PRIDE Reshake

PRIDE

More and more journals are requesting that you make your proteomics data available when publishing a proteomics manuscript. The most commonly used database for proteomics identifications is the Proteomics Identifications Database (PRIDE) which is one of the main entry points to ProteomeXchange.

PRIDE consists of two main types of projects: public and private. Public projects are freely available for everyone to inspect, while private data requires the input of a valid username and password for the given project. Private data can be very useful, for example during a review process when you do not want the data to be publicly available until the manuscript is accepted.


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Reshake

Reshake is PeptideShaker lingo for reanalyzing data, here in the case of proteomics identifications from PRIDE. All PRIDE projects have a unique ProteomeXchange identifier. These are cited in papers and links are also shown in PumMed. This makes it easy to locate a specific PRIDE project.

If you do not have a ProteomeXchange identifier, but rather want to reanalyze a certain type of data, for example data from a specific species, you can locate the available PRIDE projects using the Find feature in the Edit menu.


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Data Types

PRIDE projects are split into three types Complete, Partial and PRIDE. Complete projects contain both the proteomics identifications and the raw data, while Partial projects are missing some of the information. There are several reasons for partial projects. For example it might be difficult to convert custom project output into the standard formats, or the project might only consist of raw data. Finally, the PRIDE category is used to label mainly the older PRIDE projects that were in PRIDE before ProteomeXchange came around.


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Reshakable

In order for PeptideShaker to be able to reshake a project it has to contain at least one mgf or PRIDE XML file. If the spectra are stored in a different format you can always download and convert the files manually. Search settings from the original project can also be extracted if the project contains at least one PRIDE XML or mzIdentML file. In any case the search settings can always be added or altered before reshaking. To show all files (and not just the reshakable files) deselect the "Reshakeable Files Only" in the lower right corner below the files table.

Note that many projects are split into multiple assays. Where each assay may have its own search settings and even come from different species. When analyzing such projects it is therefore very important to pay attention to the search settings and database used, to ensure that the correct settings are used. To analyze files from multiple assays, make sure that no specific assay is selected in the assay table. To remove the assay selection, simply click on the project once more.


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