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START HERE- Raw Bruker data

If you are starting with raw Bruker data, use this flow chart to prepare your files for analysis or deposition.

*Click on the flow chart boxes for links to the required tools/pages.

flowchart TD A[Starting with raw Bruker data] --> B[Convert raw protein data to mzML via msConvert] B --> C[Download and fill out a MALDI TOF plate map] C --> D[Upload converted mzML files and plate map to GNPS2] D --> E[Run the IDBac_split_MALDI workflow] E --> F[Contribute to the IDBac database] E --> G[Analyze your data] click B href "https://proteowizard.sourceforge.io/" click C href "https://docs.google.com/spreadsheets/d/1ihFy6lQyJtWy9fp46ahMPWk7xLp2tJ3q/edit?usp=sharing&ouid=102573514213912402103&rtpof=true&sd=true" click D href "https://gnps2.org/homepage" click E href "https://gnps2.org/workflowinput?workflowname=idbac_split_maldi_workflow" click F href "https://wang-bioinformatics-lab.github.io/GNPS2_Documentation/idbacdepositions/" click G href "https://wang-bioinformatics-lab.github.io/GNPS2_Documentation/idbacsumbmitdata/" %% Styling style A fill:#FFFFFF,stroke:#000000,stroke-width:2px,font-size:18px style B fill:#FFFFFF,stroke:#000000,stroke-width:2px,font-size:18px style C fill:#FFFFFF,stroke:#000000,stroke-width:2px,font-size:18px style D fill:#FFFFFF,stroke:#000000,stroke-width:2px,font-size:18px style E fill:#FFFFFF,stroke:#000000,stroke-width:2px,font-size:18px style F fill:#FFFFFF,stroke:#000000,stroke-width:2px,font-size:18px style G fill:#FFFFFF,stroke:#000000,stroke-width:2px,font-size:18px %% Link Styling linkStyle 0 stroke:#ffcc33,stroke-width:3px linkStyle 1 stroke:#ffcc33,stroke-width:3px linkStyle 2 stroke:#ffcc33,stroke-width:3px linkStyle 3 stroke:#ffcc33,stroke-width:3px linkStyle 4 stroke:#ffcc33,stroke-width:3px linkStyle 5 stroke:#ffcc33,stroke-width:3px

More Resources

Navigating MSConvert

Use the following images to convert raw Bruker data to mzML using MSConvert

    MSConvertEDITED msconvert1 msconvert2
Uploading files to the GNPS2 File Browser
Accessing your converted files from the split_MALDI workflow

Download the converted and re-named files to your desktop (allowing for manual upload into a File Browser folder)

    Download1 UPDATED DOWNLOAD