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Vladimir Gorshkov
Aug 18, 2018, 8:42:51 AM8/18/18
to ProteomicsQA
Hi ProteomicsQA,
I have the following task that I need to perform. I have a raw file from Thermo that has MS scans iterating through different mass ranges, I would like to average the scans in each range (running average). Scans are not consequitive. The optimal result is to have a new raw file with averaged spectra, or, at least, the file in one of the open formats.
To make it more clear I can give a simple example:
My raw file is made in the following way:
scan #1 MS1 [200 - 1000]
scan #2 MS2 [200 - 400]
scan #3 MS2 [400 - 600]
scan #4 MS2 [600 - 800]
scan #5 MS2 [800 - 1000]
scan #6 MS1 [200 - 1000]
scan #7 MS2 [200 - 400]
scan #8 MS2 [400 - 600]
scan #9 MS2 [600 - 800]
scan #10 MS2 [800 - 1000]
...
(the cycle repeats to the end of file)
I would like to have a new file like this
scan #1 is MS1 scan and is avearge of scan #1 and #6 (have the same mass range and ms level)
scan #2 is MS2 scan and is avearge of scan #2 and #7
scan #3 is MS2 scan and is avearge of scan #3 and #8
scan #4 is MS2 scan and is avearge of scan #4 and #9
scan #5 is MS2 scan and is avearge of scan #5 and #10
scan #6 is MS1 scan and is avearge of scan #6 and #11
scan #7 is MS2 scan and is avearge of scan #7 and #12
scan #8 is MS2 scan and is avearge of scan #8 and #13
scan #9 is MS2 scan and is avearge of scan #9 and #14
scan #10 is MS2 scan and is avearge of scan #10 and #15
....
Scans can be both high and low resolution, profile and centroided.
Do you know any type of software that can do this type of transformation?
Thank you for your help.
Best regards,
Vladimir
Timo Sachsenberg
Aug 18, 2018, 1:33:38 PM8/18/18
to Vladimir Gorshkov, ProteomicsQA
Hi Vladimir,
I just checked if we have something ready in OpenMS and this particular use case doesn't seem to be supported.
The closest I found was:
which is used by the tool:
It seems easy to add on the library/tool side but would require some coding (I think you basically need to fill the AverageBlocks data structure which the spectra indices that get grouped together and then call averageProfile or averageCentroidSpectra).
Another option which would not require coding in C++ is to use pyOpenMS and do the merging manually.
Let me know if you want to go that road and I may be able to assist you.
Best,
Timo
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Vladimir Gorshkov
Aug 20, 2018, 4:36:24 AM8/20/18
to ProteomicsQA
Hi Timo,
thank you for your answer. I will look into it and see if I would like to go this way.
Best regards,
Vladimir
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