#Dear user, the annotation for each parameter is after the semicolon. VIP: Very Important Parameter; Default settings are recommend for other parameters.

[INI]
PATH_INI_ELEMENT=C:\pFindStudio\pLink\2.3.11\bin\element.ini;
PATH_INI_MODIFICATION=C:\pFindStudio\pLink\2.3.11\bin\modification.ini;
PATH_INI_RESIDUE=C:\pFindStudio\pLink\2.3.11\bin\aa.ini;
PATH_INI_GLYCO=C:\pFindStudio\pLink\2.3.11\bin\glyco.ini;
PATH_INI_LINKER=C:\pFindStudio\pLink\2.3.11\bin\xlink.ini;

[Performance]
PATH_BIN=;
NUMBER_MAX_PSM_PER_BLOCK=30000;
TYPE_START=0;

[MS1]
PATH_MS1=E:\Ankita_MS\PRC-6481\H0648_2p_IonOpt11_PRC-6481_Weiland_TMT-DDA-1.pf1|E:\Ankita_MS\PRC-6481\H0650_2p_IonOpt11_PRC-6481_Weiland_TMT-DDA-2.pf1|E:\Ankita_MS\PRC-6481\H0652_2p_IonOpt11_PRC-6481_Weiland_TMT-DDA-3.pf1|E:\Ankita_MS\PRC-6481\H0654_2p_IonOpt11_PRC-6481_Weiland_TMT-DDA-4.pf1|E:\Ankita_MS\PRC-6481\H0656_2p_IonOpt11_PRC-6481_Weiland_TMT-DDA-5.pf1|E:\Ankita_MS\PRC-6481\H0658_2p_IonOpt11_PRC-6481_Weiland_TMT-DDA-6.pf1|E:\Ankita_MS\PRC-6481\H0660_2p_IonOpt11_PRC-6481_Weiland_TMT-DDA-7.pf1|E:\Ankita_MS\PRC-6481\H0662_2p_IonOpt11_PRC-6481_Weiland_TMT-DDA-8.pf1|E:\Ankita_MS\PRC-6481\H0664_2p_IonOpt11_PRC-6481_Weiland_TMT-DDA-9_less.pf1|; 
EXTENSION_TEXT_MS1=pf1;

[MS2]
PATH_MS2=;VIP
EXTENSION_TEXT_MS2=ms2;VIP, case sensitive.

[Identification]
PATH_IDENTIFICATION_FILE=E:\Ankita_MS\PRC-6481\\pLink_task_2024.08.08.18.07.45\reports\Pisum_staivum_UP001058974_2023_10_02_con_2024.08.20.filtered_regular_spectra.csv|E:\Ankita_MS\PRC-6481\\pLink_task_2024.08.08.18.07.45\reports\Pisum_staivum_UP001058974_2023_10_02_con_2024.08.20.filtered_cross-linked_spectra.csv|E:\Ankita_MS\PRC-6481\\pLink_task_2024.08.08.18.07.45\reports\Pisum_staivum_UP001058974_2023_10_02_con_2024.08.20.filtered_loop-linked_spectra.csv|E:\Ankita_MS\PRC-6481\\pLink_task_2024.08.08.18.07.45\reports\Pisum_staivum_UP001058974_2023_10_02_con_2024.08.20.filtered_mono-linked_spectra.csv|;
TYPE_IDENTIFICATION_FILE=5;
THRESHOLD_FDR=0.05;

[Quantitation]
TYPE_LABEL=0;Labeling: TYPE_LABEL=0;  LabelFree: TYPE_LABEL=1;
LL_INFO_LABEL=1|none|;
LL_ELEMENT_ENRICHMENT_CALIBRATION=none;
LL_FLAG_RATIO_CALIBRATION_18O=0;
LF_INFO_SAMPLE=;

[Evidence]
NUMBER_SCANS_HALF_CMTG=200;
PPM_FOR_CALIBRATION=0.0;
PPM_HALF_WIN_ACCURACY_PEAK=15.0;
NUMBER_HOLE_IN_CMTG=2;
TYPE_SAME_START_END_BETWEEN_EVIDENCE=0;
DALTON_ISOLATION_WIDTH=1.6;

[Inference]
TYPE_PEPTIDE_RATIO=0;
TYPE_PROTEIN_RATIO_CALCULATION=0;
TYPE_UNIQUE_PEPTIDE_ONLY=0;
THRESHOLD_SCORE_INTERFERENCE=1.0;
THRESHOLD_SCORE_INTENSITY=10000.0;
TYPE_GET_GROUP=1;
PATH_FASTA=;

[Export]
DIR_EXPORT=E:\Ankita_MS\PRC-6481\\pLink_task_2024.08.08.18.07.45\pQuant;
FLAG_CREATE_NEW_FOLDER=0;