Published in Anal Chem on October 15, 2006
Impact of pretreated Switchgrass and biomass carbohydrates on Clostridium thermocellum ATCC 27405 cellulosome composition: a quantitative proteomic analysis. PLoS One (2009) 1.96
15N metabolic labeling of mammalian tissue with slow protein turnover. J Proteome Res (2007) 1.58
Relative quantification of stable isotope labeled peptides using a linear ion trap-Orbitrap hybrid mass spectrometer. Anal Chem (2007) 1.40
Quantification of the synaptosomal proteome of the rat cerebellum during post-natal development. Genome Res (2007) 1.39
A critical appraisal of techniques, software packages, and standards for quantitative proteomic analysis. OMICS (2012) 1.25
Cancer proteomics by quantitative shotgun proteomics. Mol Oncol (2007) 1.08
Statistical model to analyze quantitative proteomics data obtained by 18O/16O labeling and linear ion trap mass spectrometry: application to the study of vascular endothelial growth factor-induced angiogenesis in endothelial cells. Mol Cell Proteomics (2009) 1.06
Proteomic and metabolomic profiling of a trait anxiety mouse model implicate affected pathways. Mol Cell Proteomics (2011) 1.01
Capture and analysis of quantitative proteomic data. Proteomics (2007) 0.96
Quantitative tracking of isotope flows in proteomes of microbial communities. Mol Cell Proteomics (2011) 0.93
IsoQuant: a software tool for stable isotope labeling by amino acids in cell culture-based mass spectrometry quantitation. Anal Chem (2012) 0.88
Quantitative proteomic analyses of the response of acidophilic microbial communities to different pH conditions. ISME J (2011) 0.88
Diverse and divergent protein post-translational modifications in two growth stages of a natural microbial community. Nat Commun (2014) 0.84
Elucidation of Zymomonas mobilis physiology and stress responses by quantitative proteomics and transcriptomics. Front Microbiol (2014) 0.84
Find pairs: the module for protein quantification of the PeakQuant software suite. OMICS (2012) 0.84
A coordinated proteomic approach for identifying proteins that interact with the E. coli ribosomal protein S12. J Proteome Res (2013) 0.82
Proteome turnover in bacteria: current status for Corynebacterium glutamicum and related bacteria. Microb Biotechnol (2013) 0.81
Corynebacterium glutamicum exhibits a membrane-related response to a small ferrocene-conjugated antimicrobial peptide. J Biol Inorg Chem (2010) 0.80
IDPQuantify: combining precursor intensity with spectral counts for protein and peptide quantification. J Proteome Res (2013) 0.80
From Raw Data to Biological Discoveries: A Computational Analysis Pipeline for Mass Spectrometry-Based Proteomics. J Am Soc Mass Spectrom (2015) 0.78
Measuring dissociation rate constants of protein complexes through subunit exchange: experimental design and theoretical modeling. PLoS One (2011) 0.78
Fungi Contribute Critical but Spatially Varying Roles in Nitrogen and Carbon Cycling in Acid Mine Drainage. Front Microbiol (2016) 0.75
Fluoxetine Treatment Rescues Energy Metabolism Pathway Alterations in a Posttraumatic Stress Disorder Mouse Model. Mol Neuropsychiatry (2016) 0.75
Proteomic and mutant analysis of the CO2 concentrating mechanism of hydrothermal vent chemolithoautotroph Thiomicrospira crunogena. J Bacteriol (2017) 0.75
Skyline: an open source document editor for creating and analyzing targeted proteomics experiments. Bioinformatics (2010) 13.35
DTASelect and Contrast: tools for assembling and comparing protein identifications from shotgun proteomics. J Proteome Res (2003) 12.31
A proteomic view of the Plasmodium falciparum life cycle. Nature (2002) 10.65
Multi-site assessment of the precision and reproducibility of multiple reaction monitoring-based measurements of proteins in plasma. Nat Biotechnol (2009) 9.67
Role of Rpn11 metalloprotease in deubiquitination and degradation by the 26S proteasome. Science (2002) 7.49
Phytophthora genome sequences uncover evolutionary origins and mechanisms of pathogenesis. Science (2006) 6.74
Complete genome sequence of the metabolically versatile photosynthetic bacterium Rhodopseudomonas palustris. Nat Biotechnol (2003) 4.78
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
Assigning function to yeast proteins by integration of technologies. Mol Cell (2003) 4.58
Proteomic parsimony through bipartite graph analysis improves accuracy and transparency. J Proteome Res (2007) 4.53
A cross-platform toolkit for mass spectrometry and proteomics. Nat Biotechnol (2012) 4.48
Characterizing a model human gut microbiota composed of members of its two dominant bacterial phyla. Proc Natl Acad Sci U S A (2009) 4.09
Community proteomics of a natural microbial biofilm. Science (2005) 3.97
IDPicker 2.0: Improved protein assembly with high discrimination peptide identification filtering. J Proteome Res (2009) 3.72
Shotgun identification of protein modifications from protein complexes and lens tissue. Proc Natl Acad Sci U S A (2002) 3.70
Cln3 activates G1-specific transcription via phosphorylation of the SBF bound repressor Whi5. Cell (2004) 3.60
Detecting differential and correlated protein expression in label-free shotgun proteomics. J Proteome Res (2006) 3.51
Shotgun metaproteomics of the human distal gut microbiota. ISME J (2008) 3.43
Fermentation, hydrogen, and sulfur metabolism in multiple uncultivated bacterial phyla. Science (2012) 3.39
Determination and comparison of the baseline proteomes of the versatile microbe Rhodopseudomonas palustris under its major metabolic states. J Proteome Res (2006) 3.32
Automatic quality assessment of peptide tandem mass spectra. Bioinformatics (2004) 2.70
Tea4p links microtubule plus ends with the formin for3p in the establishment of cell polarity. Dev Cell (2005) 2.65
Swi1 and Swi3 are components of a replication fork protection complex in fission yeast. Mol Cell Biol (2004) 2.55
Strain-resolved community proteomics reveals recombining genomes of acidophilic bacteria. Nature (2007) 2.53
Interlaboratory study characterizing a yeast performance standard for benchmarking LC-MS platform performance. Mol Cell Proteomics (2009) 2.39
Proteomics analysis reveals stable multiprotein complexes in both fission and budding yeasts containing Myb-related Cdc5p/Cef1p, novel pre-mRNA splicing factors, and snRNAs. Mol Cell Biol (2002) 2.32
Proteolysis-independent regulation of the transcription factor Met4 by a single Lys 48-linked ubiquitin chain. Nat Cell Biol (2004) 2.30
Transcriptomic and proteomic characterization of the Fur modulon in the metal-reducing bacterium Shewanella oneidensis. J Bacteriol (2004) 2.23
Cid13 is a cytoplasmic poly(A) polymerase that regulates ribonucleotide reductase mRNA. Cell (2002) 2.23
Enigmatic, ultrasmall, uncultivated Archaea. Proc Natl Acad Sci U S A (2010) 2.12
Performance metrics for liquid chromatography-tandem mass spectrometry systems in proteomics analyses. Mol Cell Proteomics (2009) 2.09
Dephosphorylation of F-BAR protein Cdc15 modulates its conformation and stimulates its scaffolding activity at the cell division site. Mol Cell (2010) 2.02
Cleavage N-terminal to proline: analysis of a database of peptide tandem mass spectra. Anal Chem (2003) 1.98
Impact of pretreated Switchgrass and biomass carbohydrates on Clostridium thermocellum ATCC 27405 cellulosome composition: a quantitative proteomic analysis. PLoS One (2009) 1.96
Carcinoma and stromal enzyme activity profiles associated with breast tumor growth in vivo. Proc Natl Acad Sci U S A (2004) 1.96
Distinct microbial communities within the endosphere and rhizosphere of Populus deltoides roots across contrasting soil types. Appl Environ Microbiol (2011) 1.96
Constraining G1-specific transcription to late G1 phase: the MBF-associated corepressor Nrm1 acts via negative feedback. Mol Cell (2006) 1.92
Community genomic and proteomic analyses of chemoautotrophic iron-oxidizing "Leptospirillum rubarum" (Group II) and "Leptospirillum ferrodiazotrophum" (Group III) bacteria in acid mine drainage biofilms. Appl Environ Microbiol (2009) 1.86
Integrated metagenomics/metaproteomics reveals human host-microbiota signatures of Crohn's disease. PLoS One (2012) 1.84
Applicability of tandem affinity purification MudPIT to pathway proteomics in yeast. Mol Cell Proteomics (2003) 1.82
Systems biology: Functional analysis of natural microbial consortia using community proteomics. Nat Rev Microbiol (2009) 1.81
Niche of harmful alga Aureococcus anophagefferens revealed through ecogenomics. Proc Natl Acad Sci U S A (2011) 1.76
Helicobacter pylori exploits a unique repertoire of type IV secretion system components for pilus assembly at the bacteria-host cell interface. PLoS Pathog (2011) 1.67
The Nse5-Nse6 dimer mediates DNA repair roles of the Smc5-Smc6 complex. Mol Cell Biol (2006) 1.65
From pull-down data to protein interaction networks and complexes with biological relevance. Bioinformatics (2008) 1.62
Protein identification using customized protein sequence databases derived from RNA-Seq data. J Proteome Res (2011) 1.62
Twenty-one genome sequences from Pseudomonas species and 19 genome sequences from diverse bacteria isolated from the rhizosphere and endosphere of Populus deltoides. J Bacteriol (2012) 1.60
Community proteogenomics highlights microbial strain-variant protein expression within activated sludge performing enhanced biological phosphorus removal. ISME J (2008) 1.60
Staphylococcus aureus fur regulates the expression of virulence factors that contribute to the pathogenesis of pneumonia. Infect Immun (2010) 1.59
The sorting direct method for stochastic simulation of biochemical systems with varying reaction execution behavior. Comput Biol Chem (2006) 1.59
Proteogenomic basis for ecological divergence of closely related bacteria in natural acidophilic microbial communities. Proc Natl Acad Sci U S A (2010) 1.58
Initial Phases of biofilm formation in Shewanella oneidensis MR-1. J Bacteriol (2004) 1.56
Evaluation of strong cation exchange versus isoelectric focusing of peptides for multidimensional liquid chromatography-tandem mass spectrometry. J Proteome Res (2008) 1.55
Deletion of the Cel48S cellulase from Clostridium thermocellum. Proc Natl Acad Sci U S A (2010) 1.54
Nse1, Nse2, and a novel subunit of the Smc5-Smc6 complex, Nse3, play a crucial role in meiosis. Mol Biol Cell (2004) 1.52
The enterocyte microvillus is a vesicle-generating organelle. J Cell Biol (2009) 1.51
Replication checkpoint kinase Cds1 regulates recombinational repair protein Rad60. Mol Cell Biol (2003) 1.50
Systematic comparison of label-free, metabolic labeling, and isobaric chemical labeling for quantitative proteomics on LTQ Orbitrap Velos. J Proteome Res (2012) 1.50
Efficient and specific trypsin digestion of microgram to nanogram quantities of proteins in organic-aqueous solvent systems. Anal Chem (2006) 1.49
TagRecon: high-throughput mutation identification through sequence tagging. J Proteome Res (2010) 1.49
Azospirillum genomes reveal transition of bacteria from aquatic to terrestrial environments. PLoS Genet (2011) 1.45
Proteogenomic monitoring of Geobacter physiology during stimulated uranium bioremediation. Appl Environ Microbiol (2009) 1.45
Staphylococcus aureus LukAB cytotoxin kills human neutrophils by targeting the CD11b subunit of the integrin Mac-1. Proc Natl Acad Sci U S A (2013) 1.45
Effects of diet on resource utilization by a model human gut microbiota containing Bacteroides cellulosilyticus WH2, a symbiont with an extensive glycobiome. PLoS Biol (2013) 1.45
Identification of proteins at active, stalled, and collapsed replication forks using isolation of proteins on nascent DNA (iPOND) coupled with mass spectrometry. J Biol Chem (2013) 1.43
Characterization of the 70S Ribosome from Rhodopseudomonas palustris using an integrated "top-down" and "bottom-up" mass spectrometric approach. J Proteome Res (2004) 1.38
The Clp1/Cdc14 phosphatase contributes to the robustness of cytokinesis by association with anillin-related Mid1. J Cell Biol (2008) 1.38
MS2Grouper: group assessment and synthetic replacement of duplicate proteomic tandem mass spectra. J Am Soc Mass Spectrom (2005) 1.37
Molecular dynamics of the Shewanella oneidensis response to chromate stress. Mol Cell Proteomics (2006) 1.35
RNA-binding protein Csx1 mediates global control of gene expression in response to oxidative stress. EMBO J (2003) 1.35
A bioinformatics workflow for variant peptide detection in shotgun proteomics. Mol Cell Proteomics (2011) 1.34
MASPIC: intensity-based tandem mass spectrometry scoring scheme that improves peptide identification at high confidence. Anal Chem (2005) 1.34
Analysis of protein solvent accessible surfaces by photochemical oxidation and mass spectrometry. Anal Chem (2004) 1.33
Caldicellulosiruptor core and pangenomes reveal determinants for noncellulosomal thermophilic deconstruction of plant biomass. J Bacteriol (2012) 1.32
Direct cellular lysis/protein extraction protocol for soil metaproteomics. J Proteome Res (2010) 1.31
Impact of phenolic substrate and growth temperature on the Arthrobacter chlorophenolicus proteome. J Proteome Res (2009) 1.31
Phospho-regulation of the Cdc14/Clp1 phosphatase delays late mitotic events in S. pombe. Dev Cell (2006) 1.31
Improved genome annotation for Zymomonas mobilis. Nat Biotechnol (2009) 1.30
DBDigger: reorganized proteomic database identification that improves flexibility and speed. Anal Chem (2005) 1.30