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pmic7802-sup-0001-SupMat.docx46KSupporting Information Figure 1. Overview of the PRIDE/ProteomeXchange ‘partial’ submission workflow. First data files associated with the study are collected together and identified as particular file types needed for the submission. Then the data set is then transferred using the PX submission tool or via command line, as explained in the main manuscript.
pmic7802-sup-0002-SupMat.pdf517KSupporting Information Figure 2. Screenshot of the PRIDE Inspector ‘Protein’ view. It shows delta m/z values for peptide spectrum matches (PSMs) assigned to one protein. This screenshot was generated using the C145.mzid file, included in the example data set PXD000764.

Supporting Information Figure 3. Screenshot of the PX submission tool showing the ‘Export summary file’ functionality in the ‘Submission Summary’ screen. Then a submission.px file is generated, which can be used for a command–-line based submission.

Supporting Information Figure 4. Screenshot of the PX submission tool showing the ‘Resubmission’ option in the first step of the submission. The resubmission option is used to update a private data set.

Supporting Information Figure 5. Screenshot of the PX submission tool showing the ‘entering information required’ for performing a resubmission. The original submitter must first log–-in using their PRIDE user account and password, and then select the private data set to be resubmitted in the drop–-down menu.

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