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Discrepancies in Heavy and Light Peptide Chromatogram Import Ranges

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Discrepancies in Heavy and Light Peptide Chromatogram Import Ranges robwsprung  2017-09-21 10:07
 
Hi Brendan,

This message is in response to issue #544

I am extracting fragment ion information as well (3 fragment ions per peptide). The file in question was a DDA run in which our heavy and light peptide standards are spiked at 100fmol each (on column) into a complex matrix (1ug tumor tryptic digest on column).

The issue appears to be specific to Skyline-daily (64-bit) 3.7.1.11357.

When I import the file into Skyline (64-bit) 3.7.0.11317, I see the entire chromatogram as expected.

Let me know if you need additional information or files.

Robert
 
 
robwsprung responded:  2017-09-21 11:32
As an update, it has been brought to my attention that changing Transition Settings - MS/MS Filtering to "None" results in import of the full MS1 chromatogram, although then there is no MS/MS data to verify the ID.

Robert
 
Brendan MacLean responded:  2017-09-21 11:51
Okay. Thanks, Robert. It seems new code implemented for PRM is causing your problem.

I think that code should at least be fixed to use the same RT range for all precursors of a peptide. Beyond that, we don't give a ton of thought to MS/MS extraction from DDA, because it is not quantitative.

If just fixing it to extract the same range over all precursors of a peptide, still based on the range in which MS/MS spectra are found, is not enough for you, then we should consider how your needs could be made to not conflict with the much higher priority of supporting PRM.

Thanks for pointing this out and digging into the details.

--Brendan