new IonQuant beta version 1.2 incl. MBR
Email from IonQuant developers:
We would like to send our internal version to you for testing. You can download them from https://umich.box.com/s/6ter5g5gjqh4a39p2l0pkhf1x2bii32n. Please feel free to contact us if there is any question, error, or suggestion. You can use it inside FragPipe (the new internal version included in the above link) or the standalone jar with the following flags:
Usage:
java -jar IonQuant.jar <options> <.d/.mzML/.mzXML/.raw/.pepXML/_quant.csv files>
Options:
--threads <integer> # Number of threads. 0 = all logical cores. Default: 0
--mztol <float> # MS1 tolerance in PPM. Default: 10.0
--imtol <float> # 1/K0 tolerance. Default: 0.05
--rttol <float> # Retention time tolerance. Unit: min. Default: 0.4
--seedmz 0/1 # M/Z used as the start point of tracing. 0 = calculated M/Z; 1 = observed M/Z. Default:
--minisotopes 1/2/3 # Required isotopes in feature extraction. Default: 2
--psm <string> # Path to Philosopher's psm.tsv. One --psm indicates one psm.tsv and can have multiple --psm. Optional. Default: <blank>
--multidir <string> # Output dir for the multi experimental result. Optional. Default: <blank>
--normalization 0/1 # Normalize the intensities across all runs. Default: 1
--minions <integer> # Minimum ions required in quantifying proteins. Default: 1
--minfreq <float> # Minimum required frequency of a ion being selected for protein quantification. Default: 0.5
--tp <int> # Number of ions used in quantifying each protein. If 0, using all ions. Default: 3
--mbr 0/1 # Perform match-between-runs. Default: 0
--mbrrttol <float> # Retention time tolerance used in match-between-runs. Unit: min. Default: 1.0
--mbrimtol <float> # 1/K0 tolerance used in match-between-runs. Default: 0.05
--mbrtoprun <integer> # Maximum number of matched runs in mapping one run. Default: 3
--mbrmincorr <float> # Minimum required correlation coefficient in matching two runs. Default: 0.5
--ionmobility 0/1 # The data has ion mobility information or not (for conventional LC-MS data). Default: 0
--ionfdr <float> # Transferred ion false discovery rate threshold. Default: 0.01
--peptidefdr <float> # Transferred peptide false discovery rate threshold. Default: 0.01
--proteinfdr <float> # Transferred protein false discovery rate threshold. Default: 0.01
--label <string> # A pair of light and heavy labelling mass. Can have multiple --label for multiple pairs of light and heavy labelling, but one peptide can only have one of these pairs. Format: <light mass>;<heavy mass>. Optional. Default: <blank>
--requantify 0/1 # Re-quantify unidentified feature based on identified feature. Only activate when --label is not empty. Default: 0
Our current IonQuant jar is 1.0:
tobiasko@fgcz-r-033:/usr/local/nesvilab$ ls -la
total 79484
drwxr-sr-x 4 cpanse staff 4096 Apr 1 20:46 .
drwxrwsr-x 16 root staff 4096 Apr 1 20:34 ..
-rw-r--r-- 1 cpanse staff 8819164 Apr 1 20:40 CrystalC-1.1.0.jar
drwxr-sr-x 4 cpanse SG_Employees 4096 Feb 19 15:50 ext
-rw-r--r-- 1 cpanse staff 37648960 Apr 1 20:40 IonQuant-1.0.0.jar
-rw-r--r-- 1 cpanse staff 34901264 Apr 1 20:40 MSFragger-2.3.jar
drwxr-sr-x 3 cpanse staff 4096 Apr 1 20:39 philosopher-3.2.3
critical params for testing are:
--mbr 0/1 # Perform match-between-runs. Default: 0
--mbrrttol <float> # Retention time tolerance used in match-between-runs. Unit: min. Default: 1.0
--mbrimtol <float> # 1/K0 tolerance used in match-between-runs. Default: 0.05
--mbrtoprun <integer> # Maximum number of matched runs in mapping one run. Default: 3
--mbrmincorr <float> # Minimum required correlation coefficient in matching two runs. Default: 0.5
--ionmobility 0/1 # The data has ion mobility information or not (for conventional LC-MS data). Default: 0 (I would use 1)
These need to be available in the bf fragpipe app.