1) Convert raw MALDI data to mzML via MSConvert

For raw data file conversion using msConvert, refer to the Data Conversion tab of the IDBac documentation. The steps are the same for all vendor file formats.

2) Fill out the 'input_filename' and 'output_filename' in the msConvert_File_Merger spreadsheet

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 merge. Otherwise the workflow will write files with different 'output_filename' entries as separate mzML files.

3) Upload mzML files and completed msConvert_File_Merger spreadsheet to GNPS2.org

i) Select "File Browser" found on the GNPS2.org homepage.

ii) Create a new folder and upload your converted files.

iii) Upload your completed msConvert_File_Merger spreadsheet.

4) Merge spectra for strain replicates using 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.

5) Access your data for download and export

i) Select 'See Output Files' to access the merged mzML files in file broswer.