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False positive glycopeptide identification through in-FAIMS glycan fragmentation.

ABSTRACT: Glycosylation 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.

INSTRUMENT(S): Orbitrap Eclipse

ORGANISM(S): Homo Sapiens (human)

SUBMITTER: Valentina Rangel Angarita

LAB HEAD: Stacy Alyse Malaker

PROVIDER: PXD041217 | Pride | 2023-09-11

REPOSITORIES: Pride

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Project description:We recently discovered that human neutrophils express immunomodulatory glycoproteins carrying unusual and highly truncated paucimannosidic N-glycans (Man1-3GlcNAc2Fuc0-1), but their biosynthesis remains elusive. Guided by the well-characterised truncation pathway in invertebrates and plants in which the N-acetyl-β-D-hexosaminidase (Hex) isoenzymes catalyse paucimannosidic protein (PMP) formation, we here set out to test if the homologous human Hex α and β subunits encoded by HEXA and HEXB drive a similar truncation pathway in human neutrophils. To this end, we performed quantitative glycomics and glycoproteomics of several CRISPR-Cas9-edited Hex-disrupted neutrophil-like HL-60 mutants (HEXA-/- and HEXB-/-) and matching unedited cell lines. Hex disruption was validated using next-generation sequencing, ELISA, proteomics and Hex activity assays. Excitingly, all Hex-disrupted mutants displayed significantly reduced levels of paucimannosylation, particularly of Man2-3GlcNAc2Fuc1, relative to unedited HL-60 suggesting that both HEXA and HEXB contribute to PMP formation via a hitherto unexplored truncation pathway in neutrophils. Quantitative N-glycomics indeed demonstrated reduced utilisation of a putative non-canonical truncation pathway in favour of the canonical elongation pathway in all Hex-disrupted mutants relative to unedited controls. Quantitative glycoproteomics recapitulated the truncation-to-elongation switch in all Hex-deficient mutants and showed a pronounced switch for N-glycoproteins co-trafficking with Hex to the azurophilic granules of neutrophils such as myeloperoxidase. Finally, we supported the Hex-PMP relationship by documenting that primary neutrophils isolated from an early-onset Sandhoff disease patient (HEXB-/-) displayed dramatically reduced paucimannosylation relative to neutrophils from an age-matched unaffected donor. We conclude that both human Hex α and β mediate PMP formation via a putative non-canonical truncation pathway in neutrophils.

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False positive glycopeptide identification through in-FAIMS glycan fragmentation.

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