PXD018408

PXD018408 is an original dataset announced via ProteomeXchange.

Dataset Summary

Title	Benchmarking and Best Practices for Quantitative Proteomics
Description	We use an integrated benchmarking approach to empirically establish guidelines for data acquisition, statistical approach, and replicate numbers for accurate quantification. We evaluated three workflows for protein- and peptide-level quantitative accuracy: data dependent acquisition (DDA), data independent acquisition (DIA), and chemical labeling via tandem mass tags (TMT). The former two datasets were generated in our lab, so we have published them here.
HostingRepository	MassIVE
AnnounceDate	2021-05-14
AnnouncementXML	Submission_2021-05-14_09:02:20.383.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Logan J Wright
SpeciesList	scientific name: Escherichia coli; common name: E. coli; NCBI TaxID: 562; scientific name: Homo sapiens; common name: human; NCBI TaxID: 9606;
ModificationList	Carbamidomethyl; Oxidation; Acetyl; Deamidated
Instrument	Q Exactive

Dataset History

Revision	Datetime	Status	ChangeLog Entry
0	2020-04-06 13:50:58	ID requested
1	2020-04-07 08:49:42	announced
⏵ 2	2021-05-14 09:02:21	announced	2021-05-14: Re-announcing after manual reversion to private dataset status

Publication List

Dowell JA, Wright LJ, Armstrong EA, Denu JM, Benchmarking Quantitative Performance in Label-Free Proteomics. ACS Omega, 6(4):2494-2504(2021) [pubmed]

Dowell JA, Wright LJ, Armstrong EA, Denu JM, Benchmarking Quantitative Performance in Label-Free Proteomics. ACS Omega, 6(4):2494-2504(2021) [pubmed]

Keyword List

submitter keyword: Benchmarking, Data-Independent Quantitation, Data-Dependent Quantitation, Statistics, Best Practices

submitter keyword: Benchmarking, Data-Independent Quantitation, Data-Dependent Quantitation, Statistics, Best Practices

Contact List

John Denu
contact affiliation	University of Wisconsin - Madison
contact email	john.denu@wisc.edu
lab head
Logan J Wright
contact affiliation	University of Wisconsin - Madison
contact email	ljwright2@wisc.edu
dataset submitter

Full Dataset Link List

MassIVE dataset URI
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://massive.ucsd.edu/MSV000085239/

MassIVE dataset URI

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://massive.ucsd.edu/MSV000085239/