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PXD041217

PXD041217 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleFalse positive glycopeptide identification through in-FAIMS glycan fragmentation.
DescriptionGlycosylation is an important post-translational modification characterized by extensive heterogeneity. While mass spectrometry (MS) is the premier technique to characterize glycoproteins, the study of intact glycopeptides presents challenges often not observed in the study of unmodified species. High-field asymmetric waveform ion mobility spectrometry (FAIMS) involves in-line gas-phase separation and offers the potential to analyze glycopeptides without prior enrichment. While FAIMS has been assessed for its use in glycoproteomics, most of these studies focus heavily or exclusively on N-glycoproteomics. Therefore, we evaluated FAIMS for O-glycoprotein and mucin analysis. We generated three samples: the mucin-domain glycoprotein podocalyxin, a recombinant glycoprotein mixture, and a WGA enriched human platelet sheddome. Although FAIMS allowed for the identification of new podocalyxin O-glycosites, it yielded less glycopeptide identifications and glycoforms. FAIMS seemed to be more useful in the increasingly complex samples, since we observed a higher number of identified glycosylated species. Because of the labile nature of glycosidic bonds, and presence of a buffer gas in FAIMS separation, we investigated the possibility of increased in-source fragmentation during FAIMS analysis. We compared total ion chromatograms of identifications eluting within a minute of identifications bearing larger glycan structures, albeit with the same peptide backbone. FAIMS experiments showed a 2-5-fold increase in spectral matches from in-FAIMS fragmentation compared to control experiments. These results were also replicated in other previously published data, indicating that this is a systematic behavior. In summary, our study highlights that, although there are potential benefits gained when using FAIMS separation, caution must be exercised when using FAIMS due to in-FAIMS fragmentation, which limits its applicability in the field of O-glycoproteomics.
HostingRepositoryPRIDE
AnnounceDate2023-11-14
AnnouncementXMLSubmission_2023-11-14_08:31:21.661.xml
DigitalObjectIdentifier
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterValentina Rangel Angarita
SpeciesList scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationListcomplex glycosylation
InstrumentOrbitrap Eclipse
Dataset History
RevisionDatetimeStatusChangeLog Entry
02023-03-30 07:24:15ID requested
12023-09-11 12:44:44announced
22023-11-14 08:31:22announced2023-11-14: Updated project metadata.
Publication List
Dataset with its publication pending
Keyword List
submitter keyword: Glycoproteomics, mucinomics FAIMS, mucin-domain glycoproteomics, enrichment., ion mobility separation
Contact List
Stacy Alyse Malaker
contact affiliationDepartment of Chemistry, Yale University
contact emailstacy.malaker@yale.edu
lab head
Valentina Rangel Angarita
contact affiliationGraduate Student, Malaker Lab
contact emailvalentina.rangelangarita@yale.edu
dataset submitter
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