Mapping between peptides in main report file and input mzml spectra

[daichengxin]

Hi, Thank the developer for providing so a fantastic tool for DIA data analysis.
Is there a way to match the peptides in the main report to the spectra in input mzML file ? What does the MS2.Scan column mean in the main report file?

Best Chengxin

[vdemichev]

Hi Chengxin,

I would suggest doing it by the retention time (RT) column. But can also use MS2.Scan - it's MS2 scan number across all MS2 scans (MS1 are not counted here) - except with fancy dia-PASEF schemes MS2.Scan might not be directly interpretable.

Best, Vadim

[daichengxin]

Thanks a lot. So MS2.Scan corresponds to the scan number in the mzML file, right? eg. MS2.scan=73091 in main report -><spectrum id="controllerType=0 controllerNumber=1 scan=73091" index="73090" defaultArrayLength="441"> in mzML file.

[vdemichev]

If all MS2 scans are ordered by the RT, MS2.Scan is the number of the peak apex scan. I am not sure how scans are numbered in the mzML.

[daichengxin]

Got it. Thanks a lot.

Best, Chengxin

[daichengxin]

Hi vdemichev, I tried to use RT column to match peptides and spectra, but I didn't find the corresponding RT value in mzML. What do you think?

[vdemichev]

Use closest RT?