PXD008557

PXD008557 is an original dataset announced via ProteomeXchange.

Dataset Summary

Title	Quantifying homologous proteins and proteoforms
Description	Many proteoforms - arising from alternative splicing, post-translational modifications (PTMs), or paralogous genes - have distinct biological functions, such as histone PTM proteoforms. However, their quantification by existing bottom-up mass-spectrometry (MS) methods is undermined by peptide-specific biases. To avoid these biases, we developed and implemented a first-principles model (HIquant) for quantifying proteoform stoichiometries. We characterized when MS data allow inferring proteoform stoichiometries by HIquant, derived an algorithm for optimal inference, and demonstrated experimentally high accuracy in quantifying fractional PTM occupancy without using external standards, even in the challenging case of the histone modification code. HIquant server is implemented at: https://web.northeastern.edu/slavov/2014_HIquant/
HostingRepository	MassIVE
AnnounceDate	2017-12-22
AnnouncementXML	Submission_2017-12-22_11:54:19.xml
DigitalObjectIdentifier
ReviewLevel	Non peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Nikolai Slavov
SpeciesList	scientific name: Saccharomycetales; common name: budding yeasts; NCBI TaxID: 4892; scientific name: Homo sapiens; common name: human; NCBI TaxID: 9606;
ModificationList	Trimethyl; Methyl; Dimethyl; Pyridylethyl; CarbamidomethylDTT; Phospho
Instrument	LTQ Orbitrap Elite; Q Exactive

Dataset History

Revision	Datetime	Status	ChangeLog Entry
0	2017-12-22 11:49:04	ID requested
⏵ 1	2017-12-22 11:54:20	announced

Publication List

no publication

no publication

Keyword List

submitter keyword: proteoforms, PTM stoichiometry, histone modifications

submitter keyword: proteoforms, PTM stoichiometry, histone modifications

Contact List

Nikolai Slavov
contact affiliation	Northeastern University
contact email	nslavov@alumni.princeton.edu
lab head
Nikolai Slavov
contact affiliation	Harvard University
contact email	nslavov@alum.mit.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/MSV000081857

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/MSV000081857