Published in Proteomics on June 01, 2003
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
Precision proteomics: the case for high resolution and high mass accuracy. Proc Natl Acad Sci U S A (2008) 4.00
OpenSWATH enables automated, targeted analysis of data-independent acquisition MS data. Nat Biotechnol (2014) 2.20
Precursor acquisition independent from ion count: how to dive deeper into the proteomics ocean. Anal Chem (2009) 1.96
DIA-Umpire: comprehensive computational framework for data-independent acquisition proteomics. Nat Methods (2015) 1.77
Proteomics on an Orbitrap benchtop mass spectrometer using all-ion fragmentation. Mol Cell Proteomics (2010) 1.71
Quantifying protein interaction dynamics by SWATH mass spectrometry: application to the 14-3-3 system. Nat Methods (2013) 1.56
Multiplexed MS/MS for improved data-independent acquisition. Nat Methods (2013) 1.48
Deconvolution of mixture spectra from ion-trap data-independent-acquisition tandem mass spectrometry. Anal Chem (2010) 1.43
Tandem mass spectrometry with ultrahigh mass accuracy clarifies peptide identification by database retrieval. J Proteome Res (2009) 1.33
Analysis of tandem mass spectra by FTMS for improved large-scale proteomics with superior protein quantification. Anal Chem (2010) 1.22
Faster, quantitative, and accurate precursor acquisition independent from ion count. Anal Chem (2011) 1.11
Versatile online-offline engine for automated acquisition of high-resolution tandem mass spectra. Anal Chem (2008) 1.09
Analysis of host-cell proteins in biotherapeutic proteins by comprehensive online two-dimensional liquid chromatography/mass spectrometry. MAbs (2012) 1.08
Peptide-Centric Proteome Analysis: An Alternative Strategy for the Analysis of Tandem Mass Spectrometry Data. Mol Cell Proteomics (2015) 0.94
In-source fragmentation and the sources of partially tryptic peptides in shotgun proteomics. J Proteome Res (2013) 0.94
ETISEQ--an algorithm for automated elution time ion sequencing of concurrently fragmented peptides for mass spectrometry-based proteomics. BMC Bioinformatics (2009) 0.94
Multiplexed peptide analysis using data-independent acquisition and Skyline. Nat Protoc (2015) 0.92
Targeted identification of SUMOylation sites in human proteins using affinity enrichment and paralog-specific reporter ions. Mol Cell Proteomics (2013) 0.91
The zebrafish lens proteome during development and aging. Mol Vis (2009) 0.91
Characterization of an Ion Mobility-Multiplexed Collision Induced Dissociation-Tandem Time-of-Flight Mass Spectrometry Approach. Int J Mass Spectrom (2010) 0.87
Comparison of data acquisition strategies on quadrupole ion trap instrumentation for shotgun proteomics. J Am Soc Mass Spectrom (2014) 0.84
MS1 Peptide Ion Intensity Chromatograms in MS2 (SWATH) Data Independent Acquisitions. Improving Post Acquisition Analysis of Proteomic Experiments. Mol Cell Proteomics (2015) 0.83
Data-independent microbial metabolomics with ambient ionization mass spectrometry. J Am Soc Mass Spectrom (2013) 0.82
The revolution and evolution of shotgun proteomics for large-scale proteome analysis. J Am Chem Soc (2013) 0.82
High-precision iRT prediction in the targeted analysis of data-independent acquisition and its impact on identification and quantitation. Proteomics (2016) 0.77
Multi-laboratory assessment of reproducibility, qualitative and quantitative performance of SWATH-mass spectrometry. Nat Commun (2017) 0.76
Quantitative proteomics: challenges and opportunities in basic and applied research. Nat Protoc (2017) 0.75
Data Independent Acquisition analysis in ProHits 4.0. J Proteomics (2016) 0.75
Towards comprehensive and quantitative proteomics for diagnosis and therapy of human disease. Proteomics (2016) 0.75
A type VI secretion system of Pseudomonas aeruginosa targets a toxin to bacteria. Cell Host Microbe (2010) 4.98
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
Integration with the human genome of peptide sequences obtained by high-throughput mass spectrometry. Genome Biol (2004) 4.91
Human Plasma PeptideAtlas. Proteomics (2005) 4.52
Integrated genomic and proteomic analyses of gene expression in Mammalian cells. Mol Cell Proteomics (2004) 4.09
The B7 family member B7-H6 is a tumor cell ligand for the activating natural killer cell receptor NKp30 in humans. J Exp Med (2009) 3.17
Genetic basis of proteome variation in yeast. Nat Genet (2007) 3.04
Growth phenotypes of Pseudomonas aeruginosa lasR mutants adapted to the airways of cystic fibrosis patients. Mol Microbiol (2007) 2.87
Comparison of Francisella tularensis genomes reveals evolutionary events associated with the emergence of human pathogenic strains. Genome Biol (2007) 2.68
Experimental protein mixture for validating tandem mass spectral analysis. OMICS (2002) 2.54
The study of macromolecular complexes by quantitative proteomics. Nat Genet (2003) 2.44
Gene expression analyzed by high-resolution state array analysis and quantitative proteomics: response of yeast to mating pheromone. Mol Cell Proteomics (2004) 2.22
Pancreatic cancer proteome: the proteins that underlie invasion, metastasis, and immunologic escape. Gastroenterology (2005) 2.21
Mass spectrometry based targeted protein quantification: methods and applications. J Proteome Res (2009) 2.20
Lack of in vitro and in vivo recognition of Francisella tularensis subspecies lipopolysaccharide by Toll-like receptors. Infect Immun (2006) 2.18
Transcription factor Foxp3 and its protein partners form a complex regulatory network. Nat Immunol (2012) 2.10
A widespread bacterial type VI secretion effector superfamily identified using a heuristic approach. Cell Host Microbe (2012) 2.08
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
Genetic variation shapes protein networks mainly through non-transcriptional mechanisms. PLoS Biol (2011) 2.08
LPS remodeling is an evolved survival strategy for bacteria. Proc Natl Acad Sci U S A (2012) 2.05
Identification of TFB5, a new component of general transcription and DNA repair factor IIH. Nat Genet (2004) 1.99
Precursor acquisition independent from ion count: how to dive deeper into the proteomics ocean. Anal Chem (2009) 1.96
High throughput quantitative analysis of serum proteins using glycopeptide capture and liquid chromatography mass spectrometry. Mol Cell Proteomics (2004) 1.94
Quantitative proteomic analysis of Myc oncoprotein function. EMBO J (2002) 1.89
A microcapillary trap cartridge-microcapillary high-performance liquid chromatography electrospray ionization emitter device capable of peptide tandem mass spectrometry at the attomole level on an ion trap mass spectrometer with automated routine operation. Rapid Commun Mass Spectrom (2003) 1.85
Comparative metaproteomics reveals ocean-scale shifts in microbial nutrient utilization and energy transduction. ISME J (2010) 1.80
The SOX2 response program in glioblastoma multiforme: an integrated ChIP-seq, expression microarray, and microRNA analysis. BMC Genomics (2011) 1.79
Approaching complete peroxisome characterization by gas-phase fractionation. Electrophoresis (2002) 1.78
A tool to visualize and evaluate data obtained by liquid chromatography-electrospray ionization-mass spectrometry. Anal Chem (2004) 1.74
Human Toll-like receptor 4 responses to P. gingivalis are regulated by lipid A 1- and 4'-phosphatase activities. Cell Microbiol (2009) 1.66
Pro-CrossLink. Software tool for protein cross-linking and mass spectrometry. Anal Chem (2006) 1.61
The mobile nucleoporin Nup2p and chromatin-bound Prp20p function in endogenous NPC-mediated transcriptional control. J Cell Biol (2005) 1.59
Quantitative proteomics analysis reveals that proteins differentially expressed in chronic pancreatitis are also frequently involved in pancreatic cancer. Mol Cell Proteomics (2007) 1.58
Chemical cross-linking and mass spectrometry as a low-resolution protein structure determination technique. Anal Chem (2010) 1.58
A Francisella mutant in lipid A carbohydrate modification elicits protective immunity. PLoS Pathog (2008) 1.58
Characterization of protein cross-links via mass spectrometry and an open-modification search strategy. Anal Chem (2008) 1.56
Salivary α-synuclein and DJ-1: potential biomarkers for Parkinson's disease. Brain (2011) 1.53
Protein identification using top-down. Mol Cell Proteomics (2011) 1.50
Proteomic analysis of human prostasomes. Prostate (2003) 1.45
Genome-specific gas-phase fractionation strategy for improved shotgun proteomic profiling of proteotypic peptides. Anal Chem (2008) 1.44
UniPep--a database for human N-linked glycosites: a resource for biomarker discovery. Genome Biol (2006) 1.43
Quantitative proteomic analysis of age-related changes in human cerebrospinal fluid. Neurobiol Aging (2005) 1.39
Evidence for the presence of disease-perturbed networks in prostate cancer cells by genomic and proteomic analyses: a systems approach to disease. Cancer Res (2005) 1.39
Quantitative proteomic analysis indicates increased synthesis of a quinolone by Pseudomonas aeruginosa isolates from cystic fibrosis airways. Proc Natl Acad Sci U S A (2003) 1.39
Quantitative mass spectrometry reveals a role for the GTPase Rho1p in actin organization on the peroxisome membrane. J Cell Biol (2004) 1.38
Structural heterogeneity and environmentally regulated remodeling of Francisella tularensis subspecies novicida lipid A characterized by tandem mass spectrometry. J Am Soc Mass Spectrom (2007) 1.37
Comparison of pancreas juice proteins from cancer versus pancreatitis using quantitative proteomic analysis. Pancreas (2007) 1.35
A combined dataset of human cerebrospinal fluid proteins identified by multi-dimensional chromatography and tandem mass spectrometry. Proteomics (2007) 1.31
A Review of Tandem Mass Spectrometry Characterization of Adenosine Diphosphate-Ribosylated Peptides. Int J Mass Spectrom (2011) 1.29
Rules governing protein identification by mass spectrometry. Rapid Commun Mass Spectrom (2005) 1.29
Analysis of alpha-synuclein-associated proteins by quantitative proteomics. J Biol Chem (2004) 1.27
Quantitative proteomic profiling of pancreatic cancer juice. Proteomics (2006) 1.25
Increasing information from shotgun proteomic data by accounting for misassigned precursor ion masses. Proteomics (2008) 1.23
Multiplexed and data-independent tandem mass spectrometry for global proteome profiling. Mass Spectrom Rev (2013) 1.23
xComb: a cross-linked peptide database approach to protein-protein interaction analysis. J Proteome Res (2010) 1.22
Genetically distinct pathways guide effector export through the type VI secretion system. Mol Microbiol (2014) 1.20
Determination of pyrophosphorylated forms of lipid A in Gram-negative bacteria using a multivaried mass spectrometric approach. Proc Natl Acad Sci U S A (2008) 1.18
Assessing bias in experiment design for large scale mass spectrometry-based quantitative proteomics. Mol Cell Proteomics (2007) 1.18
MglA regulates Francisella tularensis subsp. novicida (Francisella novicida) response to starvation and oxidative stress. J Bacteriol (2007) 1.17
On the benefits of acquiring peptide fragment ions at high measured mass accuracy. J Am Soc Mass Spectrom (2008) 1.17
Mining the acute respiratory distress syndrome proteome: identification of the insulin-like growth factor (IGF)/IGF-binding protein-3 pathway in acute lung injury. Am J Pathol (2006) 1.16
Identification of the interactions between cytochrome P450 2E1 and cytochrome b5 by mass spectrometry and site-directed mutagenesis. J Biol Chem (2006) 1.15
Proteomic analysis of an extreme halophilic archaeon, Halobacterium sp. NRC-1. Mol Cell Proteomics (2003) 1.15
Improving mass and liquid chromatography based identification of proteins using bayesian scoring. J Proteome Res (2005) 1.14
Precursor ion independent algorithm for top-down shotgun proteomics. J Am Soc Mass Spectrom (2009) 1.14
Stromal mesenchyme cell genes of the human prostate and bladder. BMC Urol (2005) 1.13
Initial proteome analysis of model microorganism Haemophilus influenzae strain Rd KW20. J Bacteriol (2003) 1.13
Mapping PARP-1 auto-ADP-ribosylation sites by liquid chromatography-tandem mass spectrometry. J Proteome Res (2013) 1.11
Faster, quantitative, and accurate precursor acquisition independent from ion count. Anal Chem (2011) 1.11
System-based proteomic analysis of the interferon response in human liver cells. Genome Biol (2004) 1.09
Quantitative proteomic analysis of proteins released by neoplastic prostate epithelium. Cancer Res (2004) 1.09
Identification and type III-dependent secretion of the Yersinia pestis insecticidal-like proteins. Mol Microbiol (2007) 1.09
Detecting cross-linked peptides by searching against a database of cross-linked peptide pairs. J Proteome Res (2010) 1.09
Interactions between CusF and CusB identified by NMR spectroscopy and chemical cross-linking coupled to mass spectrometry. Biochemistry (2011) 1.08
Plasticity of cytochrome P450 2B4 as investigated by hydrogen-deuterium exchange mass spectrometry and X-ray crystallography. J Biol Chem (2010) 1.08
Quantitative proteomics investigation of pancreatic intraepithelial neoplasia. Electrophoresis (2009) 1.08
Quantitative proteomic analysis of chromatin-associated factors. J Am Soc Mass Spectrom (2003) 1.06
Multiplex targeted proteomic assay for biomarker detection in plasma: a pancreatic cancer biomarker case study. J Proteome Res (2012) 1.06
Dynamic changes in the subcellular distribution of Gpd1p in response to cell stress. J Biol Chem (2009) 1.04
Transferrin receptor-dependent cytotoxicity of artemisinin-transferrin conjugates on prostate cancer cells and induction of apoptosis. Cancer Lett (2008) 1.04
Identification of a novel phosphorylation site, Ser-170, as a regulator of bad pro-apoptotic activity. J Biol Chem (2001) 1.02
Comparison of a label-free quantitative proteomic method based on peptide ion current area to the isotope coded affinity tag method. Cancer Inform (2008) 1.02
DJ-1 isoforms in whole blood as potential biomarkers of Parkinson disease. Sci Rep (2012) 1.02
Proteomic analysis of the intestinal epithelial cell response to enteropathogenic Escherichia coli. J Biol Chem (2004) 1.02
UBR box N-recognin-4 (UBR4), an N-recognin of the N-end rule pathway, and its role in yolk sac vascular development and autophagy. Proc Natl Acad Sci U S A (2013) 1.01
VgrG-5 is a Burkholderia type VI secretion system-exported protein required for multinucleated giant cell formation and virulence. Infect Immun (2014) 1.01