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Topic: ms2Dec suggestion (Read 99 times) previous topic - next topic

ms2Dec suggestion

Dear msdial team,

I am using
 Software name and its version: msdial 4.24
 MS raw data file (a representative one): 1 ms1 followed by 7 swath experiments (window=50Da), collected by Sciex X500R (qtof). Raw file was converted with msconvert3.01 to mzML (peak picking 1-, 32bit, zlib).

I am trying to identified metabolite features in swath data using inhouse curated ms2 library.
While FAQ says that msdial doesn't support sciex swath data, it works for my file as long as i set the peak detection threshold to 10 counts otherwise ms2dec won't work (generate triangle chromatogram).  It is fine for us but just costs a lot computing resource. Is it possible to separate ms2 peak detection from ms1, since the intensity of most of ms2 scan is lower than of ms1? 

Thank you a lot, this is a great software,


Re: ms2Dec suggestion

Reply #1
Hi,

this is a difficult question for me. As I wrote in FAQ (http://prime.psc.riken.jp/compms/msdial/faq.html), yes, msdial does not support the swath data of WIFF2 format file. However, this is not true if all of scan data is included in your mzml file.
It means, as you know, ms-dial requires the scan-precurosr window dictionary. In your case, it can be like:
1 Scan 100-450
2 SWATH 100-150
3 SWATH 150-200
4 SWATH 200-250
5 SWATH 250-300
6 SWATH 300-350
7 SWATH 350-400
8 SWATH 400-450.
By the input of this experimental file, ms-dial recognizes the existences of your scan (100-450) data in the scan numbers of 1, 9, 17, 25, 33, ...in mzml file.
However, if you use msconvert, in most of cases, a scan data will be lost if the scan spectrum is empty or very low (when picked). In this case, ms-dial does not work for wiff2 swath-ms data.

>>Is it possible to separate ms2 peak detection from ms1, since the intensity of most of ms2 scan is lower than of ms1?
You can optimize the MS2 amplitude cutoff (of MS2Dec tab) to reduce the computational time.:)

Hiroshi