Waters MS/MS data not being recognized?

[gm123]

Hi,

I'm using mzMine v2.30 to open Waters Xevo G2-XS qTOF files containing data independent MS/MS acquisition. The RAW file, when imported into MZmine shows all data only as MS1. The picture below shows the transition from the end of the first scan (7.00 min) to beginning of the data from the next scan (0.76 min)





The data in those two scans are labeled as function=0 and function=1, but are they also supposed to be labeled as MS1, MS2 and MS3? (MS3 because there is a function=2 also available)



Because they are not labeled as such, I cannot use MS/MS builder or export the MS2 peaks for GNPS. Can I change the annotation of a subset of peaks from MS1 to MS2 in MZmine? Any other workaround?

[Tomas Pluskal]

Hi,

I think technically your data is MS1, not MS2. If I understand correctly, you are applying energy to induce fragmentation, but you are not selecting any precursor, so I guess it is still considered as MS1? (or maybe it depends on opinion?) 

I would suggest to try converting the data to mzML using msconvert, and then importing the mzML to MZmine. It might change something.

Your function=2 are probably your lock mass scans.

Best,

Tomas

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[gm123]

Hi Tomas,

Yes, you are right -- technically its MS and I'm applying increasing energy for fragmentation. It can loosely be interpreted as MS/MS, since all parent ions at function=0 are undergoing fragmentation at function=1 and function=2. I didn't have lockmass on this dataset, but when I have it, its function=3.

I have tried using mzML and mzXML, but I haven't been able to get all three scans imported. Only function=2 is imported in mzML.

In case there's no good, already available option, I was thinking of the following alternative:
-- Use Crop Filter to separate function=0,1,2
-- Filter, process, deisotope etc separately
-- Export all files as CSV
-- Associate fragments computationally post-export using retention time and m/z based rules
-- Generate an MGF format myself

I was hoping(!!) not to have to do the last two steps, but looks like I need to!

Thanks

On Tuesday, March 6, 2018 at 3:43:55 PM UTC-5, Tomas Pluskal wrote:

Hi,

I think technically your data is MS1, not MS2. If I understand correctly, you are applying energy to induce fragmentation, but you are not selecting any precursor, so I guess it is still considered as MS1? (or maybe it depends on opinion?) 

I would suggest to try converting the data to mzML using msconvert, and then importing the mzML to MZmine. It might change something.

Your function=2 are probably your lock mass scans.

Best,

Tomas

On Tue, Mar 6, 2018 at 3:26 PM, gm123 <gaura...@gmail.com> wrote:

Hi,

I'm using mzMine v2.30 to open Waters Xevo G2-XS qTOF files containing data independent MS/MS acquisition. The RAW file, when imported into MZmine shows all data only as MS1. The picture below shows the transition from the end of the first scan (7.00 min) to beginning of the data from the next scan (0.76 min)





The data in those two scans are labeled as function=0 and function=1, but are they also supposed to be labeled as MS1, MS2 and MS3? (MS3 because there is a function=2 also available)



Because they are not labeled as such, I cannot use MS/MS builder or export the MS2 peaks for GNPS. Can I change the annotation of a subset of peaks from MS1 to MS2 in MZmine? Any other workaround?

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[Diego]

Hello, You can try with MS-Dial, it can handle data independent adquisition mode...