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JUMP (Jumbo Mass Spectrometry-based Proteomics Tool) is a 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 a single machine (e.g. PC) as well as high-performance parallel computing systems.
JUMP is free software. The source code can be downloaded here (and also available at our Github repository) and used according to the terms of the GNU General Public License (GPL), version 2 or later.
Two sample datasets (mzXML files of TMT 11-plex and TMTpro (16-plex)) and parameter files for database search, filtering of identification and TMT-quantification can be downloaded here. Also database files for the sample datasets can be downloaded here.
In addition to the above sample files, common contaminant sequences (fasta format) and knowledge-based tables (text format) which supplement the generation of databases are available here.
Please visit our Github repository for the installation instruction and manual. JUMP is designed to work under Unix-like operating system, e.g. Linux. If you are a Windows 10 user, you can install and use JUMP through Windows Subsystem for Linux (WSL). You can install JUMP in a high-performance computing system such as a cluster with SGE, Slurm, LSF, etc. when appropriately configured.
JUMP accepts mzXML file(s) as input. The mzXML file can be converted from .RAW file by various programs, such as ReAdW (https://github.com/PedrioliLab/ReAdW) or msconvert (http://proteowizard.sourceforge.net/tools.shtml). When using msconvert, please select 32-bit for the option of "Binary encoding precision" and unselect the option of "use zlib compression".
Please contact Junmin Peng, Xusheng Wang or Ji-Hoon Cho for software support.