(Q33420619)

26 July 2017

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title

Bioinformatics analysis of mass spectrometry-based proteomics data sets (English)

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26 July 2017

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Chanchal Kumar

1

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PubMed ID

19306877

26 July 2017

Matthias Mann

series ordinal

2

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PubMed ID

19306877

26 July 2017

language of work or name

English

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publication date

21 March 2009

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26 July 2017

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26 July 2017

583

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26 July 2017

1703-1712

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26 July 2017

11

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From proteins to proteomes: large scale protein identification by two-dimensional electrophoresis and amino acid analysis

26 July 2017

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https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2009.03.035

Mass spectrometry-based proteomics

21 January 2018

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Precision proteomics: the case for high resolution and high mass accuracy

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Advances in proteomic workflows for systems biology

21 January 2018

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Introduction to computational proteomics

21 January 2018

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https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2009.03.035

MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification

21 January 2018

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The origins of bioinformatics

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Evolving research trends in bioinformatics

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Direct analysis of protein complexes using mass spectrometry

21 January 2018

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Computational prediction of proteotypic peptides for quantitative proteomics.

21 January 2018

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https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2009.03.035

Prediction of high-responding peptides for targeted protein assays by mass spectrometry

21 January 2018

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Selected reaction monitoring for quantitative proteomics: a tutorial

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PeptideAtlas: a resource for target selection for emerging targeted proteomics workflows

21 January 2018

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https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2009.03.035

Integration with the human genome of peptide sequences obtained by high-throughput mass spectrometry

21 January 2018

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Genome-scale proteomics reveals Arabidopsis thaliana gene models and proteome dynamics.

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Exponentially modified protein abundance index (emPAI) for estimation of absolute protein amount in proteomics by the number of sequenced peptides per protein

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Interpreting the protein language using proteomics.

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Global and site-specific quantitative phosphoproteomics: principles and applications

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An iterative statistical approach to the identification of protein phosphorylation motifs from large-scale data sets

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PHOSIDA (phosphorylation site database): management, structural and evolutionary investigation, and prediction of phosphosites

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Systematic Discovery of In Vivo Phosphorylation Networks

21 January 2018

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The human urinary proteome contains more than 1500 proteins, including a large proportion of membrane proteins

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Analysis of the mouse liver proteome using advanced mass spectrometry.

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Combined use of RNAi and quantitative proteomics to study gene function in Drosophila

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Gene ontology: tool for the unification of biology

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InterPro: the integrative protein signature database

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The KEGG resource for deciphering the genome

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Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

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GoMiner: a resource for biological interpretation of genomic and proteomic data

21 January 2018

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https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2009.03.035

Cytoscape: a software environment for integrated models of biomolecular interaction networks

21 January 2018

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BiNGO: a Cytoscape plugin to assess overrepresentation of gene ontology categories in biological networks

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Bioconductor: open software development for computational biology and bioinformatics

21 January 2018

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In-depth analysis of the adipocyte proteome by mass spectrometry and bioinformatics

21 January 2018

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Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research

21 January 2018

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Gene prioritization through genomic data fusion

21 January 2018

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Rabs 8A and 14 are targets of the insulin-regulated Rab-GAP AS160 regulating GLUT4 traffic in muscle cells

21 January 2018

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Integrated analysis of protein composition, tissue diversity, and gene regulation in mouse mitochondria

21 January 2018

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A mammalian organelle map by protein correlation profiling

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Systematic identification of human mitochondrial disease genes through integrative genomics

21 January 2018

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A mitochondrial protein compendium elucidates complex I disease biology

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STRING: a database of predicted functional associations between proteins

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MINT and IntAct contribute to the Second BioCreative challenge: serving the text-mining community with high quality molecular interaction data

21 January 2018

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Human protein reference database as a discovery resource for proteomics

21 January 2018

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Mass spectrometry-based proteomics turns quantitative

21 January 2018

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Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics

21 January 2018

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Functional and quantitative proteomics using SILAC

21 January 2018

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Comprehensive mass-spectrometry-based proteome quantification of haploid versus diploid yeast

21 January 2018

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Mass spectrometry as a diagnostic and a cancer biomarker discovery tool: opportunities and potential limitations

21 January 2018

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Reproducibility of SELDI-TOF protein patterns in serum: comparing datasets from different experiments

21 January 2018

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The ABC's (and XYZ's) of peptide sequencing

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Large-scale database searching using tandem mass spectra: looking up the answer in the back of the book

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Statistical and computational methods for comparative proteomic profiling using liquid chromatography-tandem mass spectrometry

21 January 2018

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An assessment of software solutions for the analysis of mass spectrometry based quantitative proteomics data

21 January 2018

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The properties of high-dimensional data spaces: implications for exploring gene and protein expression data.

21 January 2018

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RNA-Seq: a revolutionary tool for transcriptomics

21 January 2018

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Widespread changes in protein synthesis induced by microRNAs

21 January 2018

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The impact of microRNAs on protein output

21 January 2018

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Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling

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Gene expression profiling predicts clinical outcome of breast cancer

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Conserved patterns of protein interaction in multiple species

21 January 2018

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https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2009.03.035

Genome-wide maps of chromatin state in pluripotent and lineage-committed cells

21 January 2018

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Comparative proteomic phenotyping of cell lines and primary cells to assess preservation of cell type-specific functions

21 January 2018

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Temporal analysis of phosphotyrosine-dependent signaling networks by quantitative proteomics

21 January 2018

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Nucleolar proteome dynamics

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Time-resolved mass spectrometry of tyrosine phosphorylation sites in the epidermal growth factor receptor signaling network reveals dynamic modules

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Global, in vivo, and site-specific phosphorylation dynamics in signaling networks

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https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2009.03.035

Proteomics of organelles and large cellular structures

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Organellar proteomics: turning inventories into insights

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Mapping the Arabidopsis organelle proteome

21 January 2018

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https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2009.03.035

Analysis of protein complexes using mass spectrometry

21 January 2018

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https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2009.03.035

Network biology: understanding the cell's functional organization

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Dynamic Complex Formation During the Yeast Cell Cycle

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Global landscape of protein complexes in the yeast Saccharomyces cerevisiae

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Comparative assessment of large-scale data sets of protein-protein interactions

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High-quality binary protein interaction map of the yeast interactome network

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High confidence determination of specific protein-protein interactions using quantitative mass spectrometry

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A proteomics strategy to elucidate functional protein-protein interactions applied to EGF signaling

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A novel proteomic screen for peptide-protein interactions

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BioMart--biological queries made easy

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10.1016/J.FEBSLET.2009.03.035

21 January 2018

Identifiers

DOI

1 reference

26 July 2017

1 reference

PubMed ID

19306877