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Exporting Candidate peaks for ALL compounds

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Exporting Candidate peaks for ALL compounds sstewart  2023-09-22 12:36
 

I'd like to export a report that contains the candidate peaks for EVERY compound. I'd like to do it from the command line. A report exists but (see screenshot) ONLY for one file at a time and with no command line access (unless I misread the docs).

Format would be the same as in the screenshot PLUS extra columns for identifying the compound: "File Name", "Compound Name", "Product Mz", and "Precursor Charge" (see below screenshot). Each row would be a candidate peak.
 
 
Nick Shulman responded:  2023-09-22 12:46
There is a menu item which exports something similar to what you see in the Candidate Peaks grid:
File > Export > mProphet Features
Unfortunately, there is no way to invoke that from the commandline.
-- Nick
 
sstewart responded:  2023-09-29 12:08
Hi Nick,
Thanks! I didn't even know about that output. It's pretty close (not exact) to the candidate peaks. Why aren't they identical?

Is there a way to use proteowizard from the command line to export something similar, or are there a bunch of parameters that skyline uses? (peak width, snr level, etc)?

Sam
 
Brendan MacLean responded:  2023-10-01 12:07
There is quite a bit of chromatogram extraction code and peak detection code and even the generating of the mProphet scores that lives only in Skyline and no other part of ProteoWizard. If you are looking for scored peaks from chromatograms, then Skyline is really your own tool.

We might be able to implement command-line support for File > Export > mProphet Features, or Nick might have ideas on how to implement a candidate peaks report. Nothing immediate, though.

--Brendan
 
sstewart responded:  2023-10-04 09:56
Looks like Nick posted a task for mProphet command line access after our discussion yesterday. Posting here for reference.

https://skyline.ms/issues/home/issues/details.view?issueId=972