Published in J Proteome Res on June 19, 2008
A survey of computational methods and error rate estimation procedures for peptide and protein identification in shotgun proteomics. J Proteomics (2010) 3.78
The generating function of CID, ETD, and CID/ETD pairs of tandem mass spectra: applications to database search. Mol Cell Proteomics (2010) 2.64
Large-scale Arabidopsis phosphoproteome profiling reveals novel chloroplast kinase substrates and phosphorylation networks. Plant Physiol (2009) 2.38
MS-GF+ makes progress towards a universal database search tool for proteomics. Nat Commun (2014) 2.22
Confident phosphorylation site localization using the Mascot Delta Score. Mol Cell Proteomics (2010) 1.90
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
Spectral dictionaries: Integrating de novo peptide sequencing with database search of tandem mass spectra. Mol Cell Proteomics (2008) 1.60
A ranking-based scoring function for peptide-spectrum matches. J Proteome Res (2009) 1.22
Elucidating the CXCL12/CXCR4 signaling network in chronic lymphocytic leukemia through phosphoproteomics analysis. PLoS One (2010) 1.15
Phosphoproteomic profiling reveals vasopressin-regulated phosphorylation sites in collecting duct. J Am Soc Nephrol (2010) 1.13
Toward a complete in silico, multi-layered embryonic stem cell regulatory network. Wiley Interdiscip Rev Syst Biol Med (2010) 1.06
Integrated platform for manual and high-throughput statistical validation of tandem mass spectra. Proteomics (2009) 1.03
Online nanoflow multidimensional fractionation for high efficiency phosphopeptide analysis. Mol Cell Proteomics (2011) 1.02
mzResults: an interactive viewer for interrogation and distribution of proteomics results. Mol Cell Proteomics (2011) 0.98
Quantitative phosphoproteomics in nuclei of vasopressin-sensitive renal collecting duct cells. Am J Physiol Cell Physiol (2012) 0.98
iPhos: a toolkit to streamline the alkaline phosphatase-assisted comprehensive LC-MS phosphoproteome investigation. BMC Bioinformatics (2014) 0.87
Practical 4'-phosphopantetheine active site discovery from proteomic samples. J Proteome Res (2010) 0.83
Improved sequence tag generation method for peptide identification in tandem mass spectrometry. J Proteome Res (2008) 0.83
Phosphoproteomic analysis: an emerging role in deciphering cellular signaling in human embryonic stem cells and their differentiated derivatives. Stem Cell Rev (2012) 0.81
Global discovery of high-NaCl-induced changes of protein phosphorylation. Am J Physiol Cell Physiol (2014) 0.81
An Efficient Dynamic Programming Algorithm for Phosphorylation Site Assignment of Large-Scale Mass Spectrometry Data. Proceedings (IEEE Int Conf Bioinformatics Biomed) (2012) 0.81
Mass spectrometry-based proteomics: qualitative identification to activity-based protein profiling. Wiley Interdiscip Rev Syst Biol Med (2012) 0.78
The Pacific Northwest National Laboratory library of bacterial and archaeal proteomic biodiversity. Sci Data (2015) 0.77
Quantitative phosphoproteomics: New technologies and applications in the DNA damage response. Cell Cycle (2010) 0.77
Large-Scale Examination of Factors Influencing Phosphopeptide Neutral Loss during Collision Induced Dissociation. J Am Soc Mass Spectrom (2015) 0.77
A turn-key approach for large-scale identification of complex posttranslational modifications. J Proteome Res (2014) 0.76
PhosphoHunter: An Efficient Software Tool for Phosphopeptide Identification. Adv Bioinformatics (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
Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. Cell (2006) 20.92
TANDEM: matching proteins with tandem mass spectra. Bioinformatics (2004) 17.41
A probability-based approach for high-throughput protein phosphorylation analysis and site localization. Nat Biotechnol (2006) 12.13
Signaling--2000 and beyond. Cell (2000) 11.78
A uniform proteomics MS/MS analysis platform utilizing open XML file formats. Mol Syst Biol (2005) 9.81
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Comparative evaluation of mass spectrometry platforms used in large-scale proteomics investigations. Nat Methods (2005) 6.73
A systematic approach to the analysis of protein phosphorylation. Nat Biotechnol (2001) 6.66
InsPecT: identification of posttranslationally modified peptides from tandem mass spectra. Anal Chem (2005) 6.65
Large-scale phosphorylation analysis of mouse liver. Proc Natl Acad Sci U S A (2007) 6.08
What is a support vector machine? Nat Biotechnol (2006) 5.10
Analysis of phosphorylation sites on proteins from Saccharomyces cerevisiae by electron transfer dissociation (ETD) mass spectrometry. Proc Natl Acad Sci U S A (2007) 5.09
Selective isolation at the femtomole level of phosphopeptides from proteolytic digests using 2D-NanoLC-ESI-MS/MS and titanium oxide precolumns. Anal Chem (2004) 4.06
PepNovo: de novo peptide sequencing via probabilistic network modeling. Anal Chem (2005) 4.02
Global proteomic profiling of phosphopeptides using electron transfer dissociation tandem mass spectrometry. Proc Natl Acad Sci U S A (2007) 4.01
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Phosphoproteome analysis of the human mitotic spindle. Proc Natl Acad Sci U S A (2006) 3.56
Proteome-wide identification of in vivo targets of DNA damage checkpoint kinases. Proc Natl Acad Sci U S A (2007) 3.44
Isolation of phosphoproteins by immobilized metal (Fe3+) affinity chromatography. Anal Biochem (1986) 2.55
Comprehensive identification of phosphorylation sites in postsynaptic density preparations. Mol Cell Proteomics (2006) 2.51
The serine/threonine/tyrosine phosphoproteome of the model bacterium Bacillus subtilis. Mol Cell Proteomics (2007) 2.40
Interpreting the protein language using proteomics. Nat Rev Mol Cell Biol (2006) 2.23
Cleavage N-terminal to proline: analysis of a database of peptide tandem mass spectra. Anal Chem (2003) 1.98
Peptide charge state determination for low-resolution tandem mass spectra. Proc IEEE Comput Syst Bioinform Conf (2005) 1.97
Intensity-based statistical scorer for tandem mass spectrometry. Anal Chem (2003) 1.83
Automatic validation of phosphopeptide identifications from tandem mass spectra. Anal Chem (2007) 1.70
Fragmentation of phosphopeptides in an ion trap mass spectrometer. J Am Soc Mass Spectrom (1998) 1.67
Tandem mass spectrometry of very large molecules. 2. Dissociation of multiply charged proline-containing proteins from electrospray ionization. Anal Chem (1993) 1.56
Mitochondrial phosphoproteome revealed by an improved IMAC method and MS/MS/MS. Mol Cell Proteomics (2007) 1.27
Identification of phosphoproteins and their phosphorylation sites in the WEHI-231 B lymphoma cell line. Mol Cell Proteomics (2004) 1.19
Cross-correlation algorithm for calculation of peptide molecular weight from tandem mass spectra. Anal Chem (2006) 0.99
Proteome and phosphoproteome dynamic change during cell dedifferentiation in Arabidopsis. Proteomics (2007) 0.94
The diploid genome sequence of an individual human. PLoS Biol (2007) 44.80
Sequence and structural variation in a human genome uncovered by short-read, massively parallel ligation sequencing using two-base encoding. Genome Res (2009) 15.15
The Sorcerer II Global Ocean Sampling expedition: expanding the universe of protein families. PLoS Biol (2007) 13.99
InsPecT: identification of posttranslationally modified peptides from tandem mass spectra. Anal Chem (2005) 6.65
The dog genome: survey sequencing and comparative analysis. Science (2003) 5.84
Discovery and revision of Arabidopsis genes by proteogenomics. Proc Natl Acad Sci U S A (2008) 3.45
Proteome-wide identification of in vivo targets of DNA damage checkpoint kinases. Proc Natl Acad Sci U S A (2007) 3.44
De novo somatic mutations in components of the PI3K-AKT3-mTOR pathway cause hemimegalencephaly. Nat Genet (2012) 3.41
Global DNA hypomethylation coupled to repressive chromatin domain formation and gene silencing in breast cancer. Genome Res (2011) 3.36
A multidimensional chromatography technology for in-depth phosphoproteome analysis. Mol Cell Proteomics (2008) 3.13
Functional interrogation of the kinome using nucleotide acyl phosphates. Biochemistry (2007) 3.01
HapCUT: an efficient and accurate algorithm for the haplotype assembly problem. Bioinformatics (2008) 2.96
Identification of post-translational modifications by blind search of mass spectra. Nat Biotechnol (2005) 2.84
Improving gene annotation using peptide mass spectrometry. Genome Res (2006) 2.69
Whole proteome analysis of post-translational modifications: applications of mass-spectrometry for proteogenomic annotation. Genome Res (2007) 2.67
ALS-associated mutations in TDP-43 increase its stability and promote TDP-43 complexes with FUS/TLS. Proc Natl Acad Sci U S A (2010) 2.65
TANGO1 facilitates cargo loading at endoplasmic reticulum exit sites. Cell (2009) 2.58
GOLPH3 bridges phosphatidylinositol-4- phosphate and actomyosin to stretch and shape the Golgi to promote budding. Cell (2009) 2.54
iDASH: integrating data for analysis, anonymization, and sharing. J Am Med Inform Assoc (2011) 2.51
An MCMC algorithm for haplotype assembly from whole-genome sequence data. Genome Res (2008) 2.45
Evaluation of paired-end sequencing strategies for detection of genome rearrangements in cancer. PLoS Comput Biol (2008) 2.40
Global analyses of sumoylated proteins in Saccharomyces cerevisiae. Induction of protein sumoylation by cellular stresses. J Biol Chem (2004) 2.27
Compressing genomic sequence fragments using SlimGene. J Comput Biol (2011) 2.10
DNA damage signaling recruits the Rtt107-Slx4 scaffolds via Dpb11 to mediate replication stress response. Mol Cell (2010) 2.02
Clustering millions of tandem mass spectra. J Proteome Res (2007) 1.98
A covering method for detecting genetic associations between rare variants and common phenotypes. PLoS Comput Biol (2010) 1.98
Searching genomes for noncoding RNA using FastR. IEEE/ACM Trans Comput Biol Bioinform (2006) 1.90
Peptide sequence tags for fast database search in mass-spectrometry. J Proteome Res (2005) 1.74
Proteogenomics to discover the full coding content of genomes: a computational perspective. J Proteomics (2010) 1.71
Comparative proteogenomics: combining mass spectrometry and comparative genomics to analyze multiple genomes. Genome Res (2008) 1.68
Distinct SUMO ligases cooperate with Esc2 and Slx5 to suppress duplication-mediated genome rearrangements. PLoS Genet (2013) 1.67
Cell junction-associated proteins IQGAP1, MAGI-2, CASK, spectrins, and alpha-actinin are components of the nephrin multiprotein complex. Proc Natl Acad Sci U S A (2005) 1.64
TORC1 regulates endocytosis via Npr1-mediated phosphoinhibition of a ubiquitin ligase adaptor. Cell (2011) 1.63
Experimental selection of hypoxia-tolerant Drosophila melanogaster. Proc Natl Acad Sci U S A (2011) 1.60
Genome-wide lethality screen identifies new PI4,5P2 effectors that regulate the actin cytoskeleton. EMBO J (2004) 1.59
Sensitive gene fusion detection using ambiguously mapping RNA-Seq read pairs. Bioinformatics (2011) 1.58
Deconvolution and database search of complex tandem mass spectra of intact proteins: a combinatorial approach. Mol Cell Proteomics (2010) 1.53
Protein identification using top-down. Mol Cell Proteomics (2011) 1.50
A proteome-wide analysis of kinase-substrate network in the DNA damage response. J Biol Chem (2010) 1.46
Mass spectrometric and kinetic analysis of ASF/SF2 phosphorylation by SRPK1 and Clk/Sty. J Biol Chem (2005) 1.43
An FHA domain-mediated protein interaction network of Rad53 reveals its role in polarized cell growth. J Cell Biol (2006) 1.40
Dynamic changes in protein-protein interaction and protein phosphorylation probed with amine-reactive isotope tag. Mol Cell Proteomics (2005) 1.39
Robustness of inference of haplotype block structure. J Comput Biol (2003) 1.38
Negative regulation of the E3 ubiquitin ligase itch via Fyn-mediated tyrosine phosphorylation. Mol Cell (2006) 1.35
Checkpoint proteins control morphogenetic events during DNA replication stress in Saccharomyces cerevisiae. J Cell Biol (2006) 1.32
QNet: a tool for querying protein interaction networks. J Comput Biol (2008) 1.32
Expansion of the mycobacterial "PUPylome". Mol Biosyst (2009) 1.31
Accurate annotation of peptide modifications through unrestrictive database search. J Proteome Res (2007) 1.30
Evidence for large inversion polymorphisms in the human genome from HapMap data. Genome Res (2006) 1.29
Optimal haplotype block-free selection of tagging SNPs for genome-wide association studies. Genome Res (2004) 1.28
Mechanism of Dun1 activation by Rad53 phosphorylation in Saccharomyces cerevisiae. J Biol Chem (2006) 1.28
DNA-repair scaffolds dampen checkpoint signalling by counteracting the adaptor Rad9. Nature (2012) 1.22
Orthologous repeats and mammalian phylogenetic inference. Genome Res (2005) 1.20
DNA replication stress differentially regulates G1/S genes via Rad53-dependent inactivation of Nrm1. EMBO J (2012) 1.17
A decomposition theory for phylogenetic networks and incompatible characters. J Comput Biol (2007) 1.17
Impact of phosphorylation and phosphorylation-null mutants on the activity and deamination specificity of activation-induced cytidine deaminase. J Biol Chem (2008) 1.16
Linking DNA replication checkpoint to MBF cell-cycle transcription reveals a distinct class of G1/S genes. EMBO J (2012) 1.16
Shotgun protein sequencing by tandem mass spectra assembly. Anal Chem (2004) 1.15
Resistance to EGF receptor inhibitors in glioblastoma mediated by phosphorylation of the PTEN tumor suppressor at tyrosine 240. Proc Natl Acad Sci U S A (2012) 1.15
Fast and accurate alignment of multiple protein networks. J Comput Biol (2009) 1.14
Direct binding of SAS-6 to ZYG-1 recruits SAS-6 to the mother centriole for cartwheel assembly. Dev Cell (2013) 1.13
Population sequencing of two endocannabinoid metabolic genes identifies rare and common regulatory variants associated with extreme obesity and metabolite level. Genome Biol (2010) 1.12
Resurrection of a clinical antibody: template proteogenomic de novo proteomic sequencing and reverse engineering of an anti-lymphotoxin-α antibody. Proteomics (2011) 1.08
Proteogenomic database construction driven from large scale RNA-seq data. J Proteome Res (2013) 1.08
Whole-genome sequencing uncovers the genetic basis of chronic mountain sickness in Andean highlanders. Am J Hum Genet (2013) 1.06
The endocytic adaptor protein ARH associates with motor and centrosomal proteins and is involved in centrosome assembly and cytokinesis. Mol Biol Cell (2008) 1.06
A sequence-based filtering method for ncRNA identification and its application to searching for riboswitch elements. Bioinformatics (2006) 1.04
Template proteogenomics: sequencing whole proteins using an imperfect database. Mol Cell Proteomics (2010) 1.04
Local phosphocycling mediated by LOK/SLK restricts ezrin function to the apical aspect of epithelial cells. J Cell Biol (2012) 1.03
Unrestrictive identification of post-translational modifications through peptide mass spectrometry. Nat Protoc (2006) 1.03
Designing deep sequencing experiments: detecting structural variation and estimating transcript abundance. BMC Genomics (2010) 1.00
hNOA1 interacts with complex I and DAP3 and regulates mitochondrial respiration and apoptosis. J Biol Chem (2008) 0.99
Automated querying and identification of novel peptides using MALDI mass spectrometric imaging. J Proteome Res (2011) 0.97
Virmid: accurate detection of somatic mutations with sample impurity inference. Genome Biol (2013) 0.97
Whi5 regulation by site specific CDK-phosphorylation in Saccharomyces cerevisiae. PLoS One (2009) 0.97
Optimization of primer design for the detection of variable genomic lesions in cancer. Bioinformatics (2007) 0.96
On the design of clone-based haplotyping. Genome Biol (2013) 0.95
An automated proteogenomic method uses mass spectrometry to reveal novel genes in Zea mays. Mol Cell Proteomics (2013) 0.95
Quantitative protein profiling using two-dimensional gel electrophoresis, isotope-coded affinity tag labeling, and mass spectrometry. Mol Cell Proteomics (2002) 0.95
RAPID detection of gene-gene interactions in genome-wide association studies. Bioinformatics (2010) 0.94
Strobe sequence design for haplotype assembly. BMC Bioinformatics (2011) 0.94
Construction of a medicinal leech transcriptome database and its application to the identification of leech homologs of neural and innate immune genes. BMC Genomics (2010) 0.94
Whole genome sequencing of Ethiopian highlanders reveals conserved hypoxia tolerance genes. Genome Biol (2014) 0.94
AMASS: algorithm for MSI analysis by semi-supervised segmentation. J Proteome Res (2011) 0.94
Using Genome Query Language to uncover genetic variation. Bioinformatics (2013) 0.93
Accurate mass spectrometry based protein quantification via shared peptides. J Comput Biol (2012) 0.92
An ancestral variant of Secretogranin II confers regulation by PHOX2 transcription factors and association with hypertension. Hum Mol Genet (2007) 0.92
Combinatorics of the breakage-fusion-bridge mechanism. J Comput Biol (2012) 0.91
Reconstitution of Rad53 activation by Mec1 through adaptor protein Mrc1. J Biol Chem (2009) 0.91
Identification of post-translational modifications via blind search of mass-spectra. Proc IEEE Comput Syst Bioinform Conf (2005) 0.91