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Start using PeptideShaker Online
Before you start using PeptideShaker Online, you will have to get a Galaxy user API key. Although PeptideShaker Online allows you to execute tasks anonymously, your data will then be shared with anybody using the application. So, apart from testing purposes, before running tasks it is highly recommended to use a specific user in order to have your own data history and be able to manage it and execute tasks associated only to your user.
Once you have registered your user using the register user form of your Galaxy GUI instance (please note that this user should not be the same as the user configured for managing the Galaxy instance, and in this case should not have admin permissions), you can generate an API key for it. API keys allow the use of your Galaxy user account programmatically without sharing your private password. This can be easily done when logged in with your user, accessing your user preferences, and clicking "Manage API Key" - "Create a new Key".
Please keep this key in a safe place and then open the PeptideShaker Online website with your browser. Once the main PeptideShaker Online page is shown, click the bottom-right button called "Galaxy Login" and enter the previously generated API Key. Once you click on "Login" button you will be returned to the main PeptideShaker Online page logged in with your Galaxy user ready to use all of its features.
When a user has successfully log in with their private API key, they can upload their own FASTA files and spectrum files through the Search tab. Currently, the supported spectrum input formats are mgf and mzML for identification and Thermo raw files for both identification and quantification.
Users can also upload and visualize their own processed data files using the Upload Your Own Project Files tab located under the Visualize Data tab. Users need to upload FASTA, Proteins, and Peptides files. Please use Sample Files as a template.
After the users select the dataset, the "Dataset tab" will be automatically displayed, the tab contest of filters and protein table.