Goals:
I wanted to do a quick analysis of the datafiles from Danielle Swaney's group to get a sense of what they were like.
Files:
Danielle recommended files from viral baits A31R and C22L. She also recommended downloading different mCherry immunoprecipitations to use as a negative control.
- 17052023_OLMP7_C22L_01.raw
- 17052023_OLMP7_C22L_02.raw
- 17052023_OLMP7_C22L_03.raw
- 17052023_OLMP7_mcherryAp09_01.raw
- 17052023_OLMP7_mcherryAp09_02.raw
- 17052023_OLMP7_mcherryAp09_03.raw
- 17052023_OLMP7_mcherryAp11_01.raw
- 17052023_OLMP7_mcherryAp11_02.raw
- 17052023_OLMP7_mcherryAp11_03.raw
- 20230321_OLEP07_JC_APMS_DIA_A31R_1.raw
- 20230321_OLEP07_JC_APMS_DIA_A31R_2.raw
- 20230321_OLEP07_JC_APMS_DIA_A31R_3.raw
- 20230321_OLEP07_JC_APMS_DIA_mCherry1.raw
- 20230321_OLEP07_JC_APMS_DIA_mCherry2.raw
- 20230321_OLEP07_JC_APMS_DIA_mCherry3.raw
Analysis:
I did two analyses. I did an analysis with DIA-NN v2.1.0 and then a quantitative analysis with Skyline. I also did an MSFragger-DIA search in Skyline with a quantitative analysis in Skyline.