PRIDE resources, tools and libraries

PRIDE offers a collection of resources and open source tools and libraries to handle, submit, visualise and analyze Mass Spectrometry (MS)-based proteomics data. 

 

Resources

Resource (Source code)
Description
Publication
Access

PRIDE Archive

New PRIDE Archival system for Ms proteomics data (based on ProteomeXchange guidelines and PSI data standards) 

New version of the system not published yet

Previous version published: The PRoteomics IDEntifications (PRIDE) database and associated tools: status in 2013 (Nucleic Acids Research, 2013)

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PRIDE Archive Web Services

RESTful web services for PRIDE Archive

Introducing the PRIDE Archive RESTful web services (Nucleic Acids Research, 2015)

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PRIDE Proteomes Subset of the data in PRIDE Archive, containing high-quality data Not published yet View
PRIDE Cluster Web  Web to access the results of PRIDE spectral-clustering (use as quality assessment for PRIDE Proteomes)  New version not published yet

 

Tools

Tool
Description
Publication
Access

PRIDE Inspector

An integrated desktop application for visualizinig and analyzing MS dataset (such as: mzML, PRIDE XML and mzIdentML). PRIDE Inspector: a tool to visualize and validate MS proteomics data (Nature Biotechnology, 2012) Download
PRIDE Converter 2 An open source tool that converts MS data into valid PRIDE XML The PRIDE Converter 2 framework: an improved suite of tools to facilitate data submission to the PRIDE database and the ProteomeXchange consortium (Molecular and Cellular Proteomics, 2012) Download
ProteomeXchange Submission Tool An free tool that assists you with the ProteomeXchange submission

ProteomeXchange provides globally coordinated proteomics data submission and dissemination (Nature Biotechnology, 2014)

How to submit MS proteomics data to ProteomeXchange via the PRIDE database (Proteomics, 2014)

Download
PICR The Protein Identifier Cross-Reference (PICR) service is a web application that provides interactive and programmatic (SOAP and REST) access to a mapping algorithm based on 100% sequence identity to proteins from over 98 distinct source databases

The Protein Identifier Cross-Referencing (PICR) service: reconciling protein identifiers across multiple source databases (BMC Bioinformatics, 2007)

Improvements in the Protein Identifier Cross-Reference service (Nucleic Acids Research, 2012)

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Libraries for the file formats

 

Other Libraries