Waters2mzML converts and subsequently annotates Waters .raw MS1 or MSn data (both MSe and DDA) into functional .mzML files. Obtained .mzML files can be processed in MZmine 3. It is currently being tested if it works for all Waters .raw data and other processing streamlines. Feel free to try it and let me know.
Based on the raw data's "_extern" file, Waters2mzML deletes obsolete functions, e.g., lockmass (reference mass) - if present - and converts the files to .mzML using ProteoWizard‘s msconvert.exe. Obtained .mzML files are annotated as .txt files, renumbering the scans and reassigning the correct MS-levels if missing. Lockmass data is treated as MS level 1 and data will be included into MS1 data if not removed.
Our data was aquired with a Waters Synapt G2 Si, MassLynx V4.2. Waters2mzML V1.1.2 now also includes Waters Xevo G2 DDA .raw data. It is yet unclear if it will work for other Waters .raw data. Waters2mzML has so far only been tested on Windows 10, 64bit.
Order of functions for MS acquisition seem to be the same by default, but users can change them. Please don't.
- Function 1 should be MS level 1
- Following functions should be MS level 2. For MSe, this will be only function 2. For DDA it is as many functions as the number of masses fragmented for one respective MS1 scan.
- Function after MS/MS scans should be the lockmass.
- Anything higher should be irrelevant for your analysis (e.g., UV-detector trace)
- Do not delete or rename any of the initial files or folders.
- Put COPIES of your Waters .raw files into raw_files folder (files will be annotated)
- Execute Waters2mzML-1.2.0.exe
- The program will ask if you are trying to convert profile data into centroid data. Enter 'y' or 'n'. If you answer no, centroid data will remain centroid and profile data will remain profile.
- Wait for console window to show „annotation completed!“
- Find functional .mzML files in the mzML_files folder.
- Please check the output files and compare them to raw data before proceeding with your analysis.
Before converting a new batch: Remove previously processed files from mzML_files folder.
With MSe data, currently there is a precursor mass assigned to MS/MS scans. This mass is the mean of lower and upper limits you set for the isolation window. E.g., you only allowed MS/MS acquisition for m/z 50 - 2000. Precursor mass value will be set to 1025, isolation window upper and lower offset will both be set to 975. This is technically correct, but it is not clear if this aids or obstructs data processing and analysis. In case of the latter, the software will be altered to contain no precursor information with the next release.
V1.2.0 is being centroided using ProteoWizard's CWT peak picking filter. The vendor conversion appears not to be applicable to Waters .raw data. However, it is advised to centroid your profile data in MassLynx, then converting the centroided .raw data to .mzML using Waters2mzML. This should reduce sources of errors.
I developed Waters2mzML in an effort to use my Waters .raw MSn data to do nontargeted metabolomics for my master’s thesis. Feel free to let me know if the software worked for your data or if you have any comments. I am happy to have a look at data you couldn't process and make : anja.prisching@uni-oldenburg.de
- Chambers, M., Maclean, B., Burke, R. et al. A cross-platform toolkit for mass spectrometry and proteomics. Nat Biotechnol 30, 918–920 (2012).
- https://proteowizard.sourceforge.io/tools/msconvert.html