Metabolomics Society Forum

Software => MS-DIAL => Topic started by: biswapriya on July 02, 2020, 02:15:05 AM

Title: MS/MS Spectra in mzML File
Post by: biswapriya on July 02, 2020, 02:15:05 AM
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
Title: Re: MS/MS Spectra in mzML File
Post by: romanas chaleckis on July 06, 2020, 07:48:58 PM
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
Title: Re: MS/MS Spectra in mzML File
Post by: Hiroshi Tsugawa on August 13, 2020, 07:07:12 PM
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