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ExMS specifications


Unique identifier OMICS_06888
Name ExMS
Software type Package/Module
Interface Command line interface, Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages MATLAB
Computer skills Advanced
Stability Stable
Maintained Yes


No version available


  • person_outline Zhong-Yuan Kan

Publication for ExMS

ExMS citations


NAD+ analog reveals PARP 1 substrate blocking mechanism and allosteric communication from catalytic center to DNA binding domains

Nat Commun
PMCID: 5829251
PMID: 29487285
DOI: 10.1038/s41467-018-03234-8

[…] fic) with a peptide tolerance of 8 ppm and a fragment tolerance of 0.1 AMU. Deuterated samples were then analyzed on an Exactive Plus EMR-Orbritrap (Thermo Fisher Scientific). A MATLAB based program, ExMS was used for HXMS data processing. ExMS uses the list of MS/MS peptides found by the SEQUEST search, identifies individual isotopic peaks and peptide envelopes, and calculates centroid values of […]


Folding of maltose binding protein outside of and in GroEL

Proc Natl Acad Sci U S A
PMCID: 5776991
PMID: 29295923
DOI: 10.1073/pnas.1716168115

[…] de fragments, including 375 unique peptides (). We chose 92 that redundantly cover the entire length of the 370-residue MBP protein and could always be measured with high quality when analyzed by the ExMS program (). Examination of the many H/D-labeled peptides reveals the identity of folding intermediates and the folding rate, sequence of formation, stability, and dynamic properties of the protei […]


Non canonical reader modules of BAZ1A promote recovery from DNA damage

Nat Commun
PMCID: 5636791
PMID: 29021563
DOI: 10.1038/s41467-017-00866-0

[…] Peptides were identified using a combination of exact mass and MS/MS aided by Mascot algorithm search (Mascot Daemon V.2.3.2; Mascot Distiller V.2.4.2). Peptide deuterium levels were determined using EXMS and a script developed in-house. Complete peptide coverage was obtained for both uncomplexed and the DNA-bound BAZ1A-PHD protein, and peptides with identical sequence between the two samples (mat […]


Centromeres are maintained by fastening CENP A to DNA and directing an arginine anchor dependent nucleosome transition

Nat Commun
PMCID: 5472775
PMID: 28598437
DOI: 10.1038/ncomms15775

[…] The SEQUEST (Bioworks) software program was used to identify the likely sequence of parent peptides using non-deuterated samples via tandem MS. MATLAB-based MS data analysis tool, ExMS, was used for data processing. For all peptides found by SEQUEST, ExMS first analyses the non-deuterated sample to identify the peptide envelope centroid values as well as the chromatographic elu […]


Applications of hydrogen deuterium exchange (HDX) for the characterization of conformational dynamics in light activated photoreceptors

Front Mol Biosci
PMCID: 4477167
PMID: 26157802
DOI: 10.3389/fmolb.2015.00033

[…] luation of deuteration differences between different samples []. Hydra [] was the first solution capable of providing a full analysis workflow and a number of web server based programs followed [, ]. ExMS [] is a suite of MATLAB scripts which offer visualization for interactive parameterization. HDX-Workbench [] is geared toward high-resolution HDX-MS data and offers a comprehensive graphical inte […]


Both tails and the centromere targeting domain of CENP A are required for centromere establishment

PMCID: 4347640
PMID: 25713413
DOI: 10.1083/jcb.201412011
call_split See protocol

[…] entific). Nondeuterated samples were used to identify the likely sequence of the parent peptides in SEQUEST (Bioworks v3.3.1) software program (Thermo Fisher Scientific). The data were analyzed using ExMS program (), and the broad deprotection from HX reported for CENP-AS68Q–H4 is representative of results obtained in two independently performed experiments. […]


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ExMS institution(s)
Johnson Research Foundation, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA

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