What is IonQuant?

IonQuant is a label free quantification tool for timsTOF PASEF DDA and non-timsTOF (e.g., Orbitrap) data.

Why choose IonQuant?

1. Fast
2. Accurate

System requirements

1. Java 1.8+.
2. ext folder from MSFragger.

Download

The latest IonQuant stanalone JAR can be downloaded from here.

Usage

GUI

1. Download FragPipe from here.
2. Follow the tutorial.

Command line

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: 0
        --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 directory 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: 2
        --proteinquant 1/2     # Protein quantification algorithm. 1 = top-N, 2 = MaxLFQ. Default: 1
        --minfreq <float>      # Minimum required frequency of an 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

Note: in some high-performance computing (HPC) servers, you may need to explicitly specify --threads <integer> in case that Java cannot correctly get the logical core number.

Publication (preprint)

Fast quantitative analysis of timsTOF PASEF data with MSFragger and IonQuant