--pep-add-mod="Carbamidomethyl (C)" --pep-add-mod="Oxidation (M)" --pep-add-mod="Acetyl (N-term)" --pep-add-mod="GG (K)" --overwrite --new=D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\skyline-output\fragpipe_skylib.sky --full-scan-acquisition-method=DDA --import-search-cutoff-score=0.813512 --import-search-file=D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Aerabic_1\interact-PJ1314_Tamaki_7_Aerobic_Kgg_60min_DDA_timsHT_Slot2-28_1_2346.mod.pep.xml --import-search-file=D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Aerabic_1\interact-PJ1314_Tamaki_7_Aerobic_Kgg_60min_DDA_timsHT_Slot2-28_1_2346.pep.xml --import-search-file=D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Aerabic_2\interact-PJ1314_Tamaki_9_Aerobic_Kgg_60min_DDA_timsHT_Slot2-30_1_2350.mod.pep.xml --import-search-file=D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Aerabic_2\interact-PJ1314_Tamaki_9_Aerobic_Kgg_60min_DDA_timsHT_Slot2-30_1_2350.pep.xml --import-search-file=D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Aerabic_3\interact-PJ1314_Tamaki_11_Aerobic_Kgg_60min_DDA_timsHT_Slot2-32_1_2354.mod.pep.xml --import-search-file=D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Aerabic_3\interact-PJ1314_Tamaki_11_Aerobic_Kgg_60min_DDA_timsHT_Slot2-32_1_2354.pep.xml --import-search-file=D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Anaerabic_1\interact-PJ1314_Tamaki_8_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-29_1_2348.mod.pep.xml --import-search-file=D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Anaerabic_1\interact-PJ1314_Tamaki_8_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-29_1_2348.pep.xml --import-search-file=D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Anaerabic_2\interact-PJ1314_Tamaki_10_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-31_1_2352.mod.pep.xml --import-search-file=D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Anaerabic_2\interact-PJ1314_Tamaki_10_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-31_1_2352.pep.xml --import-search-file=D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Anaerabic_3\interact-PJ1314_Tamaki_12_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-33_1_2356.mod.pep.xml --import-search-file=D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Anaerabic_3\interact-PJ1314_Tamaki_12_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-33_1_2356.pep.xml --pep-max-missed-cleavages=2 --pep-min-length=7 --pep-max-length=50 --pep-exclude-nterminal-aas=0 --tran-precursor-ion-charges="2,3,4,5,6" --tran-product-ion-charges="1,2" --tran-product-ion-types="y,b,p" --tran-product-start-ion="ion 3" --tran-product-end-ion="last ion" --tran-product-clear-special-ions --library-match-tolerance=10.0ppm --library-product-ions=12 --library-min-product-ions=1 --library-pick-product-ions=filter --full-scan-precursor-analyzer=centroided --full-scan-precursor-isotopes=Count --full-scan-precursor-threshold=3 --full-scan-product-analyzer=centroided --full-scan-precursor-res=10.0 --full-scan-product-res=10.0 --full-scan-rt-filter=ms2_ids --full-scan-rt-filter-tolerance=2 --instrument-min-mz=50 --instrument-max-mz=2000 --full-scan-precursor-isotopes=Count --import-file=D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\PJ1314_Tamaki_10_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-31_1_2352.d --import-file=D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\PJ1314_Tamaki_11_Aerobic_Kgg_60min_DDA_timsHT_Slot2-32_1_2354.d --import-file=D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\PJ1314_Tamaki_12_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-33_1_2356.d --import-file=D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\PJ1314_Tamaki_7_Aerobic_Kgg_60min_DDA_timsHT_Slot2-28_1_2346.d --import-file=D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\PJ1314_Tamaki_8_Anaerobic_Kgg_60min_DDA_timsHT_Slot2-29_1_2348.d --import-file=D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\PJ1314_Tamaki_9_Aerobic_Kgg_60min_DDA_timsHT_Slot2-30_1_2350.d --import-search-exclude-library-sources --import-fasta=D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Aerabic_1\protein.fas --import-fasta=D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Aerabic_2\protein.fas --import-fasta=D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Aerabic_3\protein.fas --import-fasta=D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Anaerabic_1\protein.fas --import-fasta=D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Anaerabic_2\protein.fas --import-fasta=D:\timsTOF_HT\PJ1314_Tamaki_Kgg_DDA\result\Anaerabic_3\protein.fas --associate-proteins-shared-peptides=DuplicatedBetweenProteins 