Published in J Proteome Res on December 12, 2005
A survey of computational methods and error rate estimation procedures for peptide and protein identification in shotgun proteomics. J Proteomics (2010) 3.78
Spectral dictionaries: Integrating de novo peptide sequencing with database search of tandem mass spectra. Mol Cell Proteomics (2008) 1.60
A mixed integer linear optimization framework for the identification and quantification of targeted post-translational modifications of highly modified proteins using multiplexed electron transfer dissociation tandem mass spectrometry. Mol Cell Proteomics (2009) 1.51
MASPECTRAS: a platform for management and analysis of proteomics LC-MS/MS data. BMC Bioinformatics (2007) 1.34
GProX, a user-friendly platform for bioinformatics analysis and visualization of quantitative proteomics data. Mol Cell Proteomics (2011) 1.30
Quantitative mass spectrometry of histones H3.2 and H3.3 in Suz12-deficient mouse embryonic stem cells reveals distinct, dynamic post-translational modifications at Lys-27 and Lys-36. Mol Cell Proteomics (2010) 1.23
Metastasis-related plasma membrane proteins of human breast cancer cells identified by comparative quantitative mass spectrometry. Mol Cell Proteomics (2009) 1.21
DtaRefinery, a software tool for elimination of systematic errors from parent ion mass measurements in tandem mass spectra data sets. Mol Cell Proteomics (2009) 1.17
A novel approach for untargeted post-translational modification identification using integer linear optimization and tandem mass spectrometry. Mol Cell Proteomics (2010) 1.11
MODi: a powerful and convenient web server for identifying multiple post-translational peptide modifications from tandem mass spectra. Nucleic Acids Res (2006) 1.08
Elimination of systematic mass measurement errors in liquid chromatography-mass spectrometry based proteomics using regression models and a priori partial knowledge of the sample content. Anal Chem (2007) 1.06
Mass spectrometry-based proteomics for the analysis of chromatin structure and dynamics. Int J Mol Sci (2013) 0.97
Identification of RNA molecules by specific enzyme digestion and mass spectrometry: software for and implementation of RNA mass mapping. Nucleic Acids Res (2009) 0.89
Find pairs: the module for protein quantification of the PeakQuant software suite. OMICS (2012) 0.84
The nuclear protein ALY binds to and modulates the activity of transcription factor E2F2. Mol Cell Proteomics (2013) 0.80
Post-translational modification of LipL32 during Leptospira interrogans infection. PLoS Negl Trop Dis (2014) 0.79
PILOT_PROTEIN: identification of unmodified and modified proteins via high-resolution mass spectrometry and mixed-integer linear optimization. J Proteome Res (2012) 0.79
Computational refinement of post-translational modifications predicted from tandem mass spectrometry. Bioinformatics (2011) 0.79
SweetSEQer, simple de novo filtering and annotation of glycoconjugate mass spectra. Mol Cell Proteomics (2013) 0.78
Differential proteomics analysis reveals a role for E2F2 in the regulation of the Ahr pathway in T lymphocytes. Mol Cell Proteomics (2010) 0.78
Vitronectin and dermcidin serum levels predict the metastatic progression of AJCC I-II early-stage melanoma. Int J Cancer (2016) 0.75
Molecular and cellular responses of the pathogenic fungus Lomentospora prolificans to the antifungal drug voriconazole. PLoS One (2017) 0.75
Development of human protein reference database as an initial platform for approaching systems biology in humans. Genome Res (2003) 14.79
Mammalian Sir2 homolog SIRT3 regulates global mitochondrial lysine acetylation. Mol Cell Biol (2007) 7.97
Identification of a gene causing human cytochrome c oxidase deficiency by integrative genomics. Proc Natl Acad Sci U S A (2003) 6.87
Integrated analysis of protein composition, tissue diversity, and gene regulation in mouse mitochondria. Cell (2003) 6.77
Highly selective enrichment of phosphorylated peptides from peptide mixtures using titanium dioxide microcolumns. Mol Cell Proteomics (2005) 6.34
Reversible lysine acetylation controls the activity of the mitochondrial enzyme acetyl-CoA synthetase 2. Proc Natl Acad Sci U S A (2006) 5.96
Proteomic analysis of post-translational modifications. Nat Biotechnol (2003) 5.87
Hfq: a bacterial Sm-like protein that mediates RNA-RNA interaction. Mol Cell (2002) 5.26
Quantitative phosphoproteomics applied to the yeast pheromone signaling pathway. Mol Cell Proteomics (2005) 5.07
Human Proteinpedia enables sharing of human protein data. Nat Biotechnol (2008) 4.21
Analysis of protein phosphorylation using mass spectrometry: deciphering the phosphoproteome. Trends Biotechnol (2002) 3.85
Phosphoproteomics of the Arabidopsis plasma membrane and a new phosphorylation site database. Plant Cell (2004) 3.51
Large-scale analysis of in vivo phosphorylated membrane proteins by immobilized metal ion affinity chromatography and mass spectrometry. Mol Cell Proteomics (2003) 2.98
SIRT3 deacetylates mitochondrial 3-hydroxy-3-methylglutaryl CoA synthase 2 and regulates ketone body production. Cell Metab (2010) 2.77
The histone methyltransferase SET8 is required for S-phase progression. J Cell Biol (2007) 2.74
Highly selective enrichment of phosphorylated peptides using titanium dioxide. Nat Protoc (2006) 2.71
MSQuant, an open source platform for mass spectrometry-based quantitative proteomics. J Proteome Res (2010) 2.40
The pseudokinase domain of JAK2 is a dual-specificity protein kinase that negatively regulates cytokine signaling. Nat Struct Mol Biol (2011) 2.20
SIMAC (sequential elution from IMAC), a phosphoproteomics strategy for the rapid separation of monophosphorylated from multiply phosphorylated peptides. Mol Cell Proteomics (2007) 1.98
Identification of the receptor scavenging hemopexin-heme complexes. Blood (2005) 1.97
Comprehensive proteomic analysis of human pancreatic juice. J Proteome Res (2004) 1.93
A specific p47phox -serine phosphorylated by convergent MAPKs mediates neutrophil NADPH oxidase priming at inflammatory sites. J Clin Invest (2006) 1.92
The functional cobalamin (vitamin B12)-intrinsic factor receptor is a novel complex of cubilin and amnionless. Blood (2003) 1.91
Analytical strategies for phosphoproteomics. Proteomics (2009) 1.85
Proteasomal inhibition by alpha-synuclein filaments and oligomers. J Biol Chem (2004) 1.84
Site-specific phosphorylation dynamics of the nuclear proteome during the DNA damage response. Mol Cell Proteomics (2010) 1.81
Mechanism for activation of the growth factor-activated AGC kinases by turn motif phosphorylation. EMBO J (2007) 1.74
Modification-specific proteomics of plasma membrane proteins: identification and characterization of glycosylphosphatidylinositol-anchored proteins released upon phospholipase D treatment. J Proteome Res (2006) 1.71
The human cap-binding complex is functionally connected to the nuclear RNA exosome. Nat Struct Mol Biol (2013) 1.67
Modification-specific proteomics: strategies for characterization of post-translational modifications using enrichment techniques. Proteomics (2009) 1.66
Protein hydrogen exchange measured at single-residue resolution by electron transfer dissociation mass spectrometry. Anal Chem (2009) 1.65
A new strategy for identification of N-glycosylated proteins and unambiguous assignment of their glycosylation sites using HILIC enrichment and partial deglycosylation. J Proteome Res (2004) 1.65
Proteomic analysis of glycosylphosphatidylinositol-anchored membrane proteins. Mol Cell Proteomics (2003) 1.65
Simultaneous glycan-peptide characterization using hydrophilic interaction chromatography and parallel fragmentation by CID, higher energy collisional dissociation, and electron transfer dissociation MS applied to the N-linked glycoproteome of Campylobacter jejuni. Mol Cell Proteomics (2010) 1.63
Identification of phosphorylation sites in protein kinase A substrates using artificial neural networks and mass spectrometry. J Proteome Res (2004) 1.57
Autophosphorylation of JAK2 on tyrosines 221 and 570 regulates its activity. Mol Cell Biol (2004) 1.55
Dynamic histone H3 epigenome marking during the intraerythrocytic cycle of Plasmodium falciparum. Proc Natl Acad Sci U S A (2009) 1.54
Electron transfer dissociation facilitates the measurement of deuterium incorporation into selectively labeled peptides with single residue resolution. J Am Chem Soc (2008) 1.47
Cell cycle-specific UNG2 phosphorylations regulate protein turnover, activity and association with RPA. EMBO J (2007) 1.46
NetPhosYeast: prediction of protein phosphorylation sites in yeast. Bioinformatics (2007) 1.46
The sphingolipid long-chain base-Pkh1/2-Ypk1/2 signaling pathway regulates eisosome assembly and turnover. J Biol Chem (2008) 1.45
Identification of ischemia-regulated phosphorylation sites in connexin43: A possible target for the antiarrhythmic peptide analogue rotigaptide (ZP123). J Mol Cell Cardiol (2006) 1.45
Proteomics in chromatin biology and epigenetics: Elucidation of post-translational modifications of histone proteins by mass spectrometry. J Proteomics (2012) 1.44
A mass spectrometry-friendly database for cSNP identification. Nat Methods (2007) 1.43
Stable isotope labeling of Arabidopsis thaliana cells and quantitative proteomics by mass spectrometry. Mol Cell Proteomics (2005) 1.39
Identification of autophagosome-associated proteins and regulators by quantitative proteomic analysis and genetic screens. Mol Cell Proteomics (2012) 1.38
Quantitative proteomic assessment of very early cellular signaling events. Nat Biotechnol (2007) 1.35
Peptide sequencing and characterization of post-translational modifications by enhanced ion-charging and liquid chromatography electron-transfer dissociation tandem mass spectrometry. Anal Chem (2007) 1.35
SET8 is degraded via PCNA-coupled CRL4(CDT2) ubiquitylation in S phase and after UV irradiation. J Cell Biol (2011) 1.34
Identification by a differential proteomic approach of heat shock protein 27 as a potential marker of atherosclerosis. Circulation (2004) 1.33
Transcriptional co-activator protein p100 interacts with snRNP proteins and facilitates the assembly of the spliceosome. Nucleic Acids Res (2007) 1.31
Global histone analysis by mass spectrometry reveals a high content of acetylated lysine residues in the malaria parasite Plasmodium falciparum. J Proteome Res (2009) 1.30
Amnionless function is required for cubilin brush-border expression and intrinsic factor-cobalamin (vitamin B12) absorption in vivo. Blood (2005) 1.25
Quantitative mass spectrometry of histones H3.2 and H3.3 in Suz12-deficient mouse embryonic stem cells reveals distinct, dynamic post-translational modifications at Lys-27 and Lys-36. Mol Cell Proteomics (2010) 1.23
Metastasis-related plasma membrane proteins of human breast cancer cells identified by comparative quantitative mass spectrometry. Mol Cell Proteomics (2009) 1.21
WAVE regulatory complex activation by cooperating GTPases Arf and Rac1. Proc Natl Acad Sci U S A (2011) 1.20
A proteomic analysis of human bile. Mol Cell Proteomics (2004) 1.20
Autophosphorylation is essential for the in vivo function of the Lotus japonicus Nod factor receptor 1 and receptor-mediated signalling in cooperation with Nod factor receptor 5. Plant J (2010) 1.17
p130Cas mediates the transforming properties of the anaplastic lymphoma kinase. Blood (2005) 1.16
Functional heterogeneity within the CD44 high human breast cancer stem cell-like compartment reveals a gene signature predictive of distant metastasis. Mol Med (2012) 1.15
Phosphorylation of JAK2 at serine 523: a negative regulator of JAK2 that is stimulated by growth hormone and epidermal growth factor. Mol Cell Biol (2006) 1.12
Middle-down hybrid chromatography/tandem mass spectrometry workflow for characterization of combinatorial post-translational modifications in histones. Proteomics (2014) 1.11
Utilizing ion-pairing hydrophilic interaction chromatography solid phase extraction for efficient glycopeptide enrichment in glycoproteomics. Anal Chem (2010) 1.10
Characterization of gel-separated glycoproteins using two-step proteolytic digestion combined with sequential microcolumns and mass spectrometry. Mol Cell Proteomics (2004) 1.09
Identification of thioredoxin disulfide targets using a quantitative proteomics approach based on isotope-coded affinity tags. J Proteome Res (2008) 1.09
p25alpha relocalizes in oligodendroglia from myelin to cytoplasmic inclusions in multiple system atrophy. Am J Pathol (2007) 1.08
The tyrosine phosphatase Shp2 interacts with NPM-ALK and regulates anaplastic lymphoma cell growth and migration. Cancer Res (2007) 1.08
Analysis of posttranslational modifications of proteins by tandem mass spectrometry. Biotechniques (2006) 1.08
Analysis of histidine phosphorylation using tandem MS and ion-electron reactions. Anal Chem (2007) 1.07
An enzymatic deglycosylation scheme enabling identification of core fucosylated N-glycans and O-glycosylation site mapping of human plasma proteins. J Proteome Res (2007) 1.07
Up-regulated proteins in the fluid bathing the tumour cell microenvironment as potential serological markers for early detection of cancer of the breast. Mol Oncol (2009) 1.07
Assessment of lectin and HILIC based enrichment protocols for characterization of serum glycoproteins by mass spectrometry. J Proteomics (2008) 1.06
BRAG1, a Sec7 domain-containing protein, is a component of the postsynaptic density of excitatory synapses. Brain Res (2006) 1.06
TiO(2)-based phosphoproteomic analysis of the plasma membrane and the effects of phosphatase inhibitor treatment. J Proteome Res (2008) 1.05
Widespread abundance of functional bacterial amyloid in mycolata and other gram-positive bacteria. Appl Environ Microbiol (2009) 1.05
Efficient isolation and quantitative proteomic analysis of cancer cell plasma membrane proteins for identification of metastasis-associated cell surface markers. J Proteome Res (2009) 1.05
Proteomic profiling of Mycobacterium tuberculosis identifies nutrient-starvation-responsive toxin-antitoxin systems. Mol Cell Proteomics (2013) 1.05
Quantitative proteomics by amino acid labeling in C. elegans. Nat Methods (2011) 1.05
Furin proteolytically processes the heparin-binding region of extracellular superoxide dismutase. J Biol Chem (2002) 1.04
Feedback inactivation of D-serine synthesis by NMDA receptor-elicited translocation of serine racemase to the membrane. Proc Natl Acad Sci U S A (2009) 1.02
The dual nature of human extracellular superoxide dismutase: one sequence and two structures. Proc Natl Acad Sci U S A (2003) 1.02
p25alpha Stimulates alpha-synuclein aggregation and is co-localized with aggregated alpha-synuclein in alpha-synucleinopathies. J Biol Chem (2004) 1.02
Phosphosite mapping of P-type plasma membrane H+-ATPase in homologous and heterologous environments. J Biol Chem (2011) 1.02
High-oxygen packaging atmosphere influences protein oxidation and tenderness of porcine longissimus dorsi during chill storage. Meat Sci (2007) 1.00
Quantitative assessment of in-solution digestion efficiency identifies optimal protocols for unbiased protein analysis. Mol Cell Proteomics (2013) 0.99
Composition and proteolytic processing of corneal deposits associated with mutations in the TGFBI gene. Exp Eye Res (2011) 0.99
Quantitative proteomics identifies Gemin5, a scaffolding protein involved in ribonucleoprotein assembly, as a novel partner for eukaryotic initiation factor 4E. J Proteome Res (2006) 0.99
Utility of immonium ions for assignment of epsilon-N-acetyllysine-containing peptides by tandem mass spectrometry. Anal Chem (2008) 0.98
Serum protein profiling by solid phase extraction and mass spectrometry: a future diagnostics tool? Proteomics (2009) 0.98
Highly Efficient Phosphopeptide Enrichment by Calcium Phosphate Precipitation Combined with Subsequent IMAC Enrichment. Mol Cell Proteomics (2007) 0.98
Peptide binding specificity of the chaperone calreticulin. Biochim Biophys Acta (2007) 0.97
Efficacy and compatibility with mass spectrometry of methods for elution of proteins from sodium dodecyl sulfate-polyacrylamide gels and polyvinyldifluoride membranes. Anal Biochem (2004) 0.97
Quantitative phosphoproteomics of tomato mounting a hypersensitive response reveals a swift suppression of photosynthetic activity and a differential role for hsp90 isoforms. J Proteome Res (2009) 0.97
Quantitative proteomics analysis of Streptomyces coelicolor development demonstrates that onset of secondary metabolism coincides with hypha differentiation. Mol Cell Proteomics (2010) 0.96
Precision mapping of coexisting modifications in histone H3 tails from embryonic stem cells by ETD-MS/MS. Anal Chem (2013) 0.96
Structural analysis and tissue localization of human C4.4A: a protein homologue of the urokinase receptor. Biochem J (2004) 0.96
Reproducibility of mass spectrometry based protein profiles for diagnosis of breast cancer across clinical studies: a systematic review. J Proteome Res (2008) 0.96