Published in Anal Chem on January 15, 2006
A quantitative analysis software tool for mass spectrometry-based proteomics. Nat Methods (2008) 3.35
The proteomes of human parotid and submandibular/sublingual gland salivas collected as the ductal secretions. J Proteome Res (2008) 2.53
Human body fluid proteome analysis. Proteomics (2006) 2.39
Mass spectrometry for proteomics. Curr Opin Chem Biol (2008) 2.31
MassMatrix: a database search program for rapid characterization of proteins and peptides from tandem mass spectrometry data. Proteomics (2009) 2.27
Systems biology in immunology: a computational modeling perspective. Annu Rev Immunol (2011) 2.15
PatternLab for proteomics: a tool for differential shotgun proteomics. BMC Bioinformatics (2008) 2.13
Protein analysis by shotgun/bottom-up proteomics. Chem Rev (2013) 2.13
The impact of peptide abundance and dynamic range on stable-isotope-based quantitative proteomic analyses. J Proteome Res (2008) 2.11
A proteomics grade electron transfer dissociation-enabled hybrid linear ion trap-orbitrap mass spectrometer. J Proteome Res (2008) 1.92
Saliva: diagnostics and therapeutic perspectives. Oral Dis (2010) 1.50
A dynamic range compression and three-dimensional peptide fractionation analysis platform expands proteome coverage and the diagnostic potential of whole saliva. J Proteome Res (2009) 1.42
A proteomics search algorithm specifically designed for high-resolution tandem mass spectra. J Proteome Res (2013) 1.40
Relative quantification of stable isotope labeled peptides using a linear ion trap-Orbitrap hybrid mass spectrometer. Anal Chem (2007) 1.40
Characterization of global yeast quantitative proteome data generated from the wild-type and glucose repression saccharomyces cerevisiae strains: the comparison of two quantitative methods. J Proteome Res (2008) 1.39
Evaluation of HCD- and CID-type fragmentation within their respective detection platforms for murine phosphoproteomics. Mol Cell Proteomics (2011) 1.39
Accurate mass measurements in proteomics. Chem Rev (2007) 1.36
Large-scale phosphoprotein analysis in Medicago truncatula roots provides insight into in vivo kinase activity in legumes. Plant Physiol (2009) 1.27
Proteome-wide identification of proteins and their modifications with decreased ambiguities and improved false discovery rates using unique sequence tags. Anal Chem (2008) 1.26
Analysis of tandem mass spectra by FTMS for improved large-scale proteomics with superior protein quantification. Anal Chem (2010) 1.22
Anion and cation mixed-bed ion exchange for enhanced multidimensional separations of peptides and phosphopeptides. Anal Chem (2007) 1.18
A high confidence, manually validated human blood plasma protein reference set. BMC Med Genomics (2008) 1.16
Improvements in proteomic metrics of low abundance proteins through proteome equalization using ProteoMiner prior to MudPIT. J Proteome Res (2011) 1.14
Shotgun proteomics in neuroscience. Neuron (2009) 1.13
Proteomic analysis provides insights on venom processing in Conus textile. J Proteome Res (2010) 1.10
Versatile online-offline engine for automated acquisition of high-resolution tandem mass spectra. Anal Chem (2008) 1.09
Cancer proteomics by quantitative shotgun proteomics. Mol Oncol (2007) 1.08
ProLuCID: An improved SEQUEST-like algorithm with enhanced sensitivity and specificity. J Proteomics (2015) 1.07
GO Explorer: A gene-ontology tool to aid in the interpretation of shotgun proteomics data. Proteome Sci (2009) 1.05
Accurate localization and relative quantification of arginine methylation using nanoflow liquid chromatography coupled to electron transfer dissociation and orbitrap mass spectrometry. J Am Soc Mass Spectrom (2008) 1.03
Time series proteome profiling to study endoplasmic reticulum stress response. J Proteome Res (2008) 1.02
PeptideDepot: flexible relational database for visual analysis of quantitative proteomic data and integration of existing protein information. Proteomics (2009) 0.99
A high-throughput de novo sequencing approach for shotgun proteomics using high-resolution tandem mass spectrometry. BMC Bioinformatics (2010) 0.99
HTAPP: high-throughput autonomous proteomic pipeline. Proteomics (2010) 0.97
Accurate dereplication of bioactive secondary metabolites from marine-derived fungi by UHPLC-DAD-QTOFMS and a MS/HRMS library. Mar Drugs (2014) 0.94
Evaluation and optimization of mass spectrometric settings during data-dependent acquisition mode: focus on LTQ-Orbitrap mass analyzers. J Proteome Res (2013) 0.93
Mass spectrometry-based proteomic profiling of lung cancer. Proc Am Thorac Soc (2009) 0.93
Screening for EphB signaling effectors using SILAC with a linear ion trap-orbitrap mass spectrometer. J Proteome Res (2008) 0.90
Proteomics of Pyrococcus furiosus (Pfu): Identification of Extracted Proteins by Three Independent Methods. J Proteome Res (2013) 0.83
Systematic characterization of high mass accuracy influence on false discovery and probability scoring in peptide mass fingerprinting. Anal Biochem (2007) 0.80
Kinetics of a collagen-like polypeptide fragmentation after mid-IR free-electron laser ablation. Biophys J (2008) 0.80
Mass spectrometry-based proteomics in Chest Medicine, Gerontology, and Nephrology: subgroups omics for personalized medicine. Biomedicine (Taipei) (2014) 0.80
Identification of chromatophore membrane protein complexes formed under different nitrogen availability conditions in Rhodospirillum rubrum. J Proteome Res (2011) 0.80
Mass spectrometry-based proteomics: qualitative identification to activity-based protein profiling. Wiley Interdiscip Rev Syst Biol Med (2012) 0.78
Fourier Transform Mass Spectrometry: The Transformation of Modern Environmental Analyses. Int J Mol Sci (2016) 0.78
Improved mass accuracy for higher mass peptides by using SWIFT excitation for MALDI-FTICR mass spectrometry. J Am Soc Mass Spectrom (2007) 0.77
Mass spectrometry-based shotgun proteomic analysis of C. elegans protein complexes. WormBook (2014) 0.77
Mapping the disease protein interactome: toward a molecular medicine GPS to accelerate drug and biomarker discovery. J Proteome Res (2010) 0.76
Assessment of the red cell proteome of young patients with unexplained hemolytic anemia by two-dimensional differential in-gel electrophoresis (DIGE). PLoS One (2012) 0.76
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
Large-scale database searching using tandem mass spectra: looking up the answer in the back of the book. Nat Methods (2004) 3.62
Quantitative mass spectrometry identifies insulin signaling targets in C. elegans. Science (2007) 3.46
The proteomes of human parotid and submandibular/sublingual gland salivas collected as the ductal secretions. J Proteome Res (2008) 2.53
Dual-pressure linear ion trap mass spectrometer improving the analysis of complex protein mixtures. Anal Chem (2009) 2.20
βCaMKII in lateral habenula mediates core symptoms of depression. Science (2013) 1.96
A proteomics grade electron transfer dissociation-enabled hybrid linear ion trap-orbitrap mass spectrometer. J Proteome Res (2008) 1.92
Optimization of mass spectrometry-compatible surfactants for shotgun proteomics. J Proteome Res (2007) 1.84
Increased selectivity, analytical precision, and throughput in targeted proteomics. Mol Cell Proteomics (2010) 1.71
Multiplexed MS/MS for improved data-independent acquisition. Nat Methods (2013) 1.48
The intracellular cargo receptor ERGIC-53 is required for the production of infectious arenavirus, coronavirus, and filovirus particles. Cell Host Microbe (2013) 1.46
Quantification of the synaptosomal proteome of the rat cerebellum during post-natal development. Genome Res (2007) 1.39
HDAC4 governs a transcriptional program essential for synaptic plasticity and memory. Cell (2012) 1.35
K33-linked polyubiquitination of T cell receptor-zeta regulates proteolysis-independent T cell signaling. Immunity (2010) 1.30
Top-down mass spectrometry of integral membrane proteins. Expert Rev Proteomics (2006) 1.27
Proteomics analysis unravels the functional repertoire of coronavirus nonstructural protein 3. J Virol (2008) 1.27
Quantitative phosphoproteomic analysis of the tumor necrosis factor pathway. J Proteome Res (2006) 1.23
Protein-Sequence Polymorphisms and Post-translational Modifications in Proteins from Human Saliva using Top-Down Fourier-transform Ion Cyclotron Resonance Mass Spectrometry. Int J Mass Spectrom (2007) 1.22
YADA: a tool for taking the most out of high-resolution spectra. Bioinformatics (2009) 1.20
Neuronal morphogenesis is regulated by the interplay between cyclin-dependent kinase 5 and the ubiquitin ligase mind bomb 1. J Neurosci (2007) 1.17
Novel parallelized quadrupole/linear ion trap/Orbitrap tribrid mass spectrometer improving proteome coverage and peptide identification rates. Anal Chem (2013) 1.15
Search engine processor: Filtering and organizing peptide spectrum matches. Proteomics (2012) 1.15
Proteomic identification of novel proteins associated with Lewy bodies. Front Biosci (2008) 1.13
XDIA: improving on the label-free data-independent analysis. Bioinformatics (2010) 1.08
Mass measurement and top-down HPLC/MS analysis of intact monoclonal antibodies on a hybrid linear quadrupole ion trap-Orbitrap mass spectrometer. J Am Soc Mass Spectrom (2009) 1.03
Measurement of deamidation of intact proteins by isotopic envelope and mass defect with ion cyclotron resonance Fourier transform mass spectrometry. Rapid Commun Mass Spectrom (2006) 1.03
Quantification of post-translationally modified peptides of bovine alpha-crystallin using tandem mass tags and electron transfer dissociation. J Proteomics (2009) 1.01
Comparison of different signal thresholds on data dependent sampling in Orbitrap and LTQ mass spectrometry for the identification of peptides and proteins in complex mixtures. J Am Soc Mass Spectrom (2009) 1.01
Cross-correlation algorithm for calculation of peptide molecular weight from tandem mass spectra. Anal Chem (2006) 0.99
Essential role of Stat3 in PI3K-induced oncogenic transformation. Proc Natl Acad Sci U S A (2011) 0.98
In situ trans ligands of CD22 identified by glycan-protein photocross-linking-enabled proteomics. Mol Cell Proteomics (2010) 0.98
Toward objective evaluation of proteomic algorithms. Nat Methods (2012) 0.96
Differential proteomic analysis of mammalian tissues using SILAM. PLoS One (2011) 0.94
Charge prediction machine: tool for inferring precursor charge states of electron transfer dissociation tandem mass spectra. Anal Chem (2009) 0.94
Dynamic proteomic overview of glioblastoma cells (A172) exposed to perillyl alcohol. J Proteomics (2010) 0.93
Can the false-discovery rate be misleading? Proteomics (2011) 0.92
Neddylation pathway regulates T-cell function by targeting an adaptor protein Shc and a protein kinase Erk signaling. Proc Natl Acad Sci U S A (2012) 0.92
Dynamics of subcellular proteomes during brain development. J Proteome Res (2012) 0.91
Validation of an LC-MS based approach for profiling histones in chronic lymphocytic leukemia. Proteomics (2009) 0.90
Evaluation of front-end higher energy collision-induced dissociation on a benchtop dual-pressure linear ion trap mass spectrometer for shotgun proteomics. Anal Chem (2012) 0.89
Motif-specific sampling of phosphoproteomes. J Proteome Res (2008) 0.89
Chemo-resistant protein expression pattern of glioblastoma cells (A172) to perillyl alcohol. J Proteome Res (2010) 0.88
A computational approach to correct arginine-to-proline conversion in quantitative proteomics. Nat Methods (2009) 0.87
Severe acute respiratory syndrome coronavirus nonstructural protein 2 interacts with a host protein complex involved in mitochondrial biogenesis and intracellular signaling. J Virol (2009) 0.86
Characterization of the human submandibular/sublingual saliva glycoproteome using lectin affinity chromatography coupled to multidimensional protein identification technology. J Proteome Res (2011) 0.84
Shotgun protein identification and quantification by mass spectrometry in neuroproteomics. Methods Mol Biol (2009) 0.83
Proteomics of Pyrococcus furiosus (Pfu): Identification of Extracted Proteins by Three Independent Methods. J Proteome Res (2013) 0.83
Protein expression profiles of C3H 10T1/2 murine fibroblasts and of isogenic cells transformed by the H1047R mutant of phosphoinositide 3-kinase (PI3K). Cell Cycle (2011) 0.83
Micro-heterogeneity of human saliva Peptide P-C characterized by high-resolution top-down Fourier-transform mass spectrometry. J Am Soc Mass Spectrom (2010) 0.82
Isobaric tagging-based quantification by mass spectrometry of differentially regulated proteins in synaptosomes of HIV/gp120 transgenic mice: implications for HIV-associated neurodegeneration. Exp Neurol (2012) 0.82
Quantitative phosphoproteomic profiling of PINK1-deficient cells identifies phosphorylation changes in nuclear proteins. Mol Biosyst (2014) 0.79
Brain Proteome Changes Induced by Olfactory Learning in Drosophila. J Proteome Res (2014) 0.76
Corrigendum: Targeting BMK1 Impairs the Drug Resistance to Combined Inhibition of BRAF and MEK1/2 in Melanoma. Sci Rep (2017) 0.75