Published in J Proteome Res on June 18, 2008
A survey of computational methods and error rate estimation procedures for peptide and protein identification in shotgun proteomics. J Proteomics (2010) 3.78
iProphet: multi-level integrative analysis of shotgun proteomic data improves peptide and protein identification rates and error estimates. Mol Cell Proteomics (2011) 2.88
Protein analysis by shotgun/bottom-up proteomics. Chem Rev (2013) 2.13
Combining results of multiple search engines in proteomics. Mol Cell Proteomics (2013) 1.20
MSblender: A probabilistic approach for integrating peptide identifications from multiple database search engines. J Proteome Res (2011) 1.19
Addressing statistical biases in nucleotide-derived protein databases for proteogenomic search strategies. J Proteome Res (2012) 1.04
Proteomic analysis of seminal plasma from asthenozoospermia patients reveals proteins that affect oxidative stress responses and semen quality. Asian J Androl (2009) 0.93
Peptide identification by tandem mass spectrometry with alternate fragmentation modes. Mol Cell Proteomics (2012) 0.91
UNiquant, a program for quantitative proteomics analysis using stable isotope labeling. J Proteome Res (2011) 0.90
RAId_aPS: MS/MS analysis with multiple scoring functions and spectrum-specific statistics. PLoS One (2010) 0.89
Optimization of the Use of Consensus Methods for the Detection and Putative Identification of Peptides via Mass Spectrometry Using Protein Standard Mixtures. J Proteomics Bioinform (2009) 0.88
An assessment of false discovery rates and statistical significance in label-free quantitative proteomics with combined filters. BMC Bioinformatics (2009) 0.87
Combining independent, weighted P-values: achieving computational stability by a systematic expansion with controllable accuracy. PLoS One (2011) 0.85
Current algorithmic solutions for peptide-based proteomics data generation and identification. Curr Opin Biotechnol (2012) 0.85
Improved protein extraction and protein identification from archival formalin-fixed paraffin-embedded human aortas. Proteomics Clin Appl (2013) 0.84
Accuracy evaluation of the unified P-value from combining correlated P-values. PLoS One (2014) 0.84
Assigning statistical significance to proteotypic peptides via database searches. J Proteomics (2010) 0.80
Mass spectrometry-based protein identification with accurate statistical significance assignment. Bioinformatics (2014) 0.78
Identification of Microorganisms by High Resolution Tandem Mass Spectrometry with Accurate Statistical Significance. J Am Soc Mass Spectrom (2015) 0.77
Practical and Efficient Searching in Proteomics: A Cross Engine Comparison. Webmedcentral (2013) 0.77
A large scale Plasmodium vivax- Saimiri boliviensis trophozoite-schizont transition proteome. PLoS One (2017) 0.76
PyQuant: A Versatile Framework for Analysis of Quantitative Mass Spectrometry Data. Mol Cell Proteomics (2016) 0.75
A multi-model statistical approach for proteomic spectral count quantitation. J Proteomics (2016) 0.75
A Survey of the Impact of Deyolking on Biological Processes Covered by Shotgun Proteomic Analyses of Zebrafish Embryos. Zebrafish (2015) 0.75
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
Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search. Anal Chem (2002) 35.30
TANDEM: matching proteins with tandem mass spectra. Bioinformatics (2004) 17.41
Combining evidence using p-values: application to sequence homology searches. Bioinformatics (1998) 16.51
Open mass spectrometry search algorithm. J Proteome Res (2004) 15.25
InsPecT: identification of posttranslationally modified peptides from tandem mass spectra. Anal Chem (2005) 6.65
An evaluation, comparison, and accurate benchmarking of several publicly available MS/MS search algorithms: sensitivity and specificity analysis. Proteomics (2005) 3.51
ProbID: a probabilistic algorithm to identify peptides through sequence database searching using tandem mass spectral data. Proteomics (2002) 3.01
Experimental protein mixture for validating tandem mass spectral analysis. OMICS (2002) 2.54
Retrieval accuracy, statistical significance and compositional similarity in protein sequence database searches. Nucleic Acids Res (2006) 1.81
Calibrating E-values for MS2 database search methods. Biol Direct (2007) 1.44
RAId_DbS: peptide identification using database searches with realistic statistics. Biol Direct (2007) 1.27
Guidelines for the use and interpretation of assays for monitoring autophagy. Autophagy (2012) 20.08
Identification and proteomic profiling of exosomes in human urine. Proc Natl Acad Sci U S A (2004) 8.74
Protein database searches using compositionally adjusted substitution matrices. FEBS J (2005) 8.14
The mammalian target of rapamycin (mTOR) pathway regulates mitochondrial oxygen consumption and oxidative capacity. J Biol Chem (2006) 4.28
Quantitative phosphoproteomics of vasopressin-sensitive renal cells: regulation of aquaporin-2 phosphorylation at two sites. Proc Natl Acad Sci U S A (2006) 3.26
Preconditioning results in S-nitrosylation of proteins involved in regulation of mitochondrial energetics and calcium transport. Circ Res (2007) 2.97
Composition-based statistics and translated nucleotide searches: improving the TBLASTN module of BLAST. BMC Biol (2006) 2.90
Comparative study of three proteomic quantitative methods, DIGE, cICAT, and iTRAQ, using 2D gel- or LC-MALDI TOF/TOF. J Proteome Res (2006) 2.73
Heat conduction process on community networks as a recommendation model. Phys Rev Lett (2007) 2.72
Label-free protein quantification using LC-coupled ion trap or FT mass spectrometry: Reproducibility, linearity, and application with complex proteomes. J Proteome Res (2006) 2.64
Mitochondrial matrix phosphoproteome: effect of extra mitochondrial calcium. Biochemistry (2006) 2.06
Sumoylation of heterogeneous nuclear ribonucleoproteins, zinc finger proteins, and nuclear pore complex proteins: a proteomic analysis. Proc Natl Acad Sci U S A (2004) 1.85
Discovery of new cargo proteins that enter cells through clathrin-independent endocytosis. Traffic (2009) 1.78
Quantitative phosphoproteomic analysis reveals vasopressin V2-receptor-dependent signaling pathways in renal collecting duct cells. Proc Natl Acad Sci U S A (2010) 1.78
Information flow in interaction networks. J Comput Biol (2007) 1.75
Large scale protein identification in intracellular aquaporin-2 vesicles from renal inner medullary collecting duct. Mol Cell Proteomics (2005) 1.70
PSI-BLAST pseudocounts and the minimum description length principle. Nucleic Acids Res (2008) 1.68
DJ-1 decreases Bax expression through repressing p53 transcriptional activity. J Biol Chem (2007) 1.59
The construction and use of log-odds substitution scores for multiple sequence alignment. PLoS Comput Biol (2010) 1.54
Cyclophilin D modulates mitochondrial acetylome. Circ Res (2013) 1.53
Degradation of TDP-43 and its pathogenic form by autophagy and the ubiquitin-proteasome system. Neurosci Lett (2009) 1.53
Simultaneous measurement of protein oxidation and S-nitrosylation during preconditioning and ischemia/reperfusion injury with resin-assisted capture. Circ Res (2010) 1.48
Parkin mono-ubiquitinates Bcl-2 and regulates autophagy. J Biol Chem (2010) 1.45
The MAT locus genes play different roles in sexual reproduction and pathogenesis in Fusarium graminearum. PLoS One (2013) 1.44
Calibrating E-values for MS2 database search methods. Biol Direct (2007) 1.44
Retracted The NAD-dependent deacetylase SIRT2 is required for programmed necrosis. Nature (2012) 1.44
Cerebral ischemia-reperfusion-induced autophagy protects against neuronal injury by mitochondrial clearance. Autophagy (2013) 1.39
Characterization of potential S-nitrosylation sites in the myocardium. Am J Physiol Heart Circ Physiol (2011) 1.37
An automated platform for analysis of phosphoproteomic datasets: application to kidney collecting duct phosphoproteins. J Proteome Res (2007) 1.36
Identifying microRNA-mRNA regulatory network in colorectal cancer by a combination of expression profile and bioinformatics analysis. BMC Syst Biol (2012) 1.35
Diverse range of small peptides associated with high-density lipoprotein. Biochem Biophys Res Commun (2005) 1.34
High-throughput identification of IMCD proteins using LC-MS/MS. Physiol Genomics (2006) 1.33
Functional analysis of the kinome of the wheat scab fungus Fusarium graminearum. PLoS Pathog (2011) 1.31
Stoichiometry of STAT3 and mitochondrial proteins: Implications for the regulation of oxidative phosphorylation by protein-protein interactions. J Biol Chem (2010) 1.28
RAId_DbS: peptide identification using database searches with realistic statistics. Biol Direct (2007) 1.27
Expression of SUMO-2/3 induced senescence through p53- and pRB-mediated pathways. J Biol Chem (2006) 1.26
miR-574-5p negatively regulates Qki6/7 to impact β-catenin/Wnt signalling and the development of colorectal cancer. Gut (2012) 1.25
Steroidal saponins from Solanum nigrum. J Nat Prod (2006) 1.22
Robust accurate identification of peptides (RAId): deciphering MS2 data using a structured library search with de novo based statistics. Bioinformatics (2005) 1.21
Automated quantification tool for high-throughput proteomics using stable isotope labeling and LC-MSn. Anal Chem (2006) 1.20
MicroRNA-143 functions as a tumor suppressor in human esophageal squamous cell carcinoma. Gene (2012) 1.19
Sigma-1 receptors regulate hippocampal dendritic spine formation via a free radical-sensitive mechanism involving Rac1xGTP pathway. Proc Natl Acad Sci U S A (2009) 1.18
LC-MS/MS analysis of apical and basolateral plasma membranes of rat renal collecting duct cells. Mol Cell Proteomics (2006) 1.18
Proteomic identification of altered apolipoprotein patterns in pulmonary hypertension and vasculopathy of sickle cell disease. Blood (2008) 1.18
Quantitative protein and mRNA profiling shows selective post-transcriptional control of protein expression by vasopressin in kidney cells. Mol Cell Proteomics (2010) 1.15
Electrostatics of charged dielectric spheres with application to biological systems. Phys Rev E Stat Nonlin Soft Matter Phys (2006) 1.15
Proteomic profiling of human plasma exosomes identifies PPARgamma as an exosome-associated protein. Biochem Biophys Res Commun (2008) 1.14
Identification and quantification of basic and acidic proteins using solution-based two-dimensional protein fractionation and label-free or 18O-labeling mass spectrometry. J Proteome Res (2007) 1.14
Phosphoproteomic profiling reveals vasopressin-regulated phosphorylation sites in collecting duct. J Am Soc Nephrol (2010) 1.13
Gp78, an ER associated E3, promotes SOD1 and ataxin-3 degradation. Hum Mol Genet (2009) 1.11
Large-scale quantitative LC-MS/MS analysis of detergent-resistant membrane proteins from rat renal collecting duct. Am J Physiol Cell Physiol (2008) 1.09
Proteomic identification of proteins associated with the osmoregulatory transcription factor TonEBP/OREBP: functional effects of Hsp90 and PARP-1. Am J Physiol Renal Physiol (2006) 1.09
Robust and accurate data enrichment statistics via distribution function of sum of weights. Bioinformatics (2010) 1.08
DJ-1, a cancer and Parkinson's disease associated protein, regulates autophagy through JNK pathway in cancer cells. Cancer Lett (2010) 1.06
Global protein identification and quantification technology using two-dimensional liquid chromatography nanospray mass spectrometry. Anal Chem (2003) 1.05
The β-adrenoceptor antagonist, propranolol, induces human gastric cancer cell apoptosis and cell cycle arrest via inhibiting nuclear factor κB signaling. Oncol Rep (2010) 1.04
The 1p-encoded protein stathmin and resistance of malignant gliomas to nitrosoureas. J Natl Cancer Inst (2007) 1.03
Decoy methods for assessing false positives and false discovery rates in shotgun proteomics. Anal Chem (2009) 1.02
Refractive index sensor using microfiber-based Mach-Zehnder interferometer. Opt Lett (2012) 1.01
On the inference of dirichlet mixture priors for protein sequence comparison. J Comput Biol (2011) 1.00
Identification of CHIP as a novel causative gene for autosomal recessive cerebellar ataxia. PLoS One (2013) 1.00
NGFI-B nuclear orphan receptor Nurr1 interacts with p53 and suppresses its transcriptional activity. Mol Cancer Res (2009) 1.00
Statistical Characterization of a 1D Random Potential Problem - with applications in score statistics of MS-based peptide sequencing. Physica A (2008) 0.98
A general approach for investigating enzymatic pathways and substrates for ubiquitin-like modifiers. Arch Biochem Biophys (2006) 0.98
Assembly of lysine 63-linked ubiquitin conjugates by phosphorylated alpha-synuclein implies Lewy body biogenesis. J Biol Chem (2007) 0.97
Proteolysis of macrophage inflammatory protein-1alpha isoforms LD78beta and LD78alpha by neutrophil-derived serine proteases. J Biol Chem (2005) 0.97
Compositional adjustment of Dirichlet mixture priors. J Comput Biol (2010) 0.96
Nurr1 is phosphorylated by ERK2 in vitro and its phosphorylation upregulates tyrosine hydroxylase expression in SH-SY5Y cells. Neurosci Lett (2007) 0.96
SUMO-1 modification increases human SOD1 stability and aggregation. Biochem Biophys Res Commun (2006) 0.96
Simple electrostatic model applicable to biomolecular recognition. Phys Rev E Stat Nonlin Soft Matter Phys (2010) 0.95
RAId_DbS: mass-spectrometry based peptide identification web server with knowledge integration. BMC Genomics (2008) 0.95
The endoplasmic reticulum (ER)-associated degradation system regulates aggregation and degradation of mutant neuroserpin. J Biol Chem (2011) 0.95
The HDF1 histone deacetylase gene is important for conidiation, sexual reproduction, and pathogenesis in Fusarium graminearum. Mol Plant Microbe Interact (2011) 0.94
ITM Probe: analyzing information flow in protein networks. Bioinformatics (2009) 0.94
In vacuo isotope coded alkylation technique (IVICAT); an N-terminal stable isotopic label for quantitative liquid chromatography/mass spectrometry proteomics. Rapid Commun Mass Spectrom (2006) 0.94