Users can upload any pepxml files to the IP2 platform for downstream data analysis (e.g. the result file from the Proteome discoverer). In the pepxml file, you need to make sure the fasta database name is available in the IP2 database page. You can change the database name in a text editor before uploading. The path of the database does not matter. The pepxml file name should end with pep.xml. For example, it can be myfile.pep.xml

Figure 13.1.1: pep.xml file In the experiment page, upload ms1 and ms2 files. Then, click “Upload search result” link to upload pepxml file.


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