MSFragger is an ultrafast database search tool for peptide identification in mass spectrometry-based proteomics. It has demonstrated excellent performance across a wide range of datasets and applications. MSFragger is suitable for standard shotgun proteomics analyses as well as large datasets (including timsTOF PASEF data), enzyme unconstrained searches (e.g. peptidome), ‘open’ database searches (i.e. precursor mass tolerance set to hundreds of Daltons) for identification of modified peptides, and glycopeptide identification (N-linked and O-linked) with MSFragger Glyco mode.

Reference:

• Kong, Andy T., et al. "MSFragger: ultrafast and comprehensive peptide identification in mass spectrometry–based proteomics." Nature methods 14.5 (2017): 513-520.

• msfragger Main Site

• Module Name: msfragger (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
  • MSFRAGGER_HOME
  • MSFRAGGER_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 msfragger
[+] Loading msfragger  3.1.1  on cn0852
[+] Loading java 12.0.1  ...

[user@cn0852 ~]$ java -jar $MSFRAGGER_JAR -h | head
Usage:
        To perform a search either:
                1) java -jar MSFragger.jar  
                To generate default parameter files use --config flag. E.g. "java -jar MSFragger.jar --config"
        Or:
                2) java -jar MSFragger.jar  
Options:
--num_threads                        # Number of CPU threads to use, should be set to the
                                              # number of logical processors; A value of 0
                                              # (auto-detect) will cause MSFragger to use the

[user@cn0852 ~]$ java -Xmx16g -jar $MSFRAGGER_JAR --num_threads=8 params.conf raw.d
MSFragger version MSFragger-3.1.1
Batmass-IO version 1.19.5
timsdata library version timsdata-2-7-0
(c) University of Michigan
RawFileReader reading tool. Copyright (c) 2016 by Thermo Fisher Scientific, Inc. All rights reserved.
System OS: Linux, Architecture: amd64
Java Info: 12.0.1, Java HotSpot(TM) 64-Bit Server VM, Oracle Corporation
JVM started with 16 GB memory
[snip...]

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

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

java -Xmx${SLURM_MEM_PER_NODE}m -jar $MSFRAGGER_JAR --num_threads=${SLURM_CPUS_PER_TASK} params.conf raw.d

Submit this job using the Slurm sbatch command.

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

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

java -Xmx${SLURM_MEM_PER_NODE}m -jar $MSFRAGGER_JAR --num_threads=${SLURM_CPUS_PER_TASK} params.conf raw1.d
java -Xmx${SLURM_MEM_PER_NODE}m -jar $MSFRAGGER_JAR --num_threads=${SLURM_CPUS_PER_TASK} params.conf raw2.d
java -Xmx${SLURM_MEM_PER_NODE}m -jar $MSFRAGGER_JAR --num_threads=${SLURM_CPUS_PER_TASK} params.conf raw3.d
java -Xmx${SLURM_MEM_PER_NODE}m -jar $MSFRAGGER_JAR --num_threads=${SLURM_CPUS_PER_TASK} params.conf raw4.d

Submit this job using the swarm command.

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