Hello,
I have raw files (Thermo) that have been acquired with switching so they content both positive and negative polarities in a single file. Does anyone know how can they be split using xCalibur in order to obtain separate files, one for each polarity? I know that with msConvert it can be done, but I don't want to convert the file format, but maintain raw format.
Thank you
Hi I'm Professor Soheil Seyyed Hosseini For troubleshooting please refer to my pmc control article published by the University of Rochester.
you can share this file I would like to try with my version of XCalibur is new.
Thank you for your interest Mohammd Almajidi. Finally I was able to do it by using an uptated version of FreeStyle.
How did you manage to split positive and negative from single raw file into 2 different raw files using freestyle?
Hi Diego, once the file is open in FreeStyle (click on the Title Bar that shows ~Chromatogram to select that window) use the scan filter button and look for write to .RAW for each filter. So the steps are:
Open .RAW File
Select Ranges in Workspace Options
On lower window select Filter (+ or –)
Top window should change to only the selected filter
Click on ~Chromatogram to select that window
Write to .RAW
Let me point out that I tried to do the process with FS 1.3 but it was not possible, I was able to split the scans only by using FS 1.5.
Hi Anna. Is there a way to tell FreeStyle to do this for batches of raw files instead of for a single raw file at a time?
Hi Carl, unfortunately I think the option does not exist, and I don't understand why, we spended some time processing the samples one by one
Thanks. I'll try to contact Thermo Fisher and post what I find out here.
Word is that they've developed a utility for splitting raw files in batches. Hopefully it will be made available to the general user community soon.
In addition to your own answer using freestyle, I also found that by opening up the sequence in FreeStyle it can go alot faster (when you open the application just browse to your sequence, make sure the directories in the sequence are the correct ones where the files are: open the sequence (.sld) in Xcalibur and under path ensure or copy and paste the path your files are in as this will error everytime you move your files).
1) open sequence
2) Choose polarity (see
Anna Marqueño added an answer
November 9, 2020)
3) no export raw
4) no you don't have to repeat any steps just go to the next file and export raw, etc. the positive or negative filter will remain until you get to the end of all files, then change, and do it over again....
I know Thermo has a processing method already in XCalibur that automates exporting of positive and negative files from polarity switching data, I used it 4 years ago... but now I cannot find it, ask around and maybe one Thermo representative is familiar.
- Badges
- Science topic
- Similar topics
- Physical Sciences
- Materials Science
- Plating