cause for osteoarthritis of the hip. Clin Orthop Relat Res (2003) 12.86
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
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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
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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
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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
A guided tour of the Trans-Proteomic Pipeline. Proteomics (2010) 5.09
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
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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
High sensitivity detection of plasma proteins by multiple reaction monitoring of N-glycosites. Mol Cell Proteomics (2007) 4.72
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Scoring proteomes with proteotypic peptide probes. Nat Rev Mol Cell Biol (2005) 4.63
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Human Plasma PeptideAtlas. Proteomics (2005) 4.52
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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
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The Functional Genomics Experiment model (FuGE): an extensible framework for standards in functional genomics. Nat Biotechnol (2007) 3.55
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Reporting protein identification data: the next generation of guidelines. Mol Cell Proteomics (2006) 3.50
Reproducible isolation of distinct, overlapping segments of the phosphoproteome. Nat Methods (2007) 3.46
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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
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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
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A complete mass-spectrometric map of the yeast proteome applied to quantitative trait analysis. Nature (2013) 2.61
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A PP2A phosphatase high density interaction network identifies a novel striatin-interacting phosphatase and kinase complex linked to the cerebral cavernous malformation 3 (CCM3) protein. Mol Cell Proteomics (2008) 2.56