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how to make sure the skyline only picks up peak in 10ppm

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how to make sure the skyline only picks up peak in 10ppm dengjingjing01  2018-08-29 13:13
 

Hi,

I am using Q Exactive to do PRM running. After result importing, I found in the default setting, sometimes skyline picks up precursors at 30ppm. Although there are some fragments matched to the library, I don't think that is my peptide since the precursor error is too big. Is there any setting I can narrow the precursor to 10ppm? I am using the public library, so I could not use the retention time as a criteria to filter out false positive matches.

Thanks.

Best,
Jingjing
 
 
Brendan MacLean responded:  2018-08-29 13:38

Hi Jingjing,
For this, we recommend you use "Centroided" as your mass analyzer and then simply use 10 ppm as your mass tolerance. This has worked quite well for us and has even become our preferred mode of extracting chromatograms from Orbitrap data. With this set-up, you will not see any chromatogram peaks with mass errors greater than 10 ppm.

There is currently no way of telling Skyline that you will allow it to extract from a wider range but not allow peaks in that range to be considered.

Hope this is helpful in your data processing with Skyline.

--Brendan