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MZ_extractor

This program adds the intensities to the identification file from the mzML, reporting the ion isotopic distribution.

Usage:

python mz_extractor.py \
-i "tests/test1/msfragger/Jurkat_Fr3.tsv" \
-z "tests/test1/thermo_raw_parser/Jurkat_Fr3.mzML" \
-r "tests/test1/reporter_ion_isotopic.tsv" \
-o "tests/test1/mz_extractor"

python mz_extractor.py \
-i "tests/test1/msfragger/*.tsv" \
-z "tests/test1/thermo_raw_parser/*.mzML" \
-r "tests/test1/reporter_ion_isotopic.tsv" \
-o "tests/test1/add_quant"

Test the AnaDelVal patch

python mz_extractor.py \
-i "S:\U_Proteomica\UNIDAD\Softwares\jmrodriguezc\mz_extractor\tests\test2\RH_Heart_TMTHF_FR1WO_duplicate_SHIFTS_BestPSM_calibrated.tsv" \
-z "S:\U_Proteomica\UNIDAD\Softwares\jmrodriguezc\mz_extractor\tests\test2\RH_Heart_TMTHF_FR1WO_duplicate_SHIFTS_BestPSM_calibrated.mzML" \
-r "S:\U_Proteomica\UNIDAD\Softwares\jmrodriguezc\mz_extractor\tests\test2\XH338783_TMT10PLEX_noCORR.tsv" \
-o "S:\U_Proteomica\UNIDAD\Softwares\jmrodriguezc\mz_extractor\tests\test2" \
-p 10

-i "S:\U_Proteomica\UNIDAD\Softwares\jmrodriguezc\mz_extractor\tests\test2\RH_Heart_TMTHF_FR1WO_duplicate_SHIFTS_BestPSM_calibrated.tsv" -z "S:\U_Proteomica\UNIDAD\Softwares\jmrodriguezc\mz_extractor\tests\test2\RH_Heart_TMTHF_FR1WO_duplicate_SHIFTS_BestPSM_calibrated.mzML" -r "S:\U_Proteomica\UNIDAD\Softwares\jmrodriguezc\mz_extractor\tests\test2\XH338783_TMT10PLEX_noCORR.tsv" -o "S:\U_Proteomica\UNIDAD\Softwares\jmrodriguezc\mz_extractor\tests\test2" -p 10