PXD036813

PXD036813 is an original dataset announced via ProteomeXchange.

Title	The Deuterium Calculator HDX-MS Data Analysis
Description	Hydrogen-deuterium exchange mass spectrometry (HDX-MS) is a powerful protein footprinting technique to study protein dynamics and binding; however, HDX-MS data analysis is often challenging and time consuming. Moreover, the HDX community is expanding to investigate multi-protein and highly complex protein systems such as cell lysates which further complicates data analysis. Thus, a simple and easy-to-use open source software package designed to analyze large and highly complex protein systems is needed. In this vein, we have developed The Deuterium Calculator, a Python-based software package for HDX-MS data analysis. The Deuterium Calculator is capable of differential and nondifferential HDX-MS analysis, produces standardized data files according to the recommendations put forth by the International Conference on Hydrogen-Exchange Mass Spectrometry (IC-HDX) to increase transparency in data analysis, and generates Woods’ plots for statistical analysis and data visualization. This standard output can be used to perform further analysis on HDX such as determination of labeling time dependent deuteration and for the study of protein folding kinetics or differential uptake. Moreover, the Deuterium Calculator is capable of analyzing large HDX-MS datasets (e.g., LC-HDX-MS from complex samples such as cell lysates) to determine the extent of deuteration on individual peptides from numerous proteins, perform differential analysis under varying experimental conditions, and time-dependent deuterium exchange. The Deuterium Calculator is freely available for download at https://github.com/OUWuLab/TheDeuteriumCalculator.git.
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_08:02:37.280.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Kellye Cupp-Sutton
SpeciesList	scientific name: Escherichia coli; NCBI TaxID: 562;
ModificationList	No PTMs are included in the dataset
Instrument	LTQ Orbitrap Elite

Revision	Datetime	Status	ChangeLog Entry
0	2022-09-17 14:51:53	ID requested
1	2023-01-30 02:21:53	announced
⏵ 2	2023-11-14 08:02:39	announced	2023-11-14: Updated project metadata.

Cupp-Sutton KA, Welborn T, Fang M, Langford JB, Wang Z, Smith K, Wu S, The Deuterium Calculator: An Open-Source Tool for Hydrogen-Deuterium Exchange Mass Spectrometry Analysis. J Proteome Res, 22(2):532-538(2023) [pubmed]

submitter keyword: Hydrogen-deuterium exchange mass spectrometry, subzero temperature UPLC, HDX data analysis software, HDX-MS

Si Wu
contact affiliation	University of Oklahoma
contact email	si.wu@ou.edu
lab head
Kellye Cupp-Sutton
contact affiliation	University of Oklahoma
contact email	kellyecuppsutton@ou.edu
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2023/01/PXD036813

PRIDE project URI

• PRIDE
  1. PXD036813
     1. Label: PRIDE project
     2. Name: The Deuterium Calculator HDX-MS Data Analysis