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process of IDA (information dependent acquisition) ABSciex Qtrap 6500

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process of IDA (information dependent acquisition) ABSciex Qtrap 6500 shulei lei  2017-09-30 10:19
 
Hello,

I have a problem to open IDA data which was acquired on AB Sciex Qtrap 6500. The method for the IDA data is a scheduled MRM in experiment 1 followed by EPI full scan in experiment 2 (MRM-IDA-EPI). The purpose of IDA is to confirm the peptide sequence of precursor ions in the MRM list.

When I opened with Skyline, I can not see any chromatography and MS spectra. In the transit list, I only got a few precursor ions which have a red dot and a few product ions associated with those precursor ions, but half of precursor ions in my transit list do not even have a red dot.

Probably I did not set up right. Do you have a manual for me to follow in this specific case?

Thank you,

Shulei
 
 
Brendan MacLean responded:  2017-10-14 22:31
Hi Shulei,
Sorry for the long wait on a reply. I don't think we've seen this particular experiment set-up before, but if your Targets list matched your transition list, then you should get chromatograms. I would recommend the Existing and Quantitative Experiments tutorial:

http://skyline.ms/tutorial_existing_quant.url

It doesn't sound like you used Skyline to produce the transition list for this data, and this tutorial is explicitly written for people who produced MRM data without involving Skyline in producing the method.

You would likely want to export the MS/MS from the IDA into a format that Skyline could build a library from, either using ProteinPilot to search the spectra or converting the spectra to mzML using ProteoWizard msConvert and search them with another tool. The Targeted Method Editing tutorial goes over how to build a spectral library from peptide spectrum matching search results.

But, if all you want is to see the chromatograms properly matched to targets in your Targets view, then the Existing Experiment tutorial should help with that.

Thanks for your effort to use Skyline to analyze your data.

--Brendan