PXD036667-1

PXD036667 is an original dataset announced via ProteomeXchange.

Title	AGP nLC-MS/MS and nLC-FAIMS-MS/MS
Description	Bottom-up nLC-MS/MS glycoprotein mass spectrometry workflows rely on the generation of a mixture of unmodified and glycosylated peptides via proteolysis. Such methods are challenged by suppression of hydrophilic glycopeptide ions by more abundant, hydrophobic, and readily ionizable unmodified peptides. Commercially available high-field asymmetric waveform ion mobility spectrometry (FAIMS) devices have recently been introduced and present an opportunity for orthogonal separation following chromatic graphic separation and prior to MS/MS analysis, with potential benefits for glycoproteomic workflows. However, knowledge is lacking regarding the optimal FAIMS conditions for glycopeptide analysis. Here, we document optimal FAIMS compensation voltages for the transmission and analysis of human alpha-1-acid glycoprotein (AGP) tryptic N-glycopeptide ions. Further, we evaluate the effect of FAIMS on AGP glycopeptide assignments by comparing the number of assignments at different confidence intervals using a standard nLC-MS/MS method to an identical method with FAIMS.
HostingRepository	PRIDE
AnnounceDate	2023-03-11
AnnouncementXML	Submission_2023-03-10_21:21:34.052.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	KevinChandler
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	complex glycosylation; iodoacetamide derivatized residue
Instrument	Orbitrap Eclipse

Revision	Datetime	Status	ChangeLog Entry
0	2022-09-12 06:35:27	ID requested
⏵ 1	2023-03-10 21:21:34	announced
2	2023-11-14 08:37:24	announced	2023-11-14: Updated project metadata.

Chandler KB, Marrero Roche DE, Sackstein R, Multidimensional separation and analysis of alpha-1-acid glycoprotein N-glycopeptides using high-field asymmetric waveform ion mobility spectrometry (FAIMS) and nano-liquid chromatography tandem mass spectrometry. Anal Bioanal Chem, 415(3):379-390(2023) [pubmed]

submitter keyword: N-glycopeptide, high-field asymmetric waveform ion mobility spectrometry, glycoproteomics, AGP, alpha-1-acid glycoprotein,FAIMS

Kevin BChandler
contact affiliation	Florida International University Translational Glycobiology Institute Dept. of Translational Medicine Herbert Wertheim College of Medicine 11200 SW 8th St, Miami, FL USA
contact email	kchandle@fiu.edu
lab head
KevinChandler
contact affiliation	Florida International University
contact email	kchandle@fiu.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/2023/03/PXD036667

PRIDE project URI

• PRIDE
  1. PXD036667
     1. Label: PRIDE project
     2. Name: AGP nLC-MS/MS and nLC-FAIMS-MS/MS