Tutorial: Raw Shimadzu data conversion/ File preparation
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Overview
*Find step-by-step video guides and important links below.*
đ§Video tutorials coming soon!đ§
Step 1
Step 1
Collect protein and/or small molecule MALDI-TOF MS data in biological replicates.
Protein mass range: 2,000-20,000 Da.
Small molecule mass range: 200-2,000 Da.
Replicate Recommendations:Â Minimum of 3 biological replicates.
Raw Shimadzu Data
Raw Shimadzu Data
Step 2
For this step, you chose "Raw Shimadzu Data" as your file type.
Click here for Raw Bruker Data tutorials.
Step 3
Step 3
Download MSConvert through the free Proteowizard software package.
Step 4
Step 4
Download and fill in a MALDI-TOF MS File Merger spreadsheet.
This spreadsheet and subsequent workflow combines biological or technical replicate spectra into a single, labeled mzML file.
File Merger spreadsheet link
***Video tutorial coming soon!***
Example
You have 6 replicates of an isolate that you labeled as "Strain_1".
After completing "Step 2", each of your replicates has a unique file name (see image 'Column A, Rows 2-6').
You need to create a consensus spectrum from your replicates . To do this.................so that IDBac platform needs to know what files (replicates) belong to each of my isolates.
Using the linked spreadsheet, I have copied the filenames of my replicates in "Column A/ Input_filename", and used "Column B/ Output_filename" to assign the corresponding Isolate ID.
Now I can proceed
Step 4 Tips
Step 4 Tips
Copying filenames
Press 'shift' while selecting your files.
At the top of your file browser, click "copy path".
Paste into "Column A" of the File Merger spreadsheet.
Column A / input_filename
It is important to keep the '.mzml' tag on the end of the filename.
Take care to make sure the filenames in the spreadsheet under 'input_filename' match the filenames in your data folder.
Column B / output_filename
You do NOT need to include the '.mzml' tag when creating your isolate IDs.
Make sure the 'output_filename' is identical for all replicate spectra you want to be merged.
Step 5
Step 5
Upload your mzML files and completed File Merger Spreadsheet to GNPS2 File Browser.
Step 6
Step 6
Run the File_Merger workflow
Select mzML files under "Input Spectra Folder"
Select your File Merger Spreadsheet under "Input CSV/XLSX File"
Ensure the output format is listed as "mzML"
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