I have SWATH negative ion data acquired with Analyst 1.8 (Win10 version) on a triple TOF 6600 instrument. ABF 1.3.7328 does not recognise them. Is this a known problem with the conversion program ?
Is the file format WIFF2??The current ABF converter does not recognize wiff2 format file.
You can use the proteowizard msconvert generating mzml which can be imported in msdial program.
However, at this moment, the MS-DIAL program cannot process the SWATH-MS data written by wiff2 (it will be fixed in near future).
Therefore, if your data format file is wiff2 instead of wiff, please do the data dependent analysis (information dependent acquisition) to be used in MS-DIAL program at this moment if you wanna use the program.
Sorry for your inconvenience.
OK, finally, I did it. Now, MS-DIAL can directory import the wiff2 format file, and the SWATH-MS data was successfully analyzed. I will upload the new version within this week/weekend.
I managed to overcome the file conversion problem. The files I am using are wiff and not wiff2. As mentioned there are negative acquisition and seems that the [M+H]+ adduct is complete necessity to proceed with the data analysis. If this adduct is not selected i can not process the data. I added negative mode adducts [M-H]- but there is somewhere a bug [M+H]+ adduct to get through the analysis
Any idea why does this happen?
sorry, I cannot understand your situation.
If your data was obtained by negative ion mode of ESI, you should choose "Negative" mode in the start up window of MS-DIAL.