# JUMP quantification parameter file (Version: 1.13.1, Date: 05/01/2020)
# Input:  ID.txt or IDmod.txt
idtxt = /home/user/sum_human_TMT11/ID.txt
id_all_prot_quan = 0
# 0 = skip the generation of a pubilcation table combining whole proteome and phosphopeptides
# otherwise, put the full path of 'id_all_prot_quan.xlsx' file after whole proteome quantification analysis
save_dir = human_TMT11				# name of the directory for JUMPq results (prefix "quan-" will be added)
ppi_filter = 50					# precursor peak intensity percentage threshold

# Minimum intensity-based filtering of PSM(s)
# Multiple filters can be used
# e.g. min_intensity_method = 1, 4      -> minimum intensity and median intensity of PSM are evaluated
#      min_intensity_value = 1000, 5000 -> intensity threshold for each filtering method
min_intensity_method = 1, 4			# 0 = no use of the filter, 1 = minimum, 2 = maximum, 3 = mean, 4 = median
min_intensity_value = 1000, 5000		# Minimum intensity threshold
# Minimum intensity-based filtering of PSM(s) used for summarizing a protein
# Multiple filters can be used as above
min_intensity_method_1_2_psm = 1, 4		# 0 = no use of the filter, 1 = minimum, 2 = maximum, 3 = mean, 4 = median
min_intensity_value_1_2_psm = 2000, 10000	# Minimum intensity threshold

# Impurity correction parameters
impurity_correction = 1				# 1 = Yes; 0 = No; if only a part of reporters are used, it should be set to 0
impurity_matrix = /home/user/JUMP_v1.13.1/JUMPq/TMT11.ini	# impurity table for correction

# Loading-bias correction is generally required to remove systematic biases of mass spectrometry data
loading_bias_correction = 1			# 1 = Yes; 0 = No;
loading_bias_correction_method = 1		# 1 = mean; 2 = median;
SNratio_for_correction = 10			# define the minimal signal (SN ratio) for the correction
percentage_trimmed = 25				# percentage of most variable intensities to be trimmed for the correction

# Interference removal in TMT-quantification
interference_removal = 0			# 1 = Yes; 0 = No;

# Names of TMT reporters used
# TMT reporter ion masses are as follows
# TMT11 reporters (126.127726;127.124761;127.131081;128.128116;128.134436;129.131471;129.137790;130.134825;130.141145;131.138180;131.1445001)
# TMT10 reporters (126.127726;127.124761;127.131081;128.128116;128.134436;129.131471;129.137790;130.134825;130.141145;131.138180)
# TMT8 reporters (126.127726;127.124761;127.131081;128.134436;129.131471;129.137790;130.141145;131.138180)
# TMT6 reporters (126.127726;127.124761;128.134436;129.131471;130.141145;131.138180)
tmt_reporters_used = sig126; sig127N; sig127C; sig128N; sig128C; sig129N; sig129C; sig130N; sig130C; sig131N; sig131C
tmt_peak_extraction_second_sd = 8		# SD used for identification of reporter ions
tmt_peak_extraction_method = 1			# 1 = strongest intensity; 2 = closest to expected report ion mass

# Sample labels corresponding the reporters used
# Do NOT use any special characters other than underscore, "_" 
sig126 = S1
sig127N = S2
sig127C = S3
sig128N = S4
sig128C = S5
sig129N = S6
sig129C = S7
sig130N = S8
sig130C = S9
sig131N = S10
sig131C = S11

# The program allows multiple comparisons (e.g. comparison_groups_comp1, do not change the prefix "comparison_groups_")
# e.g. sample labels are S1, S2, S3, S4, S5 : S6, S7, S8, S9 and S10 for all TMT10 reporters (sorted by mass)
#      comparison_groups_twoGroups = S1, S2, S3, S4, S5 : S6, S7, S8, S9, S10
#      comparison_groups_threeGroups = S1, S2, S3 : S4, S5, S6, S7 : S8, S9, S10
comparison_analysis = 0							# 1 = Yes; 0 = No; for group comparison
comparison_groups_twoGroups = S1, S2, S3, S4, S5 : S6, S7, S8, S9, S10