PXD028038

PXD028038 is an original dataset announced via ProteomeXchange.

Title	Mass Dynamics 1.0: A streamlined, web-based environment for analyzing, sharing and integrating Label-Free Data
Description	Label Free Quantification (LFQ) of shotgun proteomics data is a popular and robust method for the characterization of relative protein abundance between samples. Many analytical pipelines exist for the automation of this analysis and some tools exist for the subsequent representation and inspection of the results of these pipelines. Mass Dynamics 1.0 (MD 1.0) is a web-based analysis environment that can analyse and visualize LFQ data produced by software such as MaxQuant. Unlike other tools, MD 1.0 utilizes cloud-based architecture to enable researchers to store their data, enabling researchers to not only automatically process and visualize their LFQ data but annotate and share their findings with collaborators and, if chosen, to easily publish results to the community. With a view toward increased reproducibility and standardisation in proteomics data analysis and streamlining collaboration between researchers, MD 1.0 requires minimal parameter choices and automatically generates quality control reports to verify experiment integrity. Here, we demonstrate that MD 1.0 provides reliable results for protein expression quantification, emulating Perseus on benchmark datasets over a wide dynamic range.
HostingRepository	PRIDE
AnnounceDate	2022-04-13
AnnouncementXML	Submission_2022-04-13_03:43:50.037.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Joseph Bloom
SpeciesList	scientific name: Escherichia coli; NCBI TaxID: 562; scientific name: Homo sapiens (Human); NCBI TaxID: 9606; scientific name: Saccharomyces cerevisiae (Baker's yeast); NCBI TaxID: 4932;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive; LTQ Orbitrap

Revision	Datetime	Status	ChangeLog Entry
0	2021-08-19 21:42:22	ID requested
⏵ 1	2022-04-13 03:43:50	announced

Bloom J, Triantafyllidis A, Quaglieri A, Burton Ngov P, Infusini G, Webb A, Mass Dynamics 1.0: A Streamlined, Web-Based Environment for Analyzing, Sharing, and Integrating Label-Free Data. J Proteome Res, 20(11):5180-5188(2021) [pubmed]

submitter keyword: MaxQuant, benchmarking, label-free quantification, web-based software tool, automated data analysis

Andrew Webb
contact affiliation	The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia, Department of Medical Biology, University of Melbourne, Melbourne, Victoria 3010, Australia
contact email	webb@wehi.edu.au
lab head
Joseph Bloom
contact affiliation	MassDynamics
contact email	joseph@massdynamics.com
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/2022/04/PXD028038

PRIDE project URI

• PRIDE
  1. PXD028038
     1. Label: PRIDE project
     2. Name: Mass Dynamics 1.0: A streamlined, web-based environment for analyzing, sharing and integrating Label-Free Data