PXD038673

PXD038673 is an original dataset announced via ProteomeXchange.

Title	IMPROVED N- AND O-GLYCOPEPTIDE IDENTIFICATION USING HIGH-FIELD ASYMMETRIC WAVEFORM ION MOBILITY SPECTROMETRY (FAIMS)
Description	Mass spectrometry is the premier tool for identifying and quantifying site-specific protein glycosylation globally. Analysis of intact glycopeptides often requires an enrichment step, after which the samples remain highly complex and exhibit a broad dynamic range of abundance. Here, we evaluated the analytical benefits of high-field asymmetric waveform ion mobility spectrometry (FAIMS) coupled to nano-liquid chromatography mass spectrometry (nLC-MS) for analyses of intact glycopeptide devoid of any enrichment step. We compared the effects of compensation voltage on the transmission of N- and O-glycopeptides derived from heterogeneous protein mixtures using two FAIMS devices. We comprehensively demonstrate the performance characteristics of the FAIMS device for glycopeptide analysis and recommend optimal electrode temperature and compensation voltage (CV) settings for N- and O-glycopeptide analysis. Under optimal CV settings, FAIMS-assisted gas-phase fractionation in conjunction with chromatographic reverse phase separation resulted in a 31% increase in the detection of both N- and O-glycopeptide compared to control experiments without FAIMS. Overall, our results demonstrate that FAIMS provides an alternative means to access glycopeptides without any enrichment providing an unbiased global glycoproteome landscape. In addition, our work provides the framework to verify ‘difficult-to-identify’ glycopeptide features.
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_09:08:34.605.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Kathirvel Alagesan
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	iodoacetamide derivatized residue
Instrument	Orbitrap Fusion Lumos; Orbitrap Exploris 480

Revision	Datetime	Status	ChangeLog Entry
0	2022-12-07 12:58:25	ID requested
1	2023-10-24 11:59:52	announced
⏵ 2	2023-11-14 09:08:43	announced	2023-11-14: Updated project metadata.

Rangel-Angarita V, Mahoney KE, Kwon C, Sarker R, Lucas TM, Malaker SA, False-Positive Glycopeptide Identification via In-FAIMS Fragmentation. JACS Au, 3(9):2498-2509(2023) [pubmed]

submitter keyword: FAIMS, N-GLYCOPEPTIDES, MASS SPECTROMETRY, O-GLYCOPEPTIDES,GLYCOPROTEOMICS

Kathirvel Alagesan
contact affiliation	Max Planck Unit for the Science of Pathogens, Charitéplatz 1, Berlin 10117, Germany
contact email	alagesan@mpusp.mpg.de
lab head
Kathirvel Alagesan
contact affiliation	Max Planck Unit for the Science of Pathogens
contact email	alagesan@mpusp.mpg.de
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD038673
     1. Label: PRIDE project
     2. Name: IMPROVED N- AND O-GLYCOPEPTIDE IDENTIFICATION USING HIGH-FIELD ASYMMETRIC WAVEFORM ION MOBILITY SPECTROMETRY (FAIMS)