PRIDE Inspector Toolsuite: Moving Toward a Universal Visualization Tool for Proteomics Data Standard Formats and Quality Assessment of ProteomeXchange Datasets
Published 2015 View Full Article
- Home
- Publications
- Publication Search
- Publication Details
Title
PRIDE Inspector Toolsuite: Moving Toward a Universal Visualization Tool for Proteomics Data Standard Formats and Quality Assessment of ProteomeXchange Datasets
Authors
Keywords
-
Journal
MOLECULAR & CELLULAR PROTEOMICS
Volume 15, Issue 1, Pages 305-317
Publisher
American Society for Biochemistry & Molecular Biology (ASBMB)
Online
2015-11-07
DOI
10.1074/mcp.o115.050229
References
Ask authors/readers for more resources
Related references
Note: Only part of the references are listed.- ms-data-core-api: an open-source, metadata-oriented library for computational proteomics: Fig. 1.
- (2015) Yasset Perez-Riverol et al. BIOINFORMATICS
- PIA: An Intuitive Protein Inference Engine with a Web-Based User Interface
- (2015) Julian Uszkoreit et al. JOURNAL OF PROTEOME RESEARCH
- Metrics for the Human Proteome Project 2015: Progress on the Human Proteome and Guidelines for High-Confidence Protein Identification
- (2015) Gilbert S. Omenn et al. JOURNAL OF PROTEOME RESEARCH
- PeptideShaker enables reanalysis of MS-derived proteomics data sets
- (2015) Marc Vaudel et al. NATURE BIOTECHNOLOGY
- Introducing the PRIDE Archive RESTful web services
- (2015) Florian Reisinger et al. NUCLEIC ACIDS RESEARCH
- Open source libraries and frameworks for biological data visualisation: A guide for developers
- (2015) Rui Wang et al. PROTEOMICS
- Making proteomics data accessible and reusable: Current state of proteomics databases and repositories
- (2015) Yasset Perez-Riverol et al. PROTEOMICS
- MS Amanda, a Universal Identification Algorithm Optimized for High Accuracy Tandem Mass Spectra
- (2014) Viktoria Dorfer et al. JOURNAL OF PROTEOME RESEARCH
- Analyzing the First Drafts of the Human Proteome
- (2014) Iakes Ezkurdia et al. JOURNAL OF PROTEOME RESEARCH
- The mzTab Data Exchange Format: Communicating Mass-spectrometry-based Proteomics and Metabolomics Experimental Results to a Wider Audience
- (2014) Johannes Griss et al. MOLECULAR & CELLULAR PROTEOMICS
- MS-Viewer: A Web-based Spectral Viewer for Proteomics Results
- (2014) Peter R. Baker et al. MOLECULAR & CELLULAR PROTEOMICS
- ProteomeXchange provides globally coordinated proteomics data submission and dissemination
- (2014) Juan A Vizcaíno et al. NATURE BIOTECHNOLOGY
- MS-GF+ makes progress towards a universal database search tool for proteomics
- (2014) Sangtae Kim et al. Nature Communications
- HI-Bone: A Scoring System for Identifying Phenylisothiocyanate-Derivatized Peptides Based on Precursor Mass and High Intensity Fragment Ions
- (2013) Yasset Perez-Riverol et al. ANALYTICAL CHEMISTRY
- Controlled vocabularies and ontologies in proteomics: Overview, principles and practice
- (2013) Gerhard Mayer et al. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS
- Open source libraries and frameworks for mass spectrometry based proteomics: A developer's perspective
- (2013) Yasset Perez-Riverol et al. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS
- 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
- (2013) Terry Farrah et al. JOURNAL OF PROTEOME RESEARCH
- Computational proteomics pitfalls and challenges: HavanaBioinfo 2012 Workshop report
- (2013) Yasset Perez-Riverol et al. Journal of Proteomics
- Tools (Viewer, Library and Validator) that Facilitate Use of the Peptide and Protein Identification Standard Format, Termed mzIdentML
- (2013) Fawaz Ghali et al. MOLECULAR & CELLULAR PROTEOMICS
- The Minimum Information Required for a Glycomics Experiment (MIRAGE) Project: Improving the Standards for Reporting Mass-spectrometry-based Glycoanalytic Data
- (2013) Daniel Kolarich et al. MOLECULAR & CELLULAR PROTEOMICS
- Drift time-specific collision energies enable deep-coverage data-independent acquisition proteomics
- (2013) Ute Distler et al. NATURE METHODS
- Dissemination of metabolomics results: role of MetaboLights and COSMOS
- (2013) Reza M Salek et al. GigaScience
- Isoelectric point optimization using peptide descriptors and support vector machines
- (2012) Yasset Perez-Riverol et al. Journal of Proteomics
- File Formats Commonly Used in Mass Spectrometry Proteomics
- (2012) Eric W. Deutsch MOLECULAR & CELLULAR PROTEOMICS
- The mzIdentML Data Standard for Mass Spectrometry-Based Proteomics Results
- (2012) Andrew R. Jones et al. MOLECULAR & CELLULAR PROTEOMICS
- PRIDE Inspector: a tool to visualize and validate MS proteomics data
- (2012) Rui Wang et al. NATURE BIOTECHNOLOGY
- A cross-platform toolkit for mass spectrometry and proteomics
- (2012) Matthew C Chambers et al. NATURE BIOTECHNOLOGY
- The Proteomics Identifications (PRIDE) database and associated tools: status in 2013
- (2012) Juan Antonio Vizcaíno et al. NUCLEIC ACIDS RESEARCH
- jmzReader: A Java parser library to process and visualize multiple text and XML-based mass spectrometry data formats
- (2012) Johannes Griss et al. PROTEOMICS
- Comet: An open-source MS/MS sequence database search tool
- (2012) Jimmy K. Eng et al. PROTEOMICS
- PASSEL: The PeptideAtlas SRMexperiment library
- (2012) Terry Farrah et al. PROTEOMICS
- Faster SEQUEST Searching for Peptide Identification from Tandem Mass Spectra
- (2011) Benjamin J. Diament et al. JOURNAL OF PROTEOME RESEARCH
- Andromeda: A Peptide Search Engine Integrated into the MaxQuant Environment
- (2011) Jürgen Cox et al. JOURNAL OF PROTEOME RESEARCH
- In silico analysis of accurate proteomics, complemented by selective isolation of peptides
- (2011) Yasset Perez-Riverol et al. Journal of Proteomics
- PEAKS DB:De NovoSequencing Assisted Database Search for Sensitive and Accurate Peptide Identification
- (2011) Jing Zhang et al. MOLECULAR & CELLULAR PROTEOMICS
- Recommendations for mass spectrometry data quality metrics for open access data (corollary to the Amsterdam principles)
- (2011) Christopher R. Kinsinger et al. PROTEOMICS
- mzML—a Community Standard for Mass Spectrometry Data
- (2010) Lennart Martens et al. MOLECULAR & CELLULAR PROTEOMICS
- The Ontology Lookup Service: bigger and better
- (2010) R. Cote et al. NUCLEIC ACIDS RESEARCH
- Scaffold: A bioinformatic tool for validating MS/MS-based proteomic studies
- (2010) Brian C. Searle PROTEOMICS
- Rapid Validation of Mascot Search Results via Stable Isotope Labeling, Pair Picking, and Deconvolution of Fragmentation Patterns
- (2009) Samuel L. Volchenboum et al. MOLECULAR & CELLULAR PROTEOMICS
- A practical guide to the MaxQuant computational platform for SILAC-based quantitative proteomics
- (2009) Jürgen Cox et al. Nature Protocols
- The PSI-MOD community standard for representation of protein modification data
- (2008) Luisa Montecchi-Palazzi et al. NATURE BIOTECHNOLOGY
Find Funding. Review Successful Grants.
Explore over 25,000 new funding opportunities and over 6,000,000 successful grants.
ExploreDiscover Peeref hubs
Discuss science. Find collaborators. Network.
Join a conversation