IonQuant is a fast and comprehensive tool for MS1 precursor intensity-based quantification for timsTOF PASEF DDA and non-timsTOF (e.g., Orbitrap) data. It enables label-free quantification with false discovery (FDR) controlled match-between-runs (MBR). It can also be used for quantification in labelling-based experiments such as those involving SILAC, dimethyl, or similar labelling strategies. IonQuant is available as part of FragPipe (recommended option), but can also be run as a command-line tool.

Reference:

• Yu, Fengchao., et al. "Fast quantitative analysis of timsTOF PASEF data with MSFragger and IonQuant." Molecular & Cell Proteomics 19 (2020): 1575-1585.

• ionquant Main Site

• Module Name: ionquant (see the modules page for more information)
• Multithreaded application. Use --num_threads=N to specify the number of threads to run.
• Limit memory usage with the java heap size option -Xmx (e.g. -Xmx3700m for 3700 MB or -Xmx32g for 32 GB).
• This application can be executed at the command line or invoked through the fragpipe GUI frontend.
• Environment variables set
  • IONQUANT_HOME
  • IONQUANT_JAR

Allocate an interactive session and run the program.
Sample session (user input in bold):

[user@biowulf ~]$ sinteractive --cpus-per-task=8 --mem=16g
salloc.exe: Pending job allocation 4852341
salloc.exe: job 4852341 queued and waiting for resources
salloc.exe: job 4852341 has been allocated resources
salloc.exe: Granted job allocation 4852341
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn0852 are ready for job
srun: error: x11: no local DISPLAY defined, skipping

[user@cn0852 ~]$ module load ionquant
[+] Loading ionquant  1.8.0  on cn0852
[+] Loading java 12.0.1  ...

[user@cn0852 ~]$ java -jar $IONQUANT_JAR -h | head
IonQuant version IonQuant-1.8.0
Batmass-IO version 1.25.5
timsdata library version timsdata-2-7-0
(c) University of Michigan
System OS: Linux, Architecture: amd64
Java Info: 17.0.3.1, Java HotSpot(TM) 64-Bit Server VM, Oracle Corporation
JVM started with 2 GB memory
Usage:
        java -jar IonQuant.jar  --specdir  --psm  --psm ...
        OR

Create a batch input file (e.g. ionquant.sh). For example:

#!/bin/bash
set -e
module load ionquanti
cd /path/to/data/and/conf

java -Xmx${SLURM_MEM_PER_NODE}m -jar $IONQUANT_JAR --threads=${SLURM_CPUS_PER_TASK} --filelist <files>

Submit this job using the Slurm sbatch command.

sbatch [--cpus-per-task=#] [--mem=#] ionquant.sh

Create a swarmfile (e.g. ionquant.swarm). For example:

java -Xmx${SLURM_MEM_PER_NODE}m -jar $IONQUANT_JAR --num_threads=${SLURM_CPUS_PER_TASK} --filelist <files 1>
java -Xmx${SLURM_MEM_PER_NODE}m -jar $IONQUANT_JAR --num_threads=${SLURM_CPUS_PER_TASK} --filelist <files 2>
java -Xmx${SLURM_MEM_PER_NODE}m -jar $IONQUANT_JAR --num_threads=${SLURM_CPUS_PER_TASK} --filelist <files 3>
java -Xmx${SLURM_MEM_PER_NODE}m -jar $IONQUANT_JAR --num_threads=${SLURM_CPUS_PER_TASK} --filelist <files 4>

Submit this job using the swarm command.

swarm -f ionquant.swarm [-g #] [-t #] --module ionquant