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Topic: MS/MS Spectra in mzML File (Read 236 times) previous topic - next topic

MS/MS Spectra in mzML File

Hi Hiroshi,

I am trying out a single +ve mode LC-MS/MS DDA data file (CE: 40 eV) acquired data for MS-DIAL processing.
Though, upon conversion to mzML using msConvert (oth 32 , 64 bit did not work out, peak picking all conditions did not help) can see lots of MS2 spectral data using Mass++ (See pic below) but can not see any MS/MS spectra in MS-DIAL interface (see pic). Attached are the parameters (.txt file) used too. Why is MS-DIAL not able to find the MS/MS data in my processing workflow ?

Not sure what am I doing wrong in MS-DIAL for this single data file ?

Thanks a lot for the help.

Biswa
Biswapriya B. Misra, PhD
Assistant Professor
Center for Precision Medicine
Department of Internal Medicine
Section on Molecular Medicine
Wake Forest University School of Medicine
Cell: +1-352-215-6040
Office: +1-336-713-4622
Profile: http://profiles.wakehealth.edu/display/Person/bmisra

Re: MS/MS Spectra in mzML File

Reply #1
do you have the right precursor mass in the MS2 spectra data? in your screenshot it looks like all the MS2 spectra are for m/z ~764 ion

 

Re: MS/MS Spectra in mzML File

Reply #2
Hi Biswa,

in the raw data, the MS/MS spectral record should have the isolated precursor m/z value information. After the peak picking for MS1 scan data is finished, MS-DIAL tries to assign the MS/MS spectral information by using (A) the isolated precursor m/z, (B) the m/z value of detected peak's precursor m/z, and (C) centroid MS2 tolerance within the retention time range of detected peak area.

You can check your MS records, and then, please set the proper centroid MS2 tolerance for assigning MS/MS information to detected peaks.
Thanks,

Hiroshi