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Protocols

ExMS specifications

Information


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

Versioning


No version available

Maintainer


  • person_outline Zhong-Yuan Kan <>

Publication for ExMS

ExMS citations

 (5)
library_books

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

2018
PMCID: 5829251
PMID: 29487285
DOI: 10.1038/s41467-018-03234-8

[…] 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 […]

library_books

Non canonical reader modules of BAZ1A promote recovery from DNA damage

2017
PMCID: 5636791
PMID: 29021563
DOI: 10.1038/s41467-017-00866-0

[…] 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 […]

library_books

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

2017
PMCID: 5472775
PMID: 28598437
DOI: 10.1038/ncomms15775

[…] scientific)., 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 […]

library_books

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

2015
PMCID: 4477167
PMID: 26157802
DOI: 10.3389/fmolb.2015.00033

[…] 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 […]

library_books

DAXX co folds with H3.3/H4 using high local stability conferred by the H3.3 variant recognition residues

2014
PMCID: 3985662
PMID: 24493739
DOI: 10.1093/nar/gku090

[…] v3.3.1) software program (thermo fisher scientific) was used to identify the likely sequence of the parent peptides using non-deuterated samples via tandem ms., matlab-based ms data analysis tool—exms—was used for data processing (). briefly, the exms program searches raw ms data, identifies individual isotopic peaks/envelopes from a list of ms/ms peptides obtained from sequest search […]


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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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