Peak area extraction from MS1 only data acquired in paralell with SRM data

Peak area extraction from MS1 only data acquired in paralell with SRM data wen ding  2019-03-12

Hi Brendan,
I can use Skyline to extract peak areas of ions from either MS only data or DDA only data without MS/MS being performed. But I can not do that from MS raw files with MS1 and SRM only data are acquired in parallel on LTQ or Quantiva. It appears that the results import process does take place since I can see the peaks being extracted very briefly , but eventually, no chromatograms or results are obtained. Is there a way to deal with that particular problem?

Thanks a lot in advance!


Brian Pratt responded:  2019-03-12

Hi Wen,

Can you upload the raw file, and the Skyline document you're using it with (use File > Share > Complete to create a file)? That's the quickest way for us to understand what's going on. You can upload to .

It does sound like an unusual acquisition mode, but there may be ways to work around it.


Brian Pratt

wen ding responded:  2019-03-21

Hi Brian,

It is great to see that you have replied to my question! I just uploaded the files you would need to help.
The 1st 21 min of the raw file uploaded is SRM only data. From 21 min - 30 min, SRM and MS1 are acquired in parallel. We are using MS1 to monitor the contaminating species being eluted at the end of each SRM run.
Many thanks!


Nick Shulman responded:  2019-03-21
Hi, Wen,

When Skyline extracts chromatograms from a raw file, Skyline looks at how many chromatograms the file contains in order to decide whether it is SRM or full scan.
If Skyline sees more than one chromatogram, then Skyline decides that it is an SRM file, and then Skyline does not look at any of the MS1 or MS2 scans that might be in the file.

I would recommend that you use msconvert to create a .mzXML file from your .raw file. The .mzXML file format cannot contain chromatograms, so Skyline will know to extract chromatograms from your MS2 scans.

Here is where you can learn more about msconvert:

I am attaching your .raw file converted to mzXML.
-- Nick
wen ding responded:  2019-03-21
Hi Nick,
Thanks for your prompt reply and I am happy that it works great using the mzXML format with MS1 level.
Your help and expertise are really appreciated!