(Q27311603)

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PRIDE Inspector Toolsuite: Moving Toward a Universal Visualization Tool for Proteomics Data Standard Formats and Quality Assessment of ProteomeXchange Datasets

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Europe PubMed Central

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26 June 2017

PRIDE Inspector Toolsuite: Moving Toward a Universal Visualization Tool for Proteomics Data Standard Formats and Quality Assessment of ProteomeXchange Datasets (English)

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26 June 2017

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Henning Hermjakob

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6 June 2020

Juan Antonio Vizcaíno

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6 June 2020

Yasset Perez-Riverol

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6 June 2020

Julian Uszkoreit

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6 June 2020

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6 June 2020

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6 June 2020

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6 June 2020

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6 June 2020

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Aniel Sanchez

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6 June 2020

Martin Eisenacher

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Martin Eisenacher

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6 June 2020

Florian Reisinger

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Florian Reisinger

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6 June 2020

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Qing-Wei Xu

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6 June 2020

Rui Wang

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6 June 2020

Attila Csordas

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6 June 2020

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6 November 2015

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26 June 2017

Molecular & Cellular Proteomics

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6 June 2020

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6 June 2020

1

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6 June 2020

305-317

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6 June 2020

Open source libraries and frameworks for biological data visualisation: a guide for developers

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4762524

21 March 2017

Dissemination of metabolomics results: role of MetaboLights and COSMOS

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4762524

21 March 2017

A cross-platform toolkit for mass spectrometry and proteomics

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4762524

21 March 2017

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4762524

21 March 2017

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4762524

21 March 2017

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4762524

21 March 2017

A common open representation of mass spectrometry data and its application to proteomics research

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4762524

21 March 2017

Open mass spectrometry search algorithm

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4762524

21 March 2017

Making proteomics data accessible and reusable: current state of proteomics databases and repositories

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4762524

21 March 2017

The mzTab data exchange format: communicating mass-spectrometry-based proteomics and metabolomics experimental results to a wider audience

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4762524

21 March 2017

Tools (Viewer, Library and Validator) that facilitate use of the peptide and protein identification standard format, termed mzIdentML

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4762524

21 March 2017

Open source libraries and frameworks for mass spectrometry based proteomics: a developer's perspective

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4762524

21 March 2017

The PRoteomics IDEntifications (PRIDE) database and associated tools: status in 2013

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4762524

21 March 2017

The mzIdentML data standard for mass spectrometry-based proteomics results

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4762524

21 March 2017

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4762524

21 March 2017

mzML--a community standard for mass spectrometry data

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4762524

21 March 2017

The Ontology Lookup Service: bigger and better

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4762524

21 March 2017

ProteomeXchange provides globally coordinated proteomics data submission and dissemination

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4762524

7 April 2017

Andromeda: a peptide search engine integrated into the MaxQuant environment

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4762524

7 April 2017

TANDEM: matching proteins with tandem mass spectra

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4762524

7 April 2017

PEAKS DB: De Novo Sequencing Assisted Database Search for Sensitive and Accurate Peptide Identification

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4762524

24 May 2017

Metrics for the Human Proteome Project 2015: Progress on the Human Proteome and Guidelines for High-Confidence Protein Identification

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4762524

28 September 2017

PIA: An Intuitive Protein Inference Engine with a Web-Based User Interface

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4762524

28 September 2017

ms-data-core-api: an open-source, metadata-oriented library for computational proteomics

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4762524

28 September 2017

Introducing the PRIDE Archive RESTful web services

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4762524

28 September 2017

MS-GF+ makes progress towards a universal database search tool for proteomics

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4762524

28 September 2017

MS-viewer: a web-based spectral viewer for proteomics results

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4762524

28 September 2017

Drift time-specific collision energies enable deep-coverage data-independent acquisition proteomics

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4762524

28 September 2017

State of the human proteome in 2013 as viewed through PeptideAtlas: comparing the kidney, urine, and plasma proteomes for the biology- and disease-driven Human Proteome Project

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4762524

28 September 2017

Controlled vocabularies and ontologies in proteomics: overview, principles and practice

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4762524

28 September 2017

The minimum information required for a glycomics experiment (MIRAGE) project: improving the standards for reporting mass-spectrometry-based glycoanalytic data

1 reference

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28 September 2017

Comet: an open-source MS/MS sequence database search tool

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4762524

28 September 2017

File formats commonly used in mass spectrometry proteomics

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4762524

28 September 2017

jmzReader: A Java parser library to process and visualize multiple text and XML-based mass spectrometry data formats

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4762524

28 September 2017

Isoelectric point optimization using peptide descriptors and support vector machines.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4762524

28 September 2017

PASSEL: the PeptideAtlas SRMexperiment library

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4762524

28 September 2017

Faster SEQUEST searching for peptide identification from tandem mass spectra

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4762524

28 September 2017

Rapid validation of Mascot search results via stable isotope labeling, pair picking, and deconvolution of fragmentation patterns

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28 September 2017

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

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28 September 2017

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1 reference

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28 September 2017

On best practices in the development of bioinformatics software

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31 May 2018

MS Amanda, a universal identification algorithm optimized for high accuracy tandem mass spectra

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4762524

31 May 2018

Recommendations for mass spectrometry data quality metrics for open access data (corollary to the Amsterdam principles).

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21 January 2018

Computational proteomics pitfalls and challenges: HavanaBioinfo 2012 workshop report.

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21 January 2018

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

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21 January 2018

The PSI-MOD community standard for representation of protein modification data.

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21 January 2018

Unimod: Protein modifications for mass spectrometry

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21 January 2018

PeptideShaker enables reanalysis of MS-derived proteomics data sets.

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21 January 2018

HI-bone: a scoring system for identifying phenylisothiocyanate-derivatized peptides based on precursor mass and high intensity fragment ions.

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21 January 2018

In silico analysis of accurate proteomics, complemented by selective isolation of peptides

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21 January 2018

Analyzing the first drafts of the human proteome.

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21 January 2018

Scaffold: a bioinformatic tool for validating MS/MS-based proteomic studies

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12 December 2020

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6 June 2020

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6 June 2020

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