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LCMS data for skyline viviana greco82  2014-12-01 03:37
 
dear all,
I've performed a shotgun experiment (DDA) on a nanoACQUITY UPLC MS system (waters) and processed raw data with PLGS software (waters). We found some proteins differentially expressed in two conditions and now a validation of these is required. I was thinking of building a library (fasta from uniprot) only with these proteins and use this as my database. Then I think to compare the retention times of the peptides found. is that correct? do you have any suggestions for me?
Thanks in advance.
best regards,
Viviana
 
 
Brendan MacLean responded:  2014-12-01 07:18
Hi Viviana,
Have you reviewed the MS1 Full-Scan Filtering tutorial?

https://skyline.gs.washington.edu/labkey/wiki/home/software/Skyline/page.view?name=tutorial_ms1_filtering

and the DDA webinar the Skyline Team produced recently?

https://skyline.gs.washington.edu/labkey/project/home/software/Skyline/events/2014%20Webinars/Webinar%202/begin.view?

If you do things right, Skyline should automatically pick peaks based on the retention times of the identified MS/MS scans in your DDA data, and make it very easy for you to compare visually with that information.

You can build your library from the final_fragment.csv file from a PLGS search.

Good luck. Thanks for using Skyline to verify you preliminary findings from DDA data.

--Brendan