START HERE- Raw non-Bruker data
🚧 Work In Progress¶
This page is under construction, thanks for your patience!
If you are starting with raw non-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 non-Bruker data] --> B[Convert raw data to mzML via msConvert]
B --> C[Download and fill out an msConvert_File_Merger spreadsheet]
C --> D[Upload converted mzML files and completed msConvert_File_Merger spreadsheet to File Browser]
D --> E[Merge replicate files using the msConvert_File_Merger workflow]
E --> F[Contribute to the IDBac database]
E --> G[Run an analysis workflow]
click B href "https://proteowizard.sourceforge.io/"
click C href "https://docs.google.com/spreadsheets/d/1o5K4SavD14K-LqhSeWkt4h20MTrAUpkXsaFRYqNdRvY/edit?gid=508446939#gid=508446939"
click D href "https://gnps2.org/homepage"
click E href "https://gnps2.org/workflowinput?workflowname=msConvert_File_Merger"
click F href "https://wang-bioinformatics-lab.github.io/GNPS2_Documentation/idbacdepositions/"
click G href "https://wang-bioinformatics-lab.github.io/GNPS2_Documentation/idbacsumbmitdata/"
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More Resources¶
Instructions for filling out the msConvert_File_Merger spreadsheet
i) Insert the current filenames for your individual mzML files into the 'input_filename' column. It is important to keep the '.mzml' tag on the end of the filename in this column. Take care to make sure the filenames in the spreadsheet under 'input_filename' match the filenames in your data folder.
ii) Type a new filename for replicate spectra you would like to combine into a single mzml file. You do NOT need to include the '.mzml' tag in this column. Make sure the 'output_filename' is identical for all replicate spectra you want to be merged. Otherwise the workflow will write files with different 'output_filename' entries as separate mzML files.
Uploading files to the GNPS2 File Browser
Navigating the msConvert_File_Merger workflow
This workflow will combine spectra from separate spots that correspond to the same bacterial strain (i.e. replicate spots). The output is a single mzML file (per strain) that contains the replicate spectra as separate scans.
i) Open the msConvert_File_Merger workflow.ii) Select your mzML files and your input/output spreadsheet from the dropdown menus.
iii) Select mzML or mzXML as your output data format.
iV) Submit workflow.