Skip to main content
Topic: Spectra extraction for database creation (Read 4814 times) previous topic - next topic

Spectra extraction for database creation

Dear all, we are using MS-DIAL 4.24 v for the extraction of MS and MS2 spectra in MoNA format (.msp). Our files are acquired in an Agilent QtoF 6560 by direct injection.  We have some questions:

1. In the beginning we were fragmenting 4 precursor ions per cycle resulting in a low number of scans per peak. Thus, the software didn´t pick our compound of interest and we couldn´t extract the spectra. Is there any procedure to pick up peaks with a low number of scans? After increasing the number of scans the software was able to pick up the compounds.
2. If we are applying several (up to 3) collision energies in the same file, is it possible to obtain different extraction features files for the different CE?
3.  For the identification of the peak, do we have to use the alignment result file or the individual compound file?
4. Once in MS-Finder, can we export batch files in MoNA format (.msp)?

Thanks

Re: Spectra extraction for database creation

Reply #1
Hi,

first of all, the current MS-DIAL program does not support direct infusion data. (under development)
Therefore, simply, there is a possibility that MS-DIAL does not pick the peaks up from your raw data.
As you know, even though the data was acquired by direct infusion, the metabolites are defused in a PEEK tube, and therefore, MS-DIAL can partially pick peaks in the retention time axis. But not for all.
(BTW, we will cover the data of infusion MS within this year.)

Thus, the first thing from you is due to the above reason.

>>2. If we are applying several (up to 3) collision energies in the same file, is it possible to obtain different extraction features files for the different CE?

Sorry, at this moment, MS-DIAL uses only one of the MS/MS spectra assigned to a precursor peak.

>>3.  For the identification of the peak, do we have to use the alignment result file or the individual compound file?
If you wanna make a library file, please use an individual file result. If you do a biological study, please use the result of alignment result.

>>4. Once in MS-Finder, can we export batch files in MoNA format (.msp)?
Yes. Tool -> Reflect msfinder results into msp

Thanks,

Hiroshi




 

Re: Spectra extraction for database creation

Reply #2
Thank you!

Re: Spectra extraction for database creation

Reply #3
Hi,

about the second question,  we have some questions. which collision energy (10 20 40ev) of the data import to MS dial? And now the software have been updated to version 5,  this version also uses only one of the MS/MS spectra assigned to a precursor peak? Are there any plans to consider providing new solutions, such as allowing collision energy selection, etc

Thanks

Re: Spectra extraction for database creation

Reply #4
I have a follow up MS-Finder question - how do you clear the cache or previous work when you want to start a new project or set of IDs. For some reason there isn't a 'clear all' button in the program nor can you select previous items to be cleared individually. It's rather confusing.