Published in Mol Cell Proteomics on December 17, 2004
Quantitative, multiplexed assays for low abundance proteins in plasma by targeted mass spectrometry and stable isotope dilution. Mol Cell Proteomics (2007) 6.96
A survey of computational methods and error rate estimation procedures for peptide and protein identification in shotgun proteomics. J Proteomics (2010) 3.78
A high-confidence human plasma proteome reference set with estimated concentrations in PeptideAtlas. Mol Cell Proteomics (2011) 3.37
Human body fluid proteome analysis. Proteomics (2006) 2.39
Human plasma N-glycoproteome analysis by immunoaffinity subtraction, hydrazide chemistry, and mass spectrometry. J Proteome Res (2005) 2.35
High dynamic range characterization of the trauma patient plasma proteome. Mol Cell Proteomics (2006) 2.25
Protein analysis by shotgun/bottom-up proteomics. Chem Rev (2013) 2.13
Solid-phase extraction of N-linked glycopeptides. Nat Protoc (2007) 2.05
Targeted proteomic strategy for clinical biomarker discovery. Mol Oncol (2008) 2.01
Proteomic analysis of human parotid gland exosomes by multidimensional protein identification technology (MudPIT). J Proteome Res (2009) 1.97
TraML--a standard format for exchange of selected reaction monitoring transition lists. Mol Cell Proteomics (2011) 1.65
Mass spectrometry based glycoproteomics--from a proteomics perspective. Mol Cell Proteomics (2010) 1.55
UniPep--a database for human N-linked glycosites: a resource for biomarker discovery. Genome Biol (2006) 1.43
Accurate mass measurements in proteomics. Chem Rev (2007) 1.36
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 new algorithm using cross-assignment for label-free quantitation with LC-LTQ-FT MS. J Proteome Res (2007) 1.29
Quantification of the N-glycosylated secretome by super-SILAC during breast cancer progression and in human blood samples. Mol Cell Proteomics (2012) 1.24
Membrane glycoproteins associated with breast tumor cell progression identified by a lectin affinity approach. J Proteome Res (2008) 1.21
Mass spectrometry (LC-MS/MS) site-mapping of N-glycosylated membrane proteins for breast cancer biomarkers. J Proteome Res (2009) 1.17
The mouse C2C12 myoblast cell surface N-linked glycoproteome: identification, glycosite occupancy, and membrane orientation. Mol Cell Proteomics (2009) 1.16
Analysis of cell surface proteome changes via label-free, quantitative mass spectrometry. Mol Cell Proteomics (2008) 1.11
Targeted identification of metastasis-associated cell-surface sialoglycoproteins in prostate cancer. Mol Cell Proteomics (2011) 1.09
Prolyl 4-hydroxylation of alpha-fibrinogen: a novel protein modification revealed by plasma proteomics. J Biol Chem (2009) 1.04
A systematic analysis of the effects of increasing degrees of serum immunodepletion in terms of depth of coverage and other key aspects in top-down and bottom-up proteomic analyses. Proteomics (2011) 1.02
Glycomic analysis: an array of technologies. ACS Chem Biol (2009) 1.00
Sialic acid-focused quantitative mouse serum glycoproteomics by multiple reaction monitoring assay. Mol Cell Proteomics (2010) 0.99
Proteomics: applications in transfusion medicine. Blood Transfus (2008) 0.98
Simultaneous characterization of glyco- and phosphoproteomes of mouse brain membrane proteome with electrostatic repulsion hydrophilic interaction chromatography. Mol Cell Proteomics (2010) 0.96
Identification, prioritization, and evaluation of glycoproteins for aggressive prostate cancer using quantitative glycoproteomics and antibody-based assays on tissue specimens. Proteomics (2013) 0.95
A mouse model repository for cancer biomarker discovery. J Proteome Res (2008) 0.94
Quantitative proteomic analysis of ovarian cancer cells identified mitochondrial proteins associated with Paclitaxel resistance. Proteomics Clin Appl (2009) 0.93
Mapping tissue-specific expression of extracellular proteins using systematic glycoproteomic analysis of different mouse tissues. J Proteome Res (2010) 0.91
Intelligent data acquisition blends targeted and discovery methods. J Proteome Res (2014) 0.90
Liquid Chromatography Mass Spectrometry-Based Proteomics: Biological and Technological Aspects. Ann Appl Stat (2010) 0.90
Solid phase extraction of N-linked glycopeptides using hydrazide tip. Anal Chem (2013) 0.86
Analysis of glycoproteins in human serum by means of glycospecific magnetic bead separation and LC-MALDI-TOF/TOF analysis with automated glycopeptide detection. J Biomol Tech (2007) 0.86
Comparison of N-linked Glycoproteins in Human Whole Saliva, Parotid, Submandibular, and Sublingual Glandular Secretions Identified using Hydrazide Chemistry and Mass Spectrometry. Clin Proteomics (2008) 0.86
Glycoproteomic study reveals altered plasma proteins associated with HIV elite suppressors. Theranostics (2014) 0.85
Proteomics and mass spectrometry for cancer biomarker discovery. Biomark Insights (2007) 0.84
Identification of glycoproteins from mouse skin tumors and plasma. Clin Proteomics (2008) 0.84
Comprehensive identification of novel proteins and N-glycosylation sites in royal jelly. BMC Genomics (2014) 0.84
Proteomic alteration in gastic adenocarcinomas from Japanese patients. Mol Cancer (2006) 0.83
Cleaning up the masses: exclusion lists to reduce contamination with HPLC-MS/MS. J Proteomics (2013) 0.83
Glycoproteomics using fluid-based specimens in the discovery of lung cancer protein biomarkers: promise and challenge. Proteomics Clin Appl (2013) 0.82
Pairwise protein expression classifier for candidate biomarker discovery for early detection of human disease prognosis. BMC Bioinformatics (2012) 0.81
Differential Characterization and Classification of Tissue Specific Glycosaminoglycans by Tandem Mass Spectrometry and Statistical Methods. Int J Mass Spectrom (2011) 0.80
Differential Plasma Glycoproteome of p19 Skin Cancer Mouse Model Using the Corra Label-Free LC-MS Proteomics Platform. Clin Proteomics (2008) 0.79
Targeted glycoprotein enrichment and identification in stromal cell secretomes using azido sugar metabolic labeling. Proteomics Clin Appl (2013) 0.78
Chemical Glycoproteomics. Chem Rev (2016) 0.78
Enhanced peptide quantification using spectral count clustering and cluster abundance. BMC Bioinformatics (2011) 0.77
Differential analysis of N-glycoproteome between hepatocellular carcinoma and normal human liver tissues by combination of multiple protease digestion and solid phase based labeling. Clin Proteomics (2014) 0.76
Identification of Novel N-Glycosylation Sites at Noncanonical Protein Consensus Motifs. J Proteome Res (2016) 0.75
Identification of glycoproteins containing specific glycans using a lectin-chemical method. Anal Chem (2015) 0.75
Stable isotope dimethyl labelling for quantitative proteomics and beyond. Philos Trans A Math Phys Eng Sci (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
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
ProteoWizard: open source software for rapid proteomics tools development. Bioinformatics (2008) 9.47
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
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
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
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
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
Identification of proteins in human cytomegalovirus (HCMV) particles: the HCMV proteome. J Virol (2004) 4.30
Human Proteinpedia enables sharing of human protein data. Nat Biotechnol (2008) 4.21
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
Probability-based evaluation of peptide and protein identifications from tandem mass spectrometry and SEQUEST analysis: the human proteome. J Proteome Res (2005) 4.13
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
Lung cancer signatures in plasma based on proteome profiling of mouse tumor models. Cancer Cell (2011) 3.88
Advances in proteomics data analysis and display using an accurate mass and time tag approach. Mass Spectrom Rev (2006) 3.80
Recommendations from the 2008 International Summit on Proteomics Data Release and Sharing Policy: the Amsterdam principles. J Proteome Res (2009) 3.77
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
Toward a human blood serum proteome: analysis by multidimensional separation coupled with mass spectrometry. Mol Cell Proteomics (2002) 3.57
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
DAnTE: a statistical tool for quantitative analysis of -omics data. Bioinformatics (2008) 3.51
Options and considerations when selecting a quantitative proteomics strategy. Nat Biotechnol (2010) 3.51
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
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
Comparative analysis of proteome and transcriptome variation in mouse. PLoS Genet (2011) 3.23
How much will Herceptin really cost? BMJ (2006) 3.23
Chemically etched open tubular and monolithic emitters for nanoelectrospray ionization mass spectrometry. Anal Chem (2006) 3.22
A database of mass spectrometric assays for the yeast proteome. Nat Methods (2008) 3.19
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
VIPER: an advanced software package to support high-throughput LC-MS peptide identification. Bioinformatics (2007) 3.15
Global analysis of the Deinococcus radiodurans proteome by using accurate mass tags. Proc Natl Acad Sci U S A (2002) 3.15
PASSEL: the PeptideAtlas SRMexperiment library. Proteomics (2012) 3.14
mProphet: automated data processing and statistical validation for large-scale SRM experiments. Nat Methods (2011) 3.10
Normalization approaches for removing systematic biases associated with mass spectrometry and label-free proteomics. J Proteome Res (2006) 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
High-sensitivity ion mobility spectrometry/mass spectrometry using electrodynamic ion funnel interfaces. Anal Chem (2005) 2.99
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
A targeted proteomics-based pipeline for verification of biomarkers in plasma. Nat Biotechnol (2011) 2.91
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
Quantitative phosphoproteome analysis using a dendrimer conjugation chemistry and tandem mass spectrometry. Nat Methods (2005) 2.87