add Claire's THP LOPIT data

[lmsimp]

Add peptide and protein level triplicates for both the LOPIT and timecouse

[lmsimp]

I have lots of data to contribute these are the following (all will be spreadsheets in the SI of manuscript too) -

Timecouse

• 3 reps of LPS stimulation (containing 6 time points 0, 2, 4, 6, 12, 24 hours)
• Protein and PSM data

LOPIT data

• 3 replicates per condition (0 hour and 12 hour THP stimulation) = 6 protein level datasets (where each replicate contains 2 sets)
• 2 combined protein level datasets of the above (one per condition)

LOPIT PSM I wish to add the PSM level data. This is 12 LOPIT datasets. 6 per condition (2 sets per rep, and 3 reps per condition). Would it be most useful to add just as it is and let those who are interested do their own filtering/imputation/combining etc? @lgatto @ococrook

[lgatto]

PSM is definitely great, but I would also suggest to either (1) provide the protein-level data, as was used in the paper, and on which the conclusions are based and/or (2) the exact code to generate the protein-level data.

[lmsimp]

Sorry if above comment wasn’t clear. Yes, have already added all protein level data in the branch (not yet pushed) but my question is whether I should provide PSM (1) as it is was given to me unprocessed or (2) processed/imputation etc. I thought (1) is best as this is then available for testing algorithms etc?

[lgatto]

Sure, please also add the PTM data.

[ococrook]

I assume @lgatto means PSM data unless I missed something. I theink the "raw" PSM data would be best with a script in inst on how it was processed. What do you think @lmsimp ?

[lmsimp]

Hey @ococrook yes I have assumed @lgatto meant PSM and that is what will be added when I've fixed the bugs in this PR - so lots of PSM datasets coming your way! :-)

[lmsimp]

merged in #62