(Q38063572)

28 August 2017

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title

Current methods for global proteome identification (English)

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28 August 2017

Lennart Martens

3

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author name string

Marc Vaudel

series ordinal

1

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PubMed ID

23194269

28 August 2017

Albert Sickmann

series ordinal

2

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28 August 2017

1 October 2012

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Expert Review of Proteomics

28 August 2017

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28 August 2017

9

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28 August 2017

5

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28 August 2017

519-532

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Mass spectrometry-based proteomics

28 August 2017

1 reference

A la carte proteomics with an emphasis on gel-free techniques

21 January 2018

1 reference

mzML--a community standard for mass spectrometry data

21 January 2018

1 reference

ProteoWizard: open source software for rapid proteomics tools development

21 January 2018

1 reference

Low cost, scalable proteomics data analysis using Amazon's cloud computing services and open source search algorithms.

21 January 2018

1 reference

MassSieve: panning MS/MS peptide data for proteins

21 January 2018

1 reference

DTASelect and Contrast: tools for assembling and comparing protein identifications from shotgun proteomics

21 January 2018

1 reference

A survey of computational methods and error rate estimation procedures for peptide and protein identification in shotgun proteomics

21 January 2018

1 reference

A guided tour of the Trans-Proteomic Pipeline

21 January 2018

1 reference

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

21 January 2018

1 reference

Fast algorithm for peptide sequencing by mass spectroscopy

21 January 2018

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De novo sequencing of peptides by MS/MS.

21 January 2018

1 reference

Probability-based protein identification by searching sequence databases using mass spectrometry data

21 January 2018

1 reference

Method to correlate tandem mass spectra of modified peptides to amino acid sequences in the protein database

21 January 2018

1 reference

Open mass spectrometry search algorithm

21 January 2018

1 reference

TANDEM: matching proteins with tandem mass spectra

21 January 2018

1 reference

InsPecT: identification of posttranslationally modified peptides from tandem mass spectra

21 January 2018

1 reference

MassWiz: a novel scoring algorithm with target-decoy based analysis pipeline for tandem mass spectrometry

21 January 2018

1 reference

Andromeda: a peptide search engine integrated into the MaxQuant environment

21 January 2018

1 reference

MyriMatch: highly accurate tandem mass spectral peptide identification by multivariate hypergeometric analysis

21 January 2018

1 reference

Method to compare collision-induced dissociation spectra of peptides: potential for library searching and subtractive analysis

21 January 2018

1 reference

Building and searching tandem mass spectral libraries for peptide identification

21 January 2018

1 reference

PepNovo: de novo peptide sequencing via probabilistic network modeling

21 January 2018

1 reference

PEAKS: powerful software for peptide de novo sequencing by tandem mass spectrometry

21 January 2018

1 reference

GutenTag: high-throughput sequence tagging via an empirically derived fragmentation model

21 January 2018

1 reference

DirecTag: accurate sequence tags from peptide MS/MS through statistical scoring

21 January 2018

1 reference

TOPPAS: a graphical workflow editor for the analysis of high-throughput proteomics data

21 January 2018

1 reference

SearchGUI: An open-source graphical user interface for simultaneous OMSSA and X!Tandem searches.

21 January 2018

1 reference

Optimization and testing of mass spectral library search algorithms for compound identification

21 January 2018

1 reference

Using annotated peptide mass spectrum libraries for protein identification

21 January 2018

1 reference

Open source system for analyzing, validating, and storing protein identification data

21 January 2018

1 reference

Development and validation of a spectral library searching method for peptide identification from MS/MS.

21 January 2018

1 reference

MascotDatfile: an open-source library to fully parse and analyse MASCOT MS/MS search results

21 January 2018

1 reference

OMSSA Parser: an open-source library to parse and extract data from OMSSA MS/MS search results

21 January 2018

1 reference

XTandem Parser: an open-source library to parse and analyse X!Tandem MS/MS search results

21 January 2018

1 reference

compomics-utilities: an open-source Java library for computational proteomics

21 January 2018

1 reference

Semi-supervised learning for peptide identification from shotgun proteomics datasets.

21 January 2018

1 reference

Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search

21 January 2018

1 reference

Analysis and validation of proteomic data generated by tandem mass spectrometry

21 January 2018

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Statistical significance for genomewide studies

21 January 2018

1 reference

Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry

21 January 2018

1 reference

Decoy Methods for Assessing False Positives and False Discovery Rates in Shotgun Proteomics

21 January 2018

1 reference

Artificial decoy spectral libraries for false discovery rate estimation in spectral library searching in proteomics

21 January 2018

1 reference

The standard protein mix database: a diverse data set to assist in the production of improved Peptide and protein identification software tools

21 January 2018

1 reference

On using samples of known protein content to assess the statistical calibration of scores assigned to peptide-spectrum matches in shotgun proteomics

21 January 2018

1 reference

A complex standard for protein identification, designed by evolution.

21 January 2018

1 reference

Improving sensitivity by probabilistically combining results from multiple MS/MS search methodologies.

21 January 2018

1 reference

Improving sensitivity in proteome studies by analysis of false discovery rates for multiple search engines

21 January 2018

1 reference

Maximizing the sensitivity and reliability of peptide identification in large-scale proteomic experiments by harnessing multiple search engines

21 January 2018

1 reference

Can the false-discovery rate be misleading?

21 January 2018

1 reference

Protein phosphorylation in signaling--50 years and counting

21 January 2018

1 reference

Semi-automated identification of N-Glycopeptides by hydrophilic interaction chromatography, nano-reverse-phase LC-MS/MS, and glycan database search

21 January 2018

1 reference

Glycoproteomics based on tandem mass spectrometry of glycopeptides

21 January 2018

1 reference

The role of informatics in glycobiology research with special emphasis on automatic interpretation of MS spectra

21 January 2018

1 reference

Characterization of AMPylation on threonine, serine, and tyrosine using mass spectrometry.

21 January 2018

1 reference

N-glycan analysis by CGE-LIF: profiling influenza A virus hemagglutinin N-glycosylation during vaccine production

21 January 2018

1 reference

A probability-based approach for high-throughput protein phosphorylation analysis and site localization

21 January 2018

1 reference

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

21 January 2018

1 reference

Universal and confident phosphorylation site localization using phosphoRS.

21 January 2018

1 reference

Modification site localization scoring: strategies and performance

21 January 2018

1 reference

Confident phosphorylation site localization using the Mascot Delta Score

21 January 2018

1 reference

The good, the bad, the ugly: validating the mass spectrometric analysis of modified peptides

21 January 2018

1 reference

iProphet: multi-level integrative analysis of shotgun proteomic data improves peptide and protein identification rates and error estimates

21 January 2018

1 reference

Interpretation of shotgun proteomic data: the protein inference problem

21 January 2018

1 reference

A statistical model for identifying proteins by tandem mass spectrometry

21 January 2018

1 reference

Proteomics data validation: why all must provide data

21 January 2018

1 reference

IDPicker 2.0: Improved protein assembly with high discrimination peptide identification filtering

21 January 2018

1 reference

Peptide and protein quantification: a map of the minefield.

21 January 2018

1 reference

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

21 January 2018

1 reference

Towards a human proteomics atlas

21 January 2018

1 reference

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

21 January 2018

1 reference

Quantitative proteomic analysis of distinct mammalian Mediator complexes using normalized spectral abundance factors

21 January 2018

1 reference

RIBAR and xRIBAR: Methods for reproducible relative MS/MS-based label-free protein quantification.

21 January 2018

1 reference

Rover: a tool to visualize and validate quantitative proteomics data from different sources

21 January 2018

1 reference

Charting online OMICS resources: A navigational chart for clinical researchers.

21 January 2018

1 reference

UniProt: the Universal Protein knowledgebase

21 January 2018

1 reference

The Protein Identifier Cross-Referencing (PICR) service: reconciling protein identifiers across multiple source databases

21 January 2018

1 reference

The distributed annotation system

21 January 2018

1 reference

Dasty and UniProt DAS: a perfect pair for protein feature visualization

21 January 2018

1 reference

The Ensembl automatic gene annotation system

21 January 2018

1 reference

GOTree Machine (GOTM): a web-based platform for interpreting sets of interesting genes using Gene Ontology hierarchies

21 January 2018

1 reference

Ontologizer 2.0--a multifunctional tool for GO term enrichment analysis and data exploration

21 January 2018

1 reference

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

21 January 2018

1 reference

Protein Data Bank (PDB): database of three-dimensional structural information of biological macromolecules

21 January 2018

1 reference

Jmol– a paradigm shift in crystallographic visualization

21 January 2018

1 reference

Reactome pathway analysis to enrich biological discovery in proteomics data sets

21 January 2018

1 reference

The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored

21 January 2018

1 reference

PRIDE: the proteomics identifications database

21 January 2018

1 reference

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

21 January 2018

1 reference

The problem with peptide presumption and low Mascot scoring

21 January 2018

1 reference

MASPECTRAS: a platform for management and analysis of proteomics LC-MS/MS data

21 January 2018

1 reference

The proteios software environment: an extensible multiuser platform for management and analysis of proteomics data

21 January 2018

1 reference

ms_lims, a simple yet powerful open source laboratory information management system for MS-driven proteomics.

21 January 2018

1 reference

Information management for proteomics: a perspective

21 January 2018

1 reference

Using Laboratory Information Management Systems as central part of a proteomics data workflow

21 January 2018

1 reference

PRIDE Inspector: a tool to visualize and validate MS proteomics data

21 January 2018

1 reference

Analysis of the resolution limitations of peptide identification algorithms.

21 January 2018

1 reference

A spectral clustering approach to MS/MS identification of post-translational modifications

21 January 2018

1 reference

Open MS/MS spectral library search to identify unanticipated post-translational modifications and increase spectral identification rate

21 January 2018

1 reference

Unrestricted identification of modified proteins using MS/MS.

21 January 2018

1 reference

The mzIdentML data standard for mass spectrometry-based proteomics results

21 January 2018

1 reference

jmzML, an open-source Java API for mzML, the PSI standard for MS data

21 January 2018

1 reference

A posteriori quality control for the curation and reuse of public proteomics data

21 January 2018

1 reference

Shotgun collision-induced dissociation of peptides using a time of flight mass analyzer

21 January 2018

1 reference

Automated approach for quantitative analysis of complex peptide mixtures from tandem mass spectra

21 January 2018

1 reference

Deconvolution of mixture spectra from ion-trap data-independent-acquisition tandem mass spectrometry

21 January 2018

1 reference

Mapping intact protein isoforms in discovery mode using top-down proteomics

21 January 2018

1 reference

Deconvolution and database search of complex tandem mass spectra of intact proteins: a combinatorial approach

21 January 2018

1 reference

The Chromosome-Centric Human Proteome Project for cataloging proteins encoded in the genome.

21 January 2018

1 reference

OpenMS and TOPP: Open Source Software for LC-MS Data Analysis

21 January 2018

1 reference

Probabilistic Consensus Scoring Improves Tandem Mass Spectrometry Peptide Identification

21 January 2018

1 reference

DBToolkit: processing protein databases for peptide-centric proteomics

21 January 2018

1 reference

Peptide identification quality control

21 January 2018

1 reference

21 January 2018

Identifiers

DOI

10.1586/EPR.12.51

1 reference

28 August 2017

1 reference

PubMed ID

23194269