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Topic: Orbitrap AIF experiment - conversion of data to open format (Read 921 times) previous topic - next topic

Orbitrap AIF experiment - conversion of data to open format

I have a question related to conversion of raw file form Orbitrap Exactive into mzXML (or whatever).

I have files from MS experiment designed in a way: ScanEvent1 - FullScan; followed by ScanEvent2: In source fragmentation HCD30, followed by ScanEvent3: Ion source fragmentation HCD 60, followed by ScanEvent3: In source fragmentation HCD 90.  (nota bene: NO DATA DEPENDENT SCAN). This design was used for untargeted metabolomics experiment as reported in article by Bird et al 2011 (10.1021/ac102598u)
I have a problem with annotation, because I have no software that is able to group correctly full scan data - with the one coming from other three scan events. First data management and statistics was done using Progenesis and Sieve, however both softwares are using only information from FullScan Event 1, not from SC 2-4.
I am trying to convert these files, with msconverter, into mzXML (mzML), where I wish to obtain mzXML that contains information from all four scan evens, in order to perform afterwards alignment and pc grouping. However, results obtained from converting only Level 1,  or Levels 1 to 4, give me always the same file. I do believe that I am loosing information from scan event 2,3 and 4. 

Does anybody know how can I convert files into "whatever open format", that contains information from all four scan events. Does anybody have some other solutions, how to connect data from ScanEvent 1, with those from Scan Events 2-4?
Is my situation hopeless, or ... hopeless   :'( ?  


Re: Orbitrap AIF experiment - conversion of data to open format

Reply #1
Hi Marynka,

It seems awkward that the mzXML files do not include the fragmentation files. When you say 'msconverter', do you mean 'MSconvert' from ProteoWizard? (see image attached of the GUI) If you use that, double-check that you do not filter out any MS2 scans, as it is possible to do so. With the settings as displayed, it should not do so and include all scan events of level '1' (full scan) and higher....
After reading in all the files, the scan header information contains the necessary information (like retention time etc.) to 'connect' or 'place' the scan events. 

I think there is currently a lack of software that deals with AIF data. You might have heard of MS-DIAL ( which combines the full scan data with the fragmentation data present in the AIF scan events to reconstruct MS1-MS2 pairs (by deconvolution) as if data-dependent analysis was done.

Hope this helps and otherwise I hope people with AIF data processing experience will share their solutions!

Good luck,

Cheers Justin