IDA experiment and SWATH Acqusition

[tutagem tutagem]

Hello Everyone,

We have 4600 Abi-Sciex QTOF. I can search both IDA and SWATH method data in Search GUI.Searching the same sample, I got good results for IDA experiment but I could't get good results for SWATH method. 

SWATH method contain extra peak than IDA.

Can you help me?

Best Regards

Saffet.

[Peter H]

To search SWATH files you need to use a different pipeline. You can make your own library and search the SWATH data with PeakView from Sciex. Alternatively, you can use something like DIA-NN to both build a library and search the data. DIA-NN is free and works very well. The main output *.tsv file has a lot of information and you’ll likely need some R or Python skills to get the most out of the data. There are some useful *.tsv files that are also output and a good summary PDF.

You may also want to have a look at DIA-Umpire, but I find DIA-NN more user friendly. There are other free options around if you look.

Good luck,

Peter