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A label free quantification tool.
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What is IonQuant?

IonQuant is a label free quantification tool for TIMS-TOF PASEF data.

Why choose IonQuant?

  1. Fast
  2. Accurate

System requirements

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



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

Command line

Download stanalone JAR from here.

java -jar IonQuant.jar <options> <.d/.mzML/.mzXML/.pepXML/_quant.csv files>
        --mztol <float>        # MS1 tolerance in PPM. Optional. Default: 10.0
        --imtol <float>        # 1/K0 tolerance. Optional. Default: 0.05
        --rttol <float>        # Retention time tolerance. Unit: min. Optional. Default: 0.4
        --plot 0/1             # Plot traced features or not. Optional. Default: 0
        --psm <string>         # Path to Philosopher's psm.tsv. Optional.
        --multidir <string>    # Output dir for the multi experimental result. Optional.
        --minfreq <float>      # Minimum required frequency of a ion being selected for protein quantification. Optional. Default: 0.5
        --tp <int>             # Number of ions used in quantifying each protein. If 0, using all ions. Optional. Default: 0
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