Due to the size of the data files, they are not stored on GitHub. As well, the nature of sqlite files makes the result and the data exist in the same file (result only on the local copy of the data)
There are 4 data set that is intended for this program, but only one of them was actually in use as of 2021/01/01.
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The one that is in use is on the lab Google Drive. (Project > diaPASEF) Name:
20180911_TIMS2_12-2_AnBr_SA_diaPASEF_Test10_42eV_1_A1_01_2927_test_lib_overridegroupid.osw
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The other data set that is also on the Google Drive is not used because it does not have degenerate peptides
20190507_diaPASEF
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The other one does not have pyprophet scoring and has an empty feature_ms2 table (so running pyprophet is not possible) and IDPicker uses the q-value of the peptides which comes from pyprophet scoring.
20180911_TIMS2_12-2_AnBr_SA_diaPASEF_Test10_42eV_1_A1_01_2927_test_lib_hela_maxlib.osw
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The last data set is at graham cluster /project/6011811/frankmak/tims/Mar2018_helaBenchmark/data/openswath/ProteinIsoform/merged.osw
Update 2022/09/26
Since 1 has problems with epifany, I use another set of data (5 and 6)
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This is the dataset using swissprot database Top two are the same, just one in tsv and one in osw, most of the time, I only used the osw one.
projects/def-hroest/data/diaPASEFManuscriptOutput/merged_-1.osw
projects/def-hroest/data/diaPASEFManuscriptOutput/merged_-1.tsv
projects/def-hroest/data/diaPASEFManuscriptOutput/pyprophet_export.tsv
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This is the dataset using uniprot/trembl database
projects/def-hroest/data/josh_kai_2022/2021-12-23-proteinIsoformRslts.osw
projects/def-hroest/data/josh_kai_2022/peptide.tsv
peptide.tsv is one of the output files from msfragger, which is needed for adding non-razor protein.
(Project > kairen_september2022) I have also uploaded 5 and 6 to google drive.
4 is in (Project > diaPASEF)