#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\3.0.12\bin\element.ini;
PATH_INI_MODIFICATION=C:\pFindStudio\pLink\3.0.12\bin\modification.ini;
PATH_INI_RESIDUE=C:\pFindStudio\pLink\3.0.12\bin\aa.ini;
PATH_INI_GLYCO=C:\pFindStudio\pLink\3.0.12\bin\glyco.ini;
PATH_INI_LINKER=C:\pFindStudio\pLink\3.0.12\bin\xlink.ini;

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

[MS1]
PATH_MS1=F:\20241227_500cell\raw\chai\3_3_500_FS_50.pf1|F:\20241227_500cell\raw\chai\3_3_500_FS_70.pf1|; 
EXTENSION_TEXT_MS1=pf1;

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

[Identification]
PATH_IDENTIFICATION_FILE=F:\20241227_500cell\\pLink_3_500\reports\171idmapping_2024_12_31_2025.01.01.filtered_regular_spectra.csv|F:\20241227_500cell\\pLink_3_500\reports\171idmapping_2024_12_31_2025.01.01.filtered_cross-linked_spectra.csv|F:\20241227_500cell\\pLink_3_500\reports\171idmapping_2024_12_31_2025.01.01.filtered_loop-linked_spectra.csv|F:\20241227_500cell\\pLink_3_500\reports\171idmapping_2024_12_31_2025.01.01.filtered_mono-linked_spectra.csv|;
TYPE_IDENTIFICATION_FILE=5;
THRESHOLD_FDR=0.01;

[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=F:\20241227_500cell\\pLink_3_500\pQuant;
FLAG_CREATE_NEW_FOLDER=0;
