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Peng Lab

Welcome to the lab of Junmin Peng, PhD

A software program for mass spectrometry-based peptide identification


JUMP (Jumbo Mass Spectrometry-based Proteomics Tool) is a new hybrid database search algorithm that generates amino acid tags and ranks peptide spectrum matches by the tags and pattern matching. JUMP can use all potential sequence tags, as short as only one amino acid, in database search. Thus JUMP has high sensitivity and specificity to differentiate true matches from false matches. The program also provides additional features, such as (i) identification of co-eluted peptides from mixture MS/MS spectra, and (ii) assignment of modification sites by tags. The current version is optimized for the analysis of high resolution MS/MS spectra. The program is written in perl and is designed for high performance parallel computing systems.

Download JUMP

JUMP is free software. The source code can be downloaded here (updated to version 1.2.5 on Oct. 1, 2016) and used according to the terms of the GNU General Public License (GPL), version 2 or later. The parameter file can be downloaded here. For more details, see the README file inside the distribution.

Two sample data sets can be downloaded: data set 1 for regular identification and data set 2 for post-translational modifications. Two large-scale data sets are also available for testing: data set 3 for regular identification and data set 4 for post-translational modifications. A JUMP sample database (database.tar.gz) can be downloaded here.


The basic usage of JUMP is simple. To run the JUMP software, Please use the following command:

perl /home/xxxx/JUMP/jump.pl -p <JUMP parameter file> <MS/MS data file(s) with .mzXML>

-p <file> specifies a JUMP parameter file;
<MS/MS data file(s)> specifies one or multiple MS/MS data file(s).

An example parameter file is provided in the software package.

MS/MS data file is mzXML file. The mzXML file is converted from .RAW file by various programs, such as ReAdW or msconvert. When using msconvert, please select 32-bit for the option of "Binary encoding precision" and unselect the option of "use zlib compression".


Your computer system must meet these minimum requirements to run jump.

System Requirements
  • Run on a cluster system
    • Ø SGE or LSF job management system
    • Ø 32 GB memory on each node
  • Run on a single server
    • Ø 32 GB memory
    • Ø 2 GHz CPU processors with a minimum of 4 cores


Please contact Xusheng Wang and Junmin Peng for software support.