(Q37771859)

22 August 2017

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title

Proteomics: a pragmatic perspective (English)

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22 August 2017

2

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22 August 2017

Parag Mallick

1

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22 August 2017

9 July 2010

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22 August 2017

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22 August 2017

28

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22 August 2017

695-709

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22 August 2017

7

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https://scigraph.springernature.com/pub.10.1038/nbt.1658

22 August 2017

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cites work

Quantitative proteomic analysis of protein complexes: concurrent identification of interactors and their state of phosphorylation

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Stoichiometry and absolute quantification of proteins with mass spectrometry using fluorescent and isotope-labeled concatenated peptide standards.

21 January 2018

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Large-scale mapping of human protein-protein interactions by mass spectrometry

21 January 2018

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Large scale protein profiling by combination of protein fractionation and multidimensional protein identification technology (MudPIT).

21 January 2018

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Stable isotope labeling by amino acids in cell culture (SILAC) and proteome quantitation of mouse embryonic stem cells to a depth of 5,111 proteins.

21 January 2018

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Options and considerations when selecting a quantitative proteomics strategy

21 January 2018

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Activity-based protein profiling: the serine hydrolases

21 January 2018

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12 December 2020

Integration of proteomic-based tools for improved biomarkers of myocardial injury

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12 December 2020

Advances in the analysis of dynamic protein complexes by proteomics and data processing

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12 December 2020

Functional organization of the yeast proteome by systematic analysis of protein complexes

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12 December 2020

Analysis of the Saccharomyces cerevisiae proteome with PeptideAtlas

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12 December 2020

Immunoaffinity profiling of tyrosine phosphorylation in cancer cells

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12 December 2020

Single Copies of Sec61 and TRAP Associate with a Nontranslating Mammalian Ribosome

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12 December 2020

Localization of organelle proteins by isotope tagging (LOPIT)

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12 December 2020

Quantitative phosphoproteomics applied to the yeast pheromone signaling pathway

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12 December 2020

A dynamic range compression and three-dimensional peptide fractionation analysis platform expands proteome coverage and the diagnostic potential of whole saliva

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12 December 2020

Protein biomarker discovery and validation: the long and uncertain path to clinical utility

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12 December 2020

Endogenous phosphotyrosine signaling in zebrafish embryos.

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12 December 2020

Quantification of cardiovascular biomarkers in patient plasma by targeted mass spectrometry and stable isotope dilution.

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12 December 2020

Global survey of phosphotyrosine signaling identifies oncogenic kinases in lung cancer

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12 December 2020

Large-scale phosphorylation analysis of mouse liver

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12 December 2020

Peptide separation with immobilized pI strips is an attractive alternative to in-gel protein digestion for proteome analysis.

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12 December 2020

Organellar proteomics to create the cell map.

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12 December 2020

Large-scale Arabidopsis phosphoproteome profiling reveals novel chloroplast kinase substrates and phosphorylation networks.

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12 December 2020

Integrated proteomic analysis of human cancer cells and plasma from tumor bearing mice for ovarian cancer biomarker discovery.

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12 December 2020

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

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12 December 2020

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

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12 December 2020

The absolute quantification strategy: application to phosphorylation profiling of human separase serine 1126.

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12 December 2020

Activity-based protein profiling: from enzyme chemistry to proteomic chemistry

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12 December 2020

Label-free quantitative proteomics using large peptide data sets generated by nanoflow liquid chromatography and mass spectrometry

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12 December 2020

Fractionation of isotopically labeled peptides in quantitative proteomics

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12 December 2020

Analysis of protein complexes using mass spectrometry

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12 December 2020

Approaching solid tumor heterogeneity on a cellular basis by tissue proteomics using laser capture microdissection and biological mass spectrometry

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12 December 2020

N-Terminal peptide labeling strategy for incorporation of isotopic tags: a method for the determination of site-specific absolute phosphorylation stoichiometry

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12 December 2020

Full dynamic range proteome analysis of S. cerevisiae by targeted proteomics

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12 December 2020

Femtomole sequencing of proteins from polyacrylamide gels by nano-electrospray mass spectrometry

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12 December 2020

The absolute quantification strategy: a general procedure for the quantification of proteins and post-translational modifications

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12 December 2020

Decoding protein modifications using top-down mass spectrometry

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12 December 2020

Whole proteome analysis of post-translational modifications: applications of mass-spectrometry for proteogenomic annotation

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12 December 2020

Computational prediction of proteotypic peptides for quantitative proteomics.

1 reference

12 December 2020

Global landscape of protein complexes in the yeast Saccharomyces cerevisiae

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12 December 2020

Proteomics on Fixed Tissue Specimens - A Review

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12 December 2020

Mass-spectrometric identification and relative quantification of N-linked cell surface glycoproteins

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12 December 2020

Profiling of the cell surface proteome

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12 December 2020

Global analysis of protein activities using proteome chips

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12 December 2020

A physical and functional map of the human TNF-alpha/NF-kappa B signal transduction pathway

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12 December 2020

Phosphoproteomics: unraveling the signaling web.

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12 December 2020

A robust error model for iTRAQ quantification reveals divergent signaling between oncogenic FLT3 mutants in acute myeloid leukemia.

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12 December 2020

The role of mass spectrometry in structure elucidation of dynamic protein complexes

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12 December 2020

Comparative proteogenomics: combining mass spectrometry and comparative genomics to analyze multiple genomes

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12 December 2020

Towards a proteome-scale map of the human protein–protein interaction network

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12 December 2020

A generic protein purification method for protein complex characterization and proteome exploration

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12 December 2020

Analysis of mouse brain microvascular endothelium using immuno-laser capture microdissection coupled to a hybrid linear ion trap with Fourier transform-mass spectrometry proteomics platform

1 reference

12 December 2020

Discovery and revision of Arabidopsis genes by proteogenomics

1 reference

12 December 2020

Overview of the HUPO Plasma Proteome Project: results from the pilot phase with 35 collaborating laboratories and multiple analytical groups, generating a core dataset of 3020 proteins and a publicly-available database

1 reference

12 December 2020

The Glycosylation of the Complement Regulatory Protein, Human Erythrocyte CD59

1 reference

12 December 2020

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

1 reference

12 December 2020

Identifying and quantifying in vivo methylation sites by heavy methyl SILAC

1 reference

12 December 2020

Mining the plasma proteome for cancer biomarkers

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12 December 2020

Molecular imaging of biological samples: localization of peptides and proteins using MALDI-TOF MS.

1 reference

12 December 2020

A computational strategy to analyze label-free temporal bottom-up proteomics data

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12 December 2020

The cell as a collection of protein machines: preparing the next generation of molecular biologists

1 reference

12 December 2020

Absolute quantification of multisite phosphorylation by selective reaction monitoring mass spectrometry: determination of inhibitory phosphorylation status of cyclin-dependent kinases

1 reference

12 December 2020

A mouse to human search for plasma proteome changes associated with pancreatic tumor development

1 reference

12 December 2020

The molecular architecture of the nuclear pore complex

1 reference

12 December 2020

Time-controlled transcardiac perfusion cross-linking for the study of protein interactions in complex tissues

1 reference

12 December 2020

Profiling core proteomes of human cell lines by one-dimensional PAGE and liquid chromatography-tandem mass spectrometry

1 reference

12 December 2020

Proteomic analysis of ovarian cancer cells reveals dynamic processes of protein secretion and shedding of extra-cellular domains

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12 December 2020

Reverse phase protein microarrays which capture disease progression show activation of pro-survival pathways at the cancer invasion front

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12 December 2020

Protein Equalizer Technology : the quest for a "democratic proteome".

1 reference

12 December 2020

Meaningful relationships: the regulation of the Ras/Raf/MEK/ERK pathway by protein interactions

1 reference

12 December 2020

Affinity purification-mass spectrometry. Powerful tools for the characterization of protein complexes

1 reference

12 December 2020

Proteomic analysis of post-translational modifications

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12 December 2020

Scoring proteomes with proteotypic peptide probes

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12 December 2020

Mass spectrometry identifies and quantifies 74 unique histone H4 isoforms in differentiating human embryonic stem cells

1 reference

12 December 2020

Mass spectrometry to classify non-small-cell lung cancer patients for clinical outcome after treatment with epidermal growth factor receptor tyrosine kinase inhibitors: a multicohort cross-institutional study.

1 reference

12 December 2020

Laser capture microdissection

1 reference

12 December 2020

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

1 reference

12 December 2020

Determination of stoichiometry and conformational changes in the first step of the P22 tail assembly

1 reference

12 December 2020

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

1 reference

12 December 2020

In-depth proteomics to define the cell surface and secretome of ovarian cancer cells and processes of protein shedding

1 reference

12 December 2020

Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry

1 reference

12 December 2020

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

1 reference

12 December 2020

Proteomic characterization of the human centrosome by protein correlation profiling

1 reference

12 December 2020

Optimized peptide separation and identification for mass spectrometry based proteomics via free-flow electrophoresis.

1 reference

12 December 2020

Minimizing resolution of isotopically coded peptides in comparative proteomics

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12 December 2020

Constellations in a cellular universe

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12 December 2020

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

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12 December 2020

Caenorhabditis elegans has a phosphoproteome atypical for metazoans that is enriched in developmental and sex determination proteins.

1 reference

12 December 2020

Proteome survey reveals modularity of the yeast cell machinery

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12 December 2020

Stable isotope-free relative and absolute quantitation of protein phosphorylation stoichiometry by MS

1 reference

12 December 2020

FLICE, a novel FADD-homologous ICE/CED-3-like protease, is recruited to the CD95 (Fas/APO-1) death--inducing signaling complex

1 reference

12 December 2020

InsPecT: identification of posttranslationally modified peptides from tandem mass spectra

1 reference

12 December 2020

Native mass spectrometry: a bridge between interactomics and structural biology

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12 December 2020

Computational Proteomics Analysis System (CPAS): an extensible, open-source analytic system for evaluating and publishing proteomic data and high throughput biological experiments

1 reference

12 December 2020

MALDI imaging mass spectrometry: molecular snapshots of biochemical systems

1 reference

12 December 2020

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

1 reference

12 December 2020

Structural Analysis of Multiprotein Complexes by Cross-linking, Mass Spectrometry, and Database Searching

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12 December 2020

Proteomic global profiling for cancer biomarker discovery.

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12 December 2020

High throughput protein characterization by automated reverse-phase chromatography/electrospray tandem mass spectrometry

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12 December 2020

Quality control of serum albumin depletion for proteomic analysis

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12 December 2020

Mass spectrometric quantitation of peptides and proteins using Stable Isotope Standards and Capture by Anti-Peptide Antibodies (SISCAPA).

1 reference

12 December 2020

Repeatability and reproducibility in proteomic identifications by liquid chromatography-tandem mass spectrometry

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12 December 2020

Determining the stoichiometry and interactions of macromolecular assemblies from mass spectrometry

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12 December 2020

Molecular network analysis using reverse phase protein microarrays for patient tailored therapy

1 reference

12 December 2020

Large-scale analysis of the yeast proteome by multidimensional protein identification technology

1 reference

12 December 2020

A compendium of potential biomarkers of pancreatic cancer.

1 reference

12 December 2020

A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae

1 reference

12 December 2020

PEPPeR, a platform for experimental proteomic pattern recognition.

1 reference

12 December 2020

Nucleolar proteome dynamics

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12 December 2020

Value of using multiple proteases for large-scale mass spectrometry-based proteomics

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12 December 2020

Proteomic insights into ubiquitin and ubiquitin-like proteins.

1 reference

12 December 2020

Discovery and validation of urine markers of acute pediatric appendicitis using high-accuracy mass spectrometry

1 reference

12 December 2020

A practical guide to the MaxQuant computational platform for SILAC-based quantitative proteomics

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12 December 2020

Quantitative chemical proteomics reveals mechanisms of action of clinical ABL kinase inhibitors

1 reference

12 December 2020

SuperHirn - a novel tool for high resolution LC-MS-based peptide/protein profiling

1 reference

12 December 2020

Quantitative analysis of acrylamide labeled serum proteins by LC-MS/MS.

1 reference

12 December 2020

Absolute quantification of proteins and phosphoproteins from cell lysates by tandem MS

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12 December 2020

Application of serum proteomics to the Women's Health Initiative conjugated equine estrogens trial reveals a multitude of effects relevant to clinical findings

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12 December 2020

Quantitative profiling of differentiation-induced microsomal proteins using isotope-coded affinity tags and mass spectrometry

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12 December 2020

Mass spectrometry of oligosaccharides.

1 reference

12 December 2020

Comparison of linear regression methods when both variables contain error: relation to clinical studies.

1 reference

12 December 2020

A quantitative analysis software tool for mass spectrometry-based proteomics

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12 December 2020

Multiple reaction monitoring for robust quantitative proteomic analysis of cellular signaling networks

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12 December 2020

Brain tissue lipidomics: direct probing using matrix-assisted laser desorption/ionization mass spectrometry

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12 December 2020

BAC TransgeneOmics: a high-throughput method for exploration of protein function in mammals

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12 December 2020

Proteome chips for whole-organism assays

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12 December 2020

Mapping pharmaceuticals in tissues using MALDI imaging mass spectrometry

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12 December 2020

Quantitative phosphoproteomic analysis of signaling network dynamics.

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12 December 2020

Depletion efficiency and recovery of trace markers from a multiparameter immunodepletion column

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12 December 2020

Developing multiplexed assays for troponin I and interleukin-33 in plasma by peptide immunoaffinity enrichment and targeted mass spectrometry

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12 December 2020

Contribution of protein fractionation to depth of analysis of the serum and plasma proteomes

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12 December 2020

Determination of the stoichiometry of protein complexes using liquid chromatography with fluorescence and mass spectrometric detection of fluorescently labeled proteolytic peptides

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12 December 2020

Identification of the proteins of the yeast U1 small nuclear ribonucleoprotein complex by mass spectrometry

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12 December 2020

Genome sequencing in microfabricated high-density picolitre reactors

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12 December 2020

Progress with gene-product mapping of the Mollicutes: Mycoplasma genitalium.

1 reference

12 December 2020

Plant organelle proteomics

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12 December 2020

Chemical cross-linking and mass spectrometry to map three-dimensional protein structures and protein-protein interactions.

1 reference

12 December 2020

AYUMS: an algorithm for completely automatic quantitation based on LC-MS/MS proteome data and its application to the analysis of signal transduction

1 reference

12 December 2020

Identification and quantification of N-linked glycoproteins using hydrazide chemistry, stable isotope labeling and mass spectrometry

1 reference

12 December 2020

Covalent capture of kinase-specific phosphopeptides reveals Cdk1-cyclin B substrates.

1 reference

12 December 2020

Determining the architectures of macromolecular assemblies

1 reference

12 December 2020

Halobacterium salinarum NRC-1 PeptideAtlas: toward strategies for targeted proteomics and improved proteome coverage

1 reference

12 December 2020

Label-free, normalized quantification of complex mass spectrometry data for proteomic analysis

1 reference

12 December 2020

A mouse plasma peptide atlas as a resource for disease proteomics

1 reference

12 December 2020

Highly robust, automated, and sensitive online TiO2-based phosphoproteomics applied to study endogenous phosphorylation in Drosophila melanogaster.

1 reference

12 December 2020

Human Plasma PeptideAtlas

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12 December 2020

Comparisons of mass spectrometry compatible surfactants for global analysis of the mammalian brain proteome

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12 December 2020

Quantitative mass spectrometry in proteomics: a critical review

1 reference

12 December 2020

Identifiers

DOI

10.1038/NBT.1658

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22 August 2017

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PubMed ID

20622844