Published in J Proteome Res on July 15, 2004
A dual pressure linear ion trap Orbitrap instrument with very high sequencing speed. Mol Cell Proteomics (2009) 4.75
Precision proteomics: the case for high resolution and high mass accuracy. Proc Natl Acad Sci U S A (2008) 4.00
Decoding signalling networks by mass spectrometry-based proteomics. Nat Rev Mol Cell Biol (2010) 3.78
Chemical derivatization of histones for facilitated analysis by mass spectrometry. Nat Protoc (2007) 3.78
Protein identification using sequential ion/ion reactions and tandem mass spectrometry. Proc Natl Acad Sci U S A (2005) 3.77
Mass spectrometry-based proteomics using Q Exactive, a high-performance benchtop quadrupole Orbitrap mass spectrometer. Mol Cell Proteomics (2011) 3.75
Improved peptide identification in proteomics by two consecutive stages of mass spectrometric fragmentation. Proc Natl Acad Sci U S A (2004) 3.43
Status of complete proteome analysis by mass spectrometry: SILAC labeled yeast as a model system. Genome Biol (2006) 3.34
Asymmetrically modified nucleosomes. Cell (2012) 2.79
High-speed data reduction, feature detection, and MS/MS spectrum quality assessment of shotgun proteomics data sets using high-resolution mass spectrometry. Anal Chem (2007) 2.75
Long-distance combinatorial linkage between methylation and acetylation on histone H3 N termini. Proc Natl Acad Sci U S A (2007) 2.43
Mass spectrometry analysis of Arabidopsis histone H3 reveals distinct combinations of post-translational modifications. Nucleic Acids Res (2004) 2.28
RNAi-dependent H3K27 methylation is required for heterochromatin formation and DNA elimination in Tetrahymena. Genes Dev (2007) 2.26
COMPASS: a suite of pre- and post-search proteomics software tools for OMSSA. Proteomics (2011) 2.19
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
The one hour yeast proteome. Mol Cell Proteomics (2013) 2.10
Utilizing artificial neural networks in MATLAB to achieve parts-per-billion mass measurement accuracy with a fourier transform ion cyclotron resonance mass spectrometer. J Am Soc Mass Spectrom (2009) 2.02
A proteomics grade electron transfer dissociation-enabled hybrid linear ion trap-orbitrap mass spectrometer. J Proteome Res (2008) 1.92
Implementation of electron-transfer dissociation on a hybrid linear ion trap-orbitrap mass spectrometer. Anal Chem (2007) 1.92
Identification of 491 proteins in the tear fluid proteome reveals a large number of proteases and protease inhibitors. Genome Biol (2006) 1.84
Large-scale and high-confidence proteomic analysis of human seminal plasma. Genome Biol (2006) 1.84
Implementation of ion/ion reactions in a quadrupole/time-of-flight tandem mass spectrometer. Anal Chem (2006) 1.72
A novel histone deacetylase pathway regulates mitosis by modulating Aurora B kinase activity. Genes Dev (2006) 1.70
Organellar proteomics: turning inventories into insights. EMBO Rep (2006) 1.63
Performance characteristics of a new hybrid quadrupole time-of-flight tandem mass spectrometer (TripleTOF 5600). Anal Chem (2011) 1.59
Identification of histone H3 lysine 36 acetylation as a highly conserved histone modification. J Biol Chem (2006) 1.50
Investigation of protein-tyrosine phosphatase 1B function by quantitative proteomics. Mol Cell Proteomics (2008) 1.46
A proteomics search algorithm specifically designed for high-resolution tandem mass spectra. J Proteome Res (2013) 1.40
Accurate mass measurements in proteomics. Chem Rev (2007) 1.36
Quantitative proteomic analysis of histone modifications. Chem Rev (2015) 1.32
Identification of class I MHC-associated phosphopeptides as targets for cancer immunotherapy. Proc Natl Acad Sci U S A (2006) 1.32
Automated data reduction for hydrogen/deuterium exchange experiments, enabled by high-resolution Fourier transform ion cyclotron resonance mass spectrometry. J Am Soc Mass Spectrom (2010) 1.28
Advances in proteomic workflows for systems biology. Curr Opin Biotechnol (2007) 1.26
Higher-energy collision-activated dissociation without a dedicated collision cell. Mol Cell Proteomics (2011) 1.26
Fourier transform mass spectrometry. Mol Cell Proteomics (2011) 1.24
Assessing the dynamic range and peak capacity of nanoflow LC-FAIMS-MS on an ion trap mass spectrometer for proteomics. Anal Chem (2008) 1.24
Analysis of tandem mass spectra by FTMS for improved large-scale proteomics with superior protein quantification. Anal Chem (2010) 1.22
The use of a hybrid linear trap/FT-ICR mass spectrometer for on-line high resolution/high mass accuracy bottom-up sequencing. J Biomol Tech (2005) 1.21
On the benefits of acquiring peptide fragment ions at high measured mass accuracy. J Am Soc Mass Spectrom (2008) 1.17
Top down proteomics of human membrane proteins from enriched mitochondrial fractions. Anal Chem (2013) 1.15
Analysis of intact protein isoforms by mass spectrometry. J Biol Chem (2011) 1.15
Systematic comparison of a two-dimensional ion trap and a three-dimensional ion trap mass spectrometer in proteomics. Mol Cell Proteomics (2004) 1.15
Top Down proteomics: facts and perspectives. Biochem Biophys Res Commun (2014) 1.14
Shotgun proteomics in neuroscience. Neuron (2009) 1.13
Evaluation of the utility of neutral-loss-dependent MS3 strategies in large-scale phosphorylation analysis. Proteomics (2008) 1.11
Quantitative proteomics with siRNA screening identifies novel mechanisms of trastuzumab resistance in HER2 amplified breast cancers. Mol Cell Proteomics (2012) 1.10
Comparison of Mascot and X!Tandem performance for low and high accuracy mass spectrometry and the development of an adjusted Mascot threshold. Mol Cell Proteomics (2008) 1.10
EpiProfile Quantifies Histone Peptides With Modifications by Extracting Retention Time and Intensity in High-resolution Mass Spectra. Mol Cell Proteomics (2015) 1.09
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
Comparison between procedures using SDS for shotgun proteomic analyses of complex samples. Proteomics (2011) 1.08
Modular mass spectrometric tool for analysis of composition and phosphorylation of protein complexes. PLoS One (2007) 1.02
Dual electrospray ion source for electron-transfer dissociation on a hybrid linear ion trap-orbitrap mass spectrometer. Anal Chem (2007) 1.01
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
Optimization of electron transfer dissociation via informed selection of reagents and operating parameters. Anal Chem (2012) 0.97
Nano-LC FTICR tandem mass spectrometry for top-down proteomics: routine baseline unit mass resolution of whole cell lysate proteins up to 72 kDa. Anal Chem (2012) 0.97
Neutron encoded labeling for peptide identification. Anal Chem (2013) 0.96
Quantitative profiling of histone post-translational modifications by stable isotope labeling. Methods (2007) 0.95
Mass spectrometry-based proteomic profiling of lung cancer. Proc Am Thorac Soc (2009) 0.93
NeuCode labels for relative protein quantification. Mol Cell Proteomics (2014) 0.92
Sub-part-per-million precursor and product mass accuracy for high-throughput proteomics on an electron transfer dissociation-enabled orbitrap mass spectrometer. Mol Cell Proteomics (2010) 0.92
Identification and interrogation of combinatorial histone modifications. Front Genet (2013) 0.91
Experimental Evidence for Space-Charge Effects between Ions of the Same Mass-to-Charge in Fourier-Transform Ion Cyclotron Resonance Mass Spectrometry. Int J Mass Spectrom (2007) 0.91
Combining bottom-up and top-down mass spectrometric strategies for de novo sequencing of the crustacean hyperglycemic hormone from Cancer borealis. Anal Chem (2009) 0.90
Mass spectrometric quantification of histone post-translational modifications by a hybrid chemical labeling method. Mol Cell Proteomics (2015) 0.89
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
De novo correction of mass measurement error in low resolution tandem MS spectra for shotgun proteomics. J Am Soc Mass Spectrom (2012) 0.89
High mass selectivity for top-down proteomics by application of SWIFT technology. J Am Soc Mass Spectrom (2009) 0.89
Extracted Fragment Ion Mobility Distributions: A New Method for Complex Mixture Analysis. Int J Mass Spectrom (2012) 0.88
Phosphoproteomics in the Age of Rapid and Deep Proteome Profiling. Anal Chem (2015) 0.87
Characterization of strategies for obtaining confident identifications in bottom-up proteomics measurements using hybrid FTMS instruments. Anal Chem (2008) 0.87
Unambiguous determination of isobaric histone modifications by reversed-phase retention time and high-mass accuracy. Anal Biochem (2009) 0.87
Unraveling the histone's potential: a proteomics perspective. Epigenetics (2008) 0.86
Extensive and varied modifications in histone H2B of wild-type and histone deacetylase 1 mutant Neurospora crassa. Biochemistry (2010) 0.85
Chemical and biochemical approaches in the study of histone methylation and demethylation. Med Res Rev (2012) 0.85
Modern approaches for investigating epigenetic signaling pathways. J Appl Physiol (1985) (2010) 0.84
Spectral accuracy and sulfur counting capabilities of the LTQ-FT-ICR and the LTQ-Orbitrap XL for small molecule analysis. J Am Soc Mass Spectrom (2011) 0.84
Polar aprotic modifiers for chromatographic separation and back-exchange reduction for protein hydrogen/deuterium exchange monitored by Fourier transform ion cyclotron resonance mass spectrometry. J Am Soc Mass Spectrom (2012) 0.84
Enhanced Dissociation of Intact Proteins with High Capacity Electron Transfer Dissociation. J Am Soc Mass Spectrom (2015) 0.83
Systematic investigation of lycopene effects in LNCaP cells by use of novel large-scale proteomic analysis software. Proteomics Clin Appl (2007) 0.83
Sequential proteolysis and high-field FTICR MS to determine disulfide connectivity and 4-maleimide TEMPO spin-label location in L126C GM2 activator protein. Anal Chem (2009) 0.83
Mass spectrometric analysis of histone proteoforms. Annu Rev Anal Chem (Palo Alto Calif) (2014) 0.83
Preliminary identification of differentially expressed tear proteins in keratoconus. Mol Vis (2013) 0.82
Laser-induced acoustic desorption coupled with a linear quadrupole ion trap mass spectrometer. Anal Chem (2010) 0.82
Toward a systems-level view of dynamic phosphorylation networks. Front Genet (2014) 0.82
High resolution is not a strict requirement for characterization and quantification of histone post-translational modifications. J Proteome Res (2014) 0.81
Quantitative proteomics reveals that the specific methyltransferases Txr1p and Ezl2p differentially affect the mono-, di- and trimethylation states of histone H3 lysine 27 (H3K27). Mol Cell Proteomics (2012) 0.81
Quantitative proteomic approaches to studying histone modifications. Curr Chem Genomics (2011) 0.79
Use of theoretical peptide distributions in phosphoproteome analysis. J Proteome Res (2013) 0.79
Mass recalibration of FT-ICR mass spectrometry imaging data using the average frequency shift of ambient ions. J Am Soc Mass Spectrom (2013) 0.78
Proteomic solutions for analytical challenges associated with alcohol research. Alcohol Res Health (2008) 0.78
Development and characterization of a novel plug and play liquid chromatography-mass spectrometry (LC-MS) source that automates connections between the capillary trap, column, and emitter. Mol Cell Proteomics (2013) 0.78
Mass spectrometry-based proteomics: qualitative identification to activity-based protein profiling. Wiley Interdiscip Rev Syst Biol Med (2012) 0.78
High-sensitivity nanoLC-MS/MS analysis of urinary desmosine and isodesmosine. Anal Chem (2009) 0.78
Peptide and protein sequence analysis by electron transfer dissociation mass spectrometry. Proc Natl Acad Sci U S A (2004) 13.14
Parts per million mass accuracy on an Orbitrap mass spectrometer via lock mass injection into a C-trap. Mol Cell Proteomics (2005) 10.60
Sequence and structural convergence of broad and potent HIV antibodies that mimic CD4 binding. Science (2011) 9.00
Phosphoproteome analysis by mass spectrometry and its application to Saccharomyces cerevisiae. Nat Biotechnol (2002) 8.37
The mTOR-regulated phosphoproteome reveals a mechanism of mTORC1-mediated inhibition of growth factor signaling. Science (2011) 6.75
Histone methyltransferases direct different degrees of methylation to define distinct chromatin domains. Mol Cell (2003) 6.44
Regulation of HP1-chromatin binding by histone H3 methylation and phosphorylation. Nature (2005) 6.40
A large nucleolar U3 ribonucleoprotein required for 18S ribosomal RNA biogenesis. Nature (2002) 6.19
Set2 is a nucleosomal histone H3-selective methyltransferase that mediates transcriptional repression. Mol Cell Biol (2002) 5.42
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
Higher-energy C-trap dissociation for peptide modification analysis. Nat Methods (2007) 5.04
A dual pressure linear ion trap Orbitrap instrument with very high sequencing speed. Mol Cell Proteomics (2009) 4.75
Interpreting cancer genomes using systematic host network perturbations by tumour virus proteins. Nature (2012) 4.35
Aurora B phosphorylates centromeric MCAK and regulates its localization and microtubule depolymerization activity. Curr Biol (2004) 4.20
Performance evaluation of a hybrid linear ion trap/orbitrap mass spectrometer. Anal Chem (2006) 4.10
Organismal differences in post-translational modifications in histones H3 and H4. J Biol Chem (2006) 3.84
Chemical derivatization of histones for facilitated analysis by mass spectrometry. Nat Protoc (2007) 3.78
Gene silencing: trans-histone regulatory pathway in chromatin. Nature (2002) 3.77
Protein identification using sequential ion/ion reactions and tandem mass spectrometry. Proc Natl Acad Sci U S A (2005) 3.77
Mass spectrometry-based proteomics using Q Exactive, a high-performance benchtop quadrupole Orbitrap mass spectrometer. Mol Cell Proteomics (2011) 3.75
Identification of the beta cell antigen targeted by a prevalent population of pathogenic CD8+ T cells in autoimmune diabetes. Proc Natl Acad Sci U S A (2003) 3.75
A two-dimensional quadrupole ion trap mass spectrometer. J Am Soc Mass Spectrom (2002) 3.65
Supplemental activation method for high-efficiency electron-transfer dissociation of doubly protonated peptide precursors. Anal Chem (2007) 3.32
Cathepsin L proteolytically processes histone H3 during mouse embryonic stem cell differentiation. Cell (2008) 3.09
A neutral loss activation method for improved phosphopeptide sequence analysis by quadrupole ion trap mass spectrometry. Anal Chem (2004) 3.08
Expression patterns and post-translational modifications associated with mammalian histone H3 variants. J Biol Chem (2005) 3.00
The utility of ETD mass spectrometry in proteomic analysis. Biochim Biophys Acta (2006) 2.85
Extensive crosstalk between O-GlcNAcylation and phosphorylation regulates cytokinesis. Sci Signal (2010) 2.79
Recognition of a mononucleosomal histone modification pattern by BPTF via multivalent interactions. Cell (2011) 2.68
MAPKAP kinase 2 phosphorylates tristetraprolin on in vivo sites including Ser178, a site required for 14-3-3 binding. J Biol Chem (2003) 2.53
Long-distance combinatorial linkage between methylation and acetylation on histone H3 N termini. Proc Natl Acad Sci U S A (2007) 2.43
N-terminal alpha-methylation of RCC1 is necessary for stable chromatin association and normal mitosis. Nat Cell Biol (2007) 2.36
Insulin controls subcellular localization and multisite phosphorylation of the phosphatidic acid phosphatase, lipin 1. J Biol Chem (2006) 2.32
The vertebrate Ndc80 complex contains Spc24 and Spc25 homologs, which are required to establish and maintain kinetochore-microtubule attachment. Curr Biol (2004) 2.31
Mass spectrometry analysis of Arabidopsis histone H3 reveals distinct combinations of post-translational modifications. Nucleic Acids Res (2004) 2.28
O-GlcNAc regulates FoxO activation in response to glucose. J Biol Chem (2008) 2.27
Electron transfer dissociation of peptide anions. J Am Soc Mass Spectrom (2005) 2.26
RNAi-dependent H3K27 methylation is required for heterochromatin formation and DNA elimination in Tetrahymena. Genes Dev (2007) 2.26
High-performance mass spectrometry: Fourier transform ion cyclotron resonance at 14.5 Tesla. Anal Chem (2008) 2.23
Inhibition of ALK, PI3K/MEK, and HSP90 in murine lung adenocarcinoma induced by EML4-ALK fusion oncogene. Cancer Res (2010) 2.20
Saccharomyces cerevisiae Rad9 acts as a Mec1 adaptor to allow Rad53 activation. Curr Biol (2005) 2.20
Dual-pressure linear ion trap mass spectrometer improving the analysis of complex protein mixtures. Anal Chem (2009) 2.20
Ultra high resolution linear ion trap Orbitrap mass spectrometer (Orbitrap Elite) facilitates top down LC MS/MS and versatile peptide fragmentation modes. Mol Cell Proteomics (2011) 2.13
Androgen receptor phosphorylation. Regulation and identification of the phosphorylation sites. J Biol Chem (2002) 2.01
Metabolic signatures uncover distinct targets in molecular subsets of diffuse large B cell lymphoma. Cancer Cell (2012) 1.98
Genomic and functional evolution of the Drosophila melanogaster sperm proteome. Nat Genet (2006) 1.97
Dynamic range of mass accuracy in LTQ Orbitrap hybrid mass spectrometer. J Am Soc Mass Spectrom (2006) 1.96
Phosphoproteome analysis of capacitated human sperm. Evidence of tyrosine phosphorylation of a kinase-anchoring protein 3 and valosin-containing protein/p97 during capacitation. J Biol Chem (2002) 1.96
NRMT is an alpha-N-methyltransferase that methylates RCC1 and retinoblastoma protein. Nature (2010) 1.95
Characterization of histones and their post-translational modifications by mass spectrometry. Curr Opin Chem Biol (2006) 1.92
A proteomics grade electron transfer dissociation-enabled hybrid linear ion trap-orbitrap mass spectrometer. J Proteome Res (2008) 1.92
Serine 31 phosphorylation of histone variant H3.3 is specific to regions bordering centromeres in metaphase chromosomes. Proc Natl Acad Sci U S A (2005) 1.91
Phosphoproteomic analysis reveals that PP4 dephosphorylates KAP-1 impacting the DNA damage response. EMBO J (2012) 1.91
Drug hypersensitivity caused by alteration of the MHC-presented self-peptide repertoire. Proc Natl Acad Sci U S A (2012) 1.89
Cyclin E constrains Cdk5 activity to regulate synaptic plasticity and memory formation. Dev Cell (2011) 1.89
Methods for analyzing peptides and proteins on a chromatographic timescale by electron-transfer dissociation mass spectrometry. Nat Protoc (2008) 1.87