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prot_quan_lysine_est_batch2.params
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prot_quan_lysine_est_batch2.params
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# SILAC-TMT data processing parameter file V1.0.0 and The Free Lysine Estimation Parameter file V1.0.0
# JUMPsilactmt V1.0.0
# Author : Surendhar Chepyala and Abhijit Dasgupta
# Last Modified by Abhijit on date:02-06-2024
#Input files
# input the PSM quantification data file if you already have
#psm_quant = /home/adasgupt/quan_psm_impurity_corrected.txt
# when PSM quantification data is available, comment the idtxt file; this save time of quantification
idtxt = /home/adasgupt/batch_id_results/batch2/sum_out/ID.txt
id_res_folder = /home/adasgupt/batch_id_results/batch1/sum_out/publications
output_folder_protein = Protein_quan_Batch2 #if output_folder already exists, output folder named with suffix "_1" or "_2" or so on will be generated automatically in the same folder where the program excuted;
output_folder_lysine = Batch2_freeLys_estimation #if output_folder already exists, output folder named with suffix "_1" or "_2" or so on will be generated automatically in the same folder where the program excuted;
# TMT reporter information
tmt_reporters_used = sig126; sig127N; sig127C; sig128N; sig128C; sig129N; sig129C; sig130N; sig130C; sig131N; sig131C; sig132N; sig132C; sig133N; sig133C; sig134N
# mz shift correction after 1st round of extraction
mz_shift_correction = 1 # 1 = Yes; 0 = No; Calculate m/z shift of all MS2 scans and correct in second round
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; only if multiple peaks detected within mass tolerance
# 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/adasgupt/TMT16.ini # impurity table for correction
# sample information in for each sets of pulse experiment
set_1 = sig127N, sig127C, sig128N, sig128C, sig129N
set_2 = sig129C, sig130N, sig130C, sig131N, sig131C
set_3 = sig132N, sig132C, sig133N, sig133C, sig134N
# Loading-bias correction by non-Lys PSMs 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;
percentage_trimmed = 25 # total percentage of most variable intensities to be trimmed
SNratio_for_correction = 10 # define the minimal signal (SN ratio) for the correction
# Noise removal to reduce ratio compression in TMT
noise_removal_in_lightPSM = 1 # Noise correction by fully heavy reporters ; 1 = Yes; 0 = No;
fully_heavy_reporters = sig126
noise_removal_in_heavyPSM = 1 # Noise correction by fully light reporters ; 1 = Yes; 0 = No;
fully_light_reporters = sig127N; sig129C; sig132N
NoiseThreshold_completely_labeled = 1
NoiseThreshold_completely_unlabeled = 1
nc_level = 0.75 ## Noise correction level ; may vary from 0.1 to 0.95; It prevents overcorrection
# Peptide/Protein quantification by summarizing the light PSMs
PSM_selection = 10 # 5 = select top 5 PSMs; if using all PSMs, enter a big number e.g. 100000
# Normalization of light% by protein amount in each channel obtained by non-Lys PSMs
normalization = 1 # 1 = Normalize with MS1 intensity ratio (default); 2 = Normalize each channel in eavery PSM obtained using protein amount obtained by non-Lys PSMs;
mass_tolerance_ms1 = 10 # m Tolerance for MS1 isotopic peaks
# when available, input the ms1 data quantification file and prot_absQuna_byNonKpsm
#ms1_quant = /home/adasgupt/ms1quan.txt
#pepIsoDist = /home/adasgupt/pepIsoDist_batch2.txt
#prot_absQuna_byNonKpsm = /home/adasgupt/prot_absQuna_byNonKpsm_batch2.txt
# when available, input the di-Lys peptide isotopic distribution
#pepIsoDist = /home/adasgupt/pepIsoDist_batch2.txt
trim_peptide_oulier_percent = 10 # percenatge of outliers trimmed at peptide Lys%
max_dist_bet_mixed_heavy_scan = 100 # maximum distance between mixed and heavy pepetide MS2 scan#
# Outlier removal
standard_outlier = 1 # remove outlier with generalized ESD and Dixson Q-test;1 = Yes; 0 = No;
summarize_protein_from_raw_data = 1 # 1 = PSM to peptide to protein (default), 2 = PSM to protein
outlier_removal_stratagy = 2 # 1 = entire PSM is removed if ant channel is identified as an outlier (default); 2 = only outlier data is removed and other channels of PSM are used for summarization
free_lysine_estimation = 1 # 1= yes; 0= no;
########################################################
# Parameters for the isotopic distribution calculation #
########################################################
#minimum isotopic match require to select reliable MS1 level quantification
nMatchedPeaksThreshold = 2
isotope_cutoff = 1e-2 # Intensity cutoff to filter the isotopic peaks
mass_tolerance = 10 # m Tolerance for merging close isotopic peaks
ms1_peak_extraction_method = 1 # 1 = strongest intensity; 2 = closest to expected peptide mass; only if multiple peaks detected within mass tolerance
weighted_isotopic_ peaks = 1 # 1 = merge isotopic peaks within mass_tolerance using weighted average of intensity; = 0 otherwise
method_merging_isotopic_peaks = 1 # Method of merging isotopic peaks within a tolerance, 1 = weighted average, 2 = strongest peak
strong_isotopic_peaks = 0 # 1 = select strongest isotopic peaks within mass_tolerance instead of merging isotopic peaks based on weighted average of intensity; = 0 otherwise
Tracer_1 = 13C # Denoted by 13C or 15N
Tracer_1_purity = 1 #0.99
Tracer_2 = 15N
Tracer_2_purity = 1
PTM_mono_oxidation = @ # Optional parameter, oxidation on methionine, M@
PTM_phosphorylation = # # Optional parameter, phosphorylation on STY with #, %, *
######## END of Parameter file #################