ProteomeXchange Submission Validator

This tool helps user to validate submissions in the client side before submitting to PRIDE. It is specially useful for Big submissions

Minimum requirements

Java 1.8, 64-bit
A dual-core CPU
2+ GB RAM for complex mzIdentML files.

Instructions

Download the tool as a zip archive file.
Extract the zip file to a directory.
From a terminal / command prompt, navigate to this new extracted directory and execute a command as described under the ‘usage’ section below.

Usage

PX validation.

You can create manually or with our own tool or with the submission tool the submission.px file. This file contains the metadata around the file including title, description.

$ java -jar submission-tool-validator-{version}-bin.jar -v -px /path/to/data/submission.px

Validation of mzIdentML and mzTab Files

Validation an mzTab

$ java -jar submission-tool-validator-{version}-bin.jar -v -mztab /path/to/data/file.mztab

Validation an mzIdentML

$ java -jar submission-tool-validator-{version}-bin.jar -v -mzid /path/to/data/file.mzid
$ java -jar submission-tool-validator-{version}-bin.jar -v -mzid /path/to/data/file.mzid -peak /path/to/data/file.mgf 
$ java -jar submission-tool-validator-{version}-bin.jar -v -mzid /path/to/data/file.mzid -peaks /path/to/data/file1.mgf##/path/to/data/file2.mgf

Contact

To get in touch, please either email pride-support@ebi.ac.uk or raise an issue on the issues page.