HDX data analysis workflow

ON MASCOT COMPUTER move data from MQIET normal (which is not TVable, but you can get files the server via MASCOT) to MASCOT (documents -> data folder) Make mgf file in Compass open MSMS file (.baf file within the MSMS folder for each protein) in Compass left click and drag the part of the chromatogram that isn't crap (from around 1min to around 18min) Find->compounds-AutoMS(n) Deconvolute - Mass spectra File - export that section as compounds, which will save as .mgf

Open Biotools open .mgf file Start Sequence Editor button on top toolbar file - open sequence paste sequence in, save as sqs Digest->Perform Digest new window opens, select pepsin, increase Partials to 15 change ppm to ~7ppm...max of 20ppm if hadn't been tuned in a while as of 230310, try 30ppm, bc malcolm made a script to get rid of duplicates later Digest button Once list populates, click to spectrum button (takes a while) error button pops up, click switch to floppy disk to save .mgf right click on blank box below Global peptide results and save to csv copy whole day folder to MQIET-2

ON MQIET-2 (aka MQIET-old) COMPUTER: open HDXaminer paste sequence (or click new and select txt or fasta file with sequence) in peptides, right click peptide sources and click add peptide source choose csv -will ask about columns in csv...make sure charge, RT, and score are all there. Check "add peptides directly box" add time points in analysis tab for zero time point (MSMS), mark as undeuterated

Analyze in HDXaminer