A mammalian organelle map by protein correlation profiling.

A mitochondrial protein compendium elucidates complex I disease biology. Cell (2008) 13.51

WoLF PSORT: protein localization predictor. Nucleic Acids Res (2007) 10.14

Systematic discovery of in vivo phosphorylation networks. Cell (2007) 6.94

Status of complete proteome analysis by mass spectrometry: SILAC labeled yeast as a model system. Genome Biol (2006) 3.34

Protein identification false discovery rates for very large proteomics data sets generated by tandem mass spectrometry. Mol Cell Proteomics (2009) 2.96

AT_CHLORO, a comprehensive chloroplast proteome database with subplastidial localization and curated information on envelope proteins. Mol Cell Proteomics (2010) 2.39

The mitochondrial proteome and human disease. Annu Rev Genomics Hum Genet (2010) 2.38

A mouse to human search for plasma proteome changes associated with pancreatic tumor development. PLoS Med (2008) 2.31

Mammalian long-chain acyl-CoA synthetases. Exp Biol Med (Maywood) (2008) 2.28

Accurate and sensitive peptide identification with Mascot Percolator. J Proteome Res (2009) 2.25

Systems biology in immunology: a computational modeling perspective. Annu Rev Immunol (2011) 2.15

Novel asymmetrically localizing components of human centrosomes identified by complementary proteomics methods. EMBO J (2011) 2.14

Protein analysis by shotgun/bottom-up proteomics. Chem Rev (2013) 2.13

The mitochondrial contact site complex, a determinant of mitochondrial architecture. EMBO J (2011) 1.94

Neuroscience in the era of functional genomics and systems biology. Nature (2009) 1.80

The organization of the transcriptional network in specific neuronal classes. Mol Syst Biol (2009) 1.74

A quantitative proteomics analysis of subcellular proteome localization and changes induced by DNA damage. Mol Cell Proteomics (2009) 1.74

Three-dimensional structure of the human cytomegalovirus cytoplasmic virion assembly complex includes a reoriented secretory apparatus. J Virol (2007) 1.73

Proteomics of the lysosome. Biochim Biophys Acta (2008) 1.68

The dynamic phagosomal proteome and the contribution of the endoplasmic reticulum. Proc Natl Acad Sci U S A (2007) 1.66

Organellar proteomics: turning inventories into insights. EMBO Rep (2006) 1.63

Proteomics of photoreceptor outer segments identifies a subset of SNARE and Rab proteins implicated in membrane vesicle trafficking and fusion. Mol Cell Proteomics (2008) 1.56

A high-throughput approach for measuring temporal changes in the interactome. Nat Methods (2012) 1.55

Proteomic analysis of the secretome of Leishmania donovani. Genome Biol (2008) 1.54

Fluorogenic label for biomolecular imaging. ACS Chem Biol (2006) 1.54

Systematic characterization of the murine mitochondrial proteome using functionally validated cardiac mitochondria. Proteomics (2008) 1.51

Quantitative phosphoproteomics by mass spectrometry: past, present, and future. Proteomics (2008) 1.50

Integrated proteomic and transcriptomic profiling of mouse lung development and Nmyc target genes. Mol Syst Biol (2007) 1.50

The potential of high-content high-throughput microscopy in drug discovery. Br J Pharmacol (2007) 1.42

Proteomic mapping of the human mitochondrial intermembrane space in live cells via ratiometric APEX tagging. Mol Cell (2014) 1.41

Nitrate and ammonium lead to distinct global dynamic phosphorylation patterns when resupplied to nitrogen-starved Arabidopsis seedlings. Plant J (2012) 1.36

A bioinformatics workflow for variant peptide detection in shotgun proteomics. Mol Cell Proteomics (2011) 1.34

Assessing systems properties of yeast mitochondria through an interaction map of the organelle. PLoS Genet (2006) 1.31

Cardiovascular networks: systems-based approaches to cardiovascular disease. Circulation (2010) 1.30

Multidimensional proteomics for cell biology. Nat Rev Mol Cell Biol (2015) 1.26

Characterization of the mouse pancreatic islet proteome and comparative analysis with other mouse tissues. J Proteome Res (2008) 1.23

Comparative systems biology of human and mouse as a tool to guide the modeling of human placental pathology. Mol Syst Biol (2009) 1.23

Sensitive multiplexed analysis of kinase activities and activity-based kinase identification. Nat Biotechnol (2009) 1.21

Network-assisted protein identification and data interpretation in shotgun proteomics. Mol Syst Biol (2009) 1.19

Use of fluorescence-activated vesicle sorting for isolation of Naked2-associated, basolaterally targeted exocytic vesicles for proteomics analysis. Mol Cell Proteomics (2008) 1.18

MitoMiner, an integrated database for the storage and analysis of mitochondrial proteomics data. Mol Cell Proteomics (2009) 1.17

Integrated proteomic analysis of human cancer cells and plasma from tumor bearing mice for ovarian cancer biomarker discovery. PLoS One (2009) 1.17

Nuclear Proteomics Uncovers Diurnal Regulatory Landscapes in Mouse Liver. Cell Metab (2016) 1.17

A quantitative map of the liver mitochondrial phosphoproteome reveals posttranslational control of ketogenesis. Cell Metab (2012) 1.16

A high confidence, manually validated human blood plasma protein reference set. BMC Med Genomics (2008) 1.16

The organelle proteome of the DT40 lymphocyte cell line. Mol Cell Proteomics (2009) 1.14

Evolutionary origins of metabolic compartmentalization in eukaryotes. Philos Trans R Soc Lond B Biol Sci (2010) 1.14

Multilayered genetic and omics dissection of mitochondrial activity in a mouse reference population. Cell (2014) 1.13

The innate immune and systemic response in honey bees to a bacterial pathogen, Paenibacillus larvae. BMC Genomics (2009) 1.12

Metabolic labeling of plant cell cultures with K(15)NO3 as a tool for quantitative analysis of proteins and metabolites. Plant Methods (2006) 1.12

Protein correlation profiles identify lipid droplet proteins with high confidence. Mol Cell Proteomics (2013) 1.11

Quantitative organellar proteomics analysis of rough endoplasmic reticulum from normal and acute pancreatitis rat pancreas. J Proteome Res (2010) 1.11

Peptide separations by on-line MudPIT compared to isoelectric focusing in an off-gel format: application to a membrane-enriched fraction from C2C12 mouse skeletal muscle cells. J Proteome Res (2009) 1.11

eSLDB: eukaryotic subcellular localization database. Nucleic Acids Res (2006) 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

Gene expression analysis, proteomics, and network discovery. Plant Physiol (2009) 1.09

Mitochondria do not contain lipid rafts, and lipid rafts do not contain mitochondrial proteins. J Lipid Res (2009) 1.08

MAPU 2.0: high-accuracy proteomes mapped to genomes. Nucleic Acids Res (2008) 1.06

MAPU: Max-Planck Unified database of organellar, cellular, tissue and body fluid proteomes. Nucleic Acids Res (2006) 1.06

The leukocyte nuclear envelope proteome varies with cell activation and contains novel transmembrane proteins that affect genome architecture. Mol Cell Proteomics (2010) 1.05

The nuclear envelope proteome differs notably between tissues. Nucleus (2012) 1.05

A systematic search for endoplasmic reticulum (ER) membrane-associated RING finger proteins identifies Nixin/ZNRF4 as a regulator of calnexin stability and ER homeostasis. J Biol Chem (2011) 1.04

Comparative Bioinformatics Analyses and Profiling of Lysosome-Related Organelle Proteomes. Int J Mass Spectrom (2007) 1.04

Mitochondrial outer membrane proteome of Trypanosoma brucei reveals novel factors required to maintain mitochondrial morphology. Mol Cell Proteomics (2012) 1.03

Cell-specific and lamin-dependent targeting of novel transmembrane proteins in the nuclear envelope. Cell Mol Life Sci (2010) 1.02

DBMLoc: a Database of proteins with multiple subcellular localizations. BMC Bioinformatics (2008) 1.02

Several novel nuclear envelope transmembrane proteins identified in skeletal muscle have cytoskeletal associations. Mol Cell Proteomics (2010) 1.02

Proteomic profiling of a layered tissue reveals unique glycolytic specializations of photoreceptor cells. Mol Cell Proteomics (2010) 1.01

Deciphering preferential interactions within supramolecular protein complexes: the proteasome case. Mol Syst Biol (2015) 1.00

Gene expression elucidates functional impact of polygenic risk for schizophrenia. Nat Neurosci (2016) 1.00

Enhancing identifications of lipid-embedded proteins by mass spectrometry for improved mapping of endothelial plasma membranes in vivo. Mol Cell Proteomics (2009) 0.99

Contributions of proteomics to understanding phagosome maturation. Cell Microbiol (2008) 0.97

Subcellular proteomics of Trypanosoma cruzi reservosomes. Proteomics (2009) 0.97

Proteomics of a fuzzy organelle: interphase chromatin. EMBO J (2014) 0.96

A label free quantitative proteomic analysis of the Saccharomyces cerevisiae nucleus. J Proteomics (2008) 0.96

Quantitative organelle proteomics of MCF-7 breast cancer cells reveals multiple subcellular locations for proteins in cellular functional processes. J Proteome Res (2010) 0.96

Tissue specificity in the nuclear envelope supports its functional complexity. Nucleus (2013) 0.96

Proteomic study of the mucin granulae in an intestinal goblet cell model. J Proteome Res (2012) 0.95

Specialized compartments of cardiac nuclei exhibit distinct proteomic anatomy. Mol Cell Proteomics (2010) 0.95

PathLocdb: a comprehensive database for the subcellular localization of metabolic pathways and its application to multiple localization analysis. BMC Genomics (2010) 0.95

Copy number analysis of the murine platelet proteome spanning the complete abundance range. Mol Cell Proteomics (2014) 0.94

Analysis of 953 human proteins from a mitochondrial HEK293 fraction by complexome profiling. PLoS One (2013) 0.94

Global, quantitative and dynamic mapping of protein subcellular localization. Elife (2016) 0.94

The proteome of human liver peroxisomes: identification of five new peroxisomal constituents by a label-free quantitative proteomics survey. PLoS One (2013) 0.94

Spatial distribution of cellular function: the partitioning of proteins between mitochondria and the nucleus in MCF7 breast cancer cells. J Proteome Res (2012) 0.93

Enrichment of distinct microfilament-associated and GTP-binding-proteins in membrane/microvilli fractions from lymphoid cells. J Proteome Res (2008) 0.93

Ion channels at the nucleus: electrophysiology meets the genome. Mol Plant (2010) 0.91

Genomes, proteomes, and the central dogma. Circ Cardiovasc Genet (2011) 0.91

Proteomic-based identification of maternal proteins in mature mouse oocytes. BMC Genomics (2009) 0.91

Mass spectrometry analysis and quantitation of peptides presented on the MHC II molecules of mouse spleen dendritic cells. J Proteome Res (2011) 0.91

Prostate cancer regulatory networks. J Cell Biochem (2009) 0.91

The subcellular localization of the mammalian proteome comes a fraction closer. Genome Biol (2006) 0.90

Imbalanced multi-modal multi-label learning for subcellular localization prediction of human proteins with both single and multiple sites. PLoS One (2012) 0.89

Fractionation profiling: a fast and versatile approach for mapping vesicle proteomes and protein-protein interactions. Mol Biol Cell (2014) 0.89

Identification of trans-golgi network proteins in Arabidopsis thaliana root tissue. J Proteome Res (2014) 0.88

Molecular characterization of the endoplasmic reticulum: insights from proteomic studies. Proteomics (2010) 0.88

A foundation for reliable spatial proteomics data analysis. Mol Cell Proteomics (2014) 0.87

Proteomic identification of unique photoreceptor disc components reveals the presence of PRCD, a protein linked to retinal degeneration. J Proteome Res (2013) 0.87

Evolution of organelle-associated protein profiling. J Proteomics (2008) 0.87

Bioanalysis of eukaryotic organelles. Chem Rev (2013) 0.86

Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci U S A (2005) 167.46

Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature (2007) 65.18

A bivalent chromatin structure marks key developmental genes in embryonic stem cells. Cell (2006) 48.80

A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Science (2002) 42.78

MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification. Nat Biotechnol (2008) 38.00

Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature (2002) 37.66

Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics. Mol Cell Proteomics (2002) 30.58

Mass spectrometry-based proteomics. Nature (2003) 28.94

Genome sequence, comparative analysis and haplotype structure of the domestic dog. Nature (2005) 23.04

Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. Cell (2006) 20.92

Lysine acetylation targets protein complexes and co-regulates major cellular functions. Science (2009) 20.49

miRNPs: a novel class of ribonucleoproteins containing numerous microRNAs. Genes Dev (2002) 19.24

Genome-wide detection and characterization of positive selection in human populations. Nature (2007) 17.27

Universal sample preparation method for proteome analysis. Nat Methods (2009) 16.88

In-gel digestion for mass spectrometric characterization of proteins and proteomes. Nat Protoc (2006) 16.56

Efficient design and assembly of custom TALEN and other TAL effector-based constructs for DNA targeting. Nucleic Acids Res (2011) 16.53

Andromeda: a peptide search engine integrated into the MaxQuant environment. J Proteome Res (2011) 14.82

FoxA1 translates epigenetic signatures into enhancer-driven lineage-specific transcription. Cell (2008) 14.18

Bis[bis(methoxycarbimido)amine-kappa2N,N']bis(perchlorato-kappaO)copper(II) bis[bis(methoxycarbimido)amine-kappa2N,N']bis(methanol-kappaO)copper(II) bis(perchlorate) methanol disolvate. Acta Crystallogr C (2006) 14.17

Stop and go extraction tips for matrix-assisted laser desorption/ionization, nanoelectrospray, and LC/MS sample pretreatment in proteomics. Anal Chem (2003) 13.58

A mitochondrial protein compendium elucidates complex I disease biology. Cell (2008) 13.51

WEGO: a web tool for plotting GO annotations. Nucleic Acids Res (2006) 13.06

Metabolite profiles and the risk of developing diabetes. Nat Med (2011) 12.22

Sequencing of 50 human exomes reveals adaptation to high altitude. Science (2010) 11.27

Genomewide analysis of PRC1 and PRC2 occupancy identifies two classes of bivalent domains. PLoS Genet (2008) 11.17

Protocol for micro-purification, enrichment, pre-fractionation and storage of peptides for proteomics using StageTips. Nat Protoc (2007) 10.71

Exponentially modified protein abundance index (emPAI) for estimation of absolute protein amount in proteomics by the number of sequenced peptides per protein. Mol Cell Proteomics (2005) 10.67

Parts per million mass accuracy on an Orbitrap mass spectrometer via lock mass injection into a C-trap. Mol Cell Proteomics (2005) 10.60

Comprehensive mass-spectrometry-based proteome quantification of haploid versus diploid yeast. Nature (2008) 10.28

The minimum information about a proteomics experiment (MIAPE). Nat Biotechnol (2007) 10.24

Proteomic characterization of the human centrosome by protein correlation profiling. Nature (2003) 8.74

A high-resolution map of human evolutionary constraint using 29 mammals. Nature (2011) 8.67

Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis. Sci Signal (2010) 8.61

Defects in adaptive energy metabolism with CNS-linked hyperactivity in PGC-1alpha null mice. Cell (2004) 8.58

The genome of the cucumber, Cucumis sativus L. Nat Genet (2009) 8.19

Distinguishing protein-coding and noncoding genes in the human genome. Proc Natl Acad Sci U S A (2007) 8.00

An abundance of rare functional variants in 202 drug target genes sequenced in 14,002 people. Science (2012) 7.94

Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences. Nature (2007) 7.91

The Genomes of Oryza sativa: a history of duplications. PLoS Biol (2005) 7.67

Mass spectrometry-based proteomics turns quantitative. Nat Chem Biol (2005) 7.52

Nucleolar proteome dynamics. Nature (2005) 7.32

mTOR controls mitochondrial oxidative function through a YY1-PGC-1alpha transcriptional complex. Nature (2007) 7.12

Androgen receptor regulates a distinct transcription program in androgen-independent prostate cancer. Cell (2009) 7.09

Directed proteomic analysis of the human nucleolus. Curr Biol (2002) 7.04

Identification of a gene causing human cytochrome c oxidase deficiency by integrative genomics. Proc Natl Acad Sci U S A (2003) 6.87

Metabolite profiling identifies a key role for glycine in rapid cancer cell proliferation. Science (2012) 6.79

Integrated analysis of protein composition, tissue diversity, and gene regulation in mouse mitochondria. Cell (2003) 6.77

A draft sequence for the genome of the domesticated silkworm (Bombyx mori). Science (2004) 6.62

Selective anchoring of TFIID to nucleosomes by trimethylation of histone H3 lysine 4. Cell (2007) 6.62

Erralpha and Gabpa/b specify PGC-1alpha-dependent oxidative phosphorylation gene expression that is altered in diabetic muscle. Proc Natl Acad Sci U S A (2004) 6.53

Integrative genomics identifies MCU as an essential component of the mitochondrial calcium uniporter. Nature (2011) 6.48

Epidemiological serosurvey of hepatitis B in China--declining HBV prevalence due to hepatitis B vaccination. Vaccine (2009) 6.30

Mechanism of regulation of WAVE1-induced actin nucleation by Rac1 and Nck. Nature (2002) 6.26

Nucleosome dynamics define transcriptional enhancers. Nat Genet (2010) 5.94

CPC: assess the protein-coding potential of transcripts using sequence features and support vector machine. Nucleic Acids Res (2007) 5.88

Common inherited variation in mitochondrial genes is not enriched for associations with type 2 diabetes or related glycemic traits. PLoS Genet (2010) 5.79

Comparative genomics reveals mobile pathogenicity chromosomes in Fusarium. Nature (2010) 5.79

Large-scale proteomic analysis of the human spliceosome. Genome Res (2002) 5.75

Specificity in Toll-like receptor signalling through distinct effector functions of TRAF3 and TRAF6. Nature (2005) 5.72

Analysis of the Plasmodium falciparum proteome by high-accuracy mass spectrometry. Nature (2002) 5.48

Deep proteome and transcriptome mapping of a human cancer cell line. Mol Syst Biol (2011) 5.48

Kinase-selective enrichment enables quantitative phosphoproteomics of the kinome across the cell cycle. Mol Cell (2008) 5.38

Tsc tumour suppressor proteins antagonize amino-acid-TOR signalling. Nat Cell Biol (2002) 5.37

The oyster genome reveals stress adaptation and complexity of shell formation. Nature (2012) 5.30

A genetic variation map for chicken with 2.8 million single-nucleotide polymorphisms. Nature (2004) 5.24

Temporal analysis of phosphotyrosine-dependent signaling networks by quantitative proteomics. Nat Biotechnol (2004) 5.22

A practical recipe for stable isotope labeling by amino acids in cell culture (SILAC). Nat Protoc (2006) 5.21

Quantitative phosphoproteomics applied to the yeast pheromone signaling pathway. Mol Cell Proteomics (2005) 5.07

Higher-energy C-trap dissociation for peptide modification analysis. Nat Methods (2007) 5.04

SILAC mouse for quantitative proteomics uncovers kindlin-3 as an essential factor for red blood cell function. Cell (2008) 5.02

MICU1 encodes a mitochondrial EF hand protein required for Ca(2+) uptake. Nature (2010) 4.88

Unbiased quantitative proteomics of lipid rafts reveals high specificity for signaling factors. Proc Natl Acad Sci U S A (2003) 4.87

A practical guide to the MaxQuant computational platform for SILAC-based quantitative proteomics. Nat Protoc (2009) 4.84

PPARgamma and C/EBP factors orchestrate adipocyte biology via adjacent binding on a genome-wide scale. Genes Dev (2008) 4.83

Trypsin cleaves exclusively C-terminal to arginine and lysine residues. Mol Cell Proteomics (2004) 4.79

Proteome-wide analysis of chaperonin-dependent protein folding in Escherichia coli. Cell (2005) 4.78

A dual pressure linear ion trap Orbitrap instrument with very high sequencing speed. Mol Cell Proteomics (2009) 4.75

Systematic identification of human mitochondrial disease genes through integrative genomics. Nat Genet (2006) 4.67

PHOSIDA (phosphorylation site database): management, structural and evolutionary investigation, and prediction of phosphosites. Genome Biol (2007) 4.66

Upstream open reading frames cause widespread reduction of protein expression and are polymorphic among humans. Proc Natl Acad Sci U S A (2009) 4.58

A proteome-wide, quantitative survey of in vivo ubiquitylation sites reveals widespread regulatory roles. Mol Cell Proteomics (2011) 4.40

RePS: a sequence assembler that masks exact repeats identified from the shotgun data. Genome Res (2002) 4.35

Quantitative interaction proteomics and genome-wide profiling of epigenetic histone marks and their readers. Cell (2010) 4.31

Identifying novel constrained elements by exploiting biased substitution patterns. Bioinformatics (2009) 4.30

The ABC's (and XYZ's) of peptide sequencing. Nat Rev Mol Cell Biol (2004) 4.24

Human Proteinpedia enables sharing of human protein data. Nat Biotechnol (2008) 4.21

Paraspeckles: a novel nuclear domain. Curr Biol (2002) 4.19

Cistrome: an integrative platform for transcriptional regulation studies. Genome Biol (2011) 4.13

Formation of ArF from LPdAr(F): catalytic conversion of aryl triflates to aryl fluorides. Science (2009) 4.13

Production of offspring from a germline stem cell line derived from neonatal ovaries. Nat Cell Biol (2009) 4.11

Quantitative proteomics reveals subset-specific viral recognition in dendritic cells. Immunity (2010) 4.03

Molecular diagnosis of infantile mitochondrial disease with targeted next-generation sequencing. Sci Transl Med (2012) 4.02

In vitro studies with recombinant Plasmodium falciparum apical membrane antigen 1 (AMA1): production and activity of an AMA1 vaccine and generation of a multiallelic response. Infect Immun (2002) 4.02

A transcriptional signature and common gene networks link cancer with lipid metabolism and diverse human diseases. Cancer Cell (2010) 4.02

Mutation of FIG4 causes neurodegeneration in the pale tremor mouse and patients with CMT4J. Nature (2007) 3.91

An emerging recombinant human enterovirus 71 responsible for the 2008 outbreak of hand foot and mouth disease in Fuyang city of China. Virol J (2010) 3.90

Metabolic profiling of the human response to a glucose challenge reveals distinct axes of insulin sensitivity. Mol Syst Biol (2008) 3.82

Axin-mediated CKI phosphorylation of beta-catenin at Ser 45: a molecular switch for the Wnt pathway. Genes Dev (2002) 3.80