PXD042039-1

PXD042039 is an original dataset announced via ProteomeXchange.

Title	New avenues for human blood plasma biomarker discovery via improved in-depth analysis of the low-abundant N-glycoproteome
Description	An in-depth N-glycoproteomic analysis of human blood plasma was achieved by the combination of a top 14-High Abundant Protein (HAP) depletion step and protein fractionation via a GLEFrEE system. The sample preparation workflow included a tryptic digestion and glycopeptide enrichment, followed by an intact N-glycopeptide LC-MS/MS-based analysis, established by us. Two MS/MS acquisitions were applied using different fragmentation energies HCD.step and HCD.low (HCD: Higher Energy Collision Dissociation). A proteomic analysis was conducted, to assess the gain in the identification of middle- and low-abundant proteins. The protein search was applied on the three stages of the workflow: 1) untreated blood plasma, 2) top 14-HAP depleted sample, and 3) top 14-HAP depleted and GELFrEE fractionated sample. (Search engine Proteome Discoverer v 2.5) An N-glycoproteomic analysis was performed on the HCD.low and HCD.step raw data from the top 14-HAP depleted and GELFrEE fractionated sample (search engine Byonic v4.2.10). No FDR cuts nor decoys search was applied and manual validation was conducted instead. After the validation, we achieved the identification of 1929 N-glycopeptides, 942 N-glycosylation sites, and 805 glycoproteins.
HostingRepository	MassIVE
AnnounceDate	2023-05-27
AnnouncementXML	Submission_2023-05-27_01:47:06.684.xml
DigitalObjectIdentifier
ReviewLevel	Non peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Frania Jaqueline Zuniga Banuelos
SpeciesList	scientific name: Homo sapiens; common name: human; NCBI TaxID: 9606;
ModificationList	unknown modification
Instrument	LTQ Orbitrap Elite

Revision	Datetime	Status	ChangeLog Entry
0	2023-05-06 10:03:28	ID requested
⏵ 1	2023-05-27 01:47:07	announced

no publication

submitter keyword: data validation, disialyl Lewis C epitope, intact N-glycopeptides, glucuronidated glycan, glycoproteomic workflow, human blood plasma, low-abundant protein, phosphorylated glycan, protein fractionation, rare glycan, sulfated glycan

Frania Jaqueline Zuniga-Banuelos
contact affiliation	Max Planck Institute for Dynamics of Complex Technical Systems
contact email	zuniga@mpi.magdeburg.de
lab head
Erdmann Rapp
contact affiliation	Max Planck Institute for Dynamics of Complex Technical Systems
contact email	rapp@mpi-magdeburg.mpg.de
lab head
Udo Reichl
contact affiliation	Max Planck Institute for Dynamics of Complex Technical Systems
contact email	ureichl@mpi-magdeburg.mpg.de
lab head
Marcus Hoffmann
contact affiliation	Max Planck Institute for Dynamics of Complex Technical Systems
contact email	mhoffmann@mpi-magdeburg.mpg.de
lab head
Frania Jaqueline Zuniga Banuelos
contact affiliation	Max Planck Institute
contact email	zuniga@mpi-magdbeurg.mpg.de
dataset submitter

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/MSV000091870/