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both the glycan and peptide portions can be obtained through distinct yet complementary tandem fragmentation strategies. Indeed, hybrid fragmentation methods
3
combining parallel (alternating) or sequential (MS
) fragmentation approaches provide more comprehensive structural information on both the peptidic and glycan
moieties of glycopeptides[198, 199]. Collision‐induced dissociation (CID) represents one of the most prevalent approaches for the tandem fragmentation of glycans
and glycoconjugates and for the generation of diagnostic ions. Lower energy CID‐
based fragmentation preferentially cleaves the glycosidic bonds between monosaccharides, which are more labile than peptidic amide bonds, generating B‐ and Y‐ions
that inform glycan composition and sequence[200]. Higher collision energies, on
the other hand, generate cross‐ring A‐ and X‐ions and internal double cleavage fragments for the identification of glycan branching sites and the resolution of isobaric
structures[199, 201]. This kind of fragmentation does not produce information on
the glycopeptide peptidic sequence and, thus, is rarely used individually for glycopeptide assignment[201]. Indeed, CID‐derived parent B‐ and Y‐ions with sufficient
3
signal intensity can be selected to undergo sequential fragmentation cycles (MS
),
where complementary b‐ and y‐ions from the peptidic backbone can be generated
by higher collision energies. Since distinct collision energies give rise to differential
fragmentation, current glycan‐ and glycopeptide‐directed MS workflows make use
of collision energy‐stepping, i.e. the use of incremental CID fragmentation energies
on the same set of precursor ions within a single mass spectrum scan, which yields
richer and more informative fragmentation spectra[198, 202]. Higher energy collisional dissociation (HCD), a higher energy variant of CID, is unique to more modern Orbitrap‐based instruments. HCD offers improved accuracy in the detection of
small diagnostic oxonium ions, particularly in the low m/z range[201]. HCD produces both glycan B‐ and Y‐oxonium ions and b‐ and y‐type ions derived from peptide backbone fragmentation, which tend to lose all or part of their glycan
modifications during fragmentation. HCD‐based stepping workflows not only produce both glycan and peptide backbone fragments from a single fragmentation
event but also generate more detectable cross‐ring fragment ions, which are fundamental to pinpoint glycosidic linkages and identify isomeric species [198, 199].
Electron transfer dissociation (ETD) constitutes a widely used fragmentation
method for intact glycopeptide analysis. In ETD‐based fragmentation, protonated
glycopeptides receive electrons generated from radical anions, which cause fragmentation along the peptidic backbone in the form of c‐ and z‐type ions [203].
Distinctively from CID‐based fragmentation, ETD retains labile post-translational
modifications such as glycosylation on the protein backbone and, therefore, does
not generate valuable information on glycan composition or sequence[199, 204].
However, generated c‐ and z‐type ions are extremely useful to pinpoint glycosylation
sites and retrieve peptidic sequences.
Aiming to gather more comprehensive structural information on both peptide and
glycan moieties of glycopeptides, many modern‐day Orbitrap‐based mass spectrometers are able to combine complementary dissociation workflows. For instance, in a
product‐triggered targeted method, the detection of HCD‐derived glycan oxonium
ions generated by glycopeptide fragmentation triggers subsequent ETD
181

182
fragmentation events of the respective parent ions, while nonglycosylated peptides
are not selected for tandem MS analysis[205]. This strategy has been employed to
comprehensively characterize the site‐specific glycosylation profiles of the ErbB2
and EGFR RTKs in gastric and colorectal carcinoma cells, respectively, using the
HexNAc oxonium ion (m/z 204.087) as a product ion trigger to select HexNAc‐
containing parent ions for additional fragmentation rounds [48, 206]. Product‐
triggered fragmentation approaches have been successfully used to unravel the
target‐specific O‐glycoproteome of colorectal and leukemia cancer cell lines[207, 208].
The manual interpretation of data generated from the MS‐based analysis of free
glycans or glycoproteins is challenging, laborious, time‐consuming, and requires significant expertise. The inclusion of fragmentation spectral data further increases the
complexity of this analytical exercise. Contrarily to genomic databases, the establishment of both glycomic and glycoproteomic software‐based tools represents a more
challenging task since glycans constitute secondary gene products whose structure
cannot be fully predicted by a given genetic sequence. The establishment of comprehensive glycan structural databases rather relies on the global deposition of glycan
analytical data and the development of bioinformatic tools capable of querying this
data in a high‐throughput manner for the quick and targeted prediction of a given
glycan 3D structure, binding partner, biosynthetic pathway, associated pathologies,
and host organism[209]. Several open‐source and commercial software tools have
been developed to aid in the interpretation of glycopeptide mass spectra. These
include: SimGlycan[210], Glyco‐DIA[211], GlypID 2.0/GlycoFragWork[212, 213],
ByOnic [214], MassyTools [215], GlycoPepGrader [216], SweetSEQer [217],
ArMone[218], GlycoPepDetector[219], GRIP[220], MAGIC[221], GP Finder[222],
Sweet‐Heart [223], GPQuest [224], GlycoFinder [201], GlycopeptideSearch
(GPS) [225], pGlyco 2.0 [226], O‐Pair Search [227], GPSeeker [228], pMatchGlyco[229], glyXtoolMS[230], SugarQB[231], GlycoPAT[232], I‐GPA [233], and
GlycoMasterDB[234].
6.8 Concluding Remarks
Glycans undoubtedly play an essential role in maintaining mammalian cell homeostasis. Strategically localized at the interface of a cell and its surrounding microenvironment, glycans act as crucial molecular gatekeepers, actively governing virtually
every cellular process. Moreover, since the posttranslational glycosylation cellular
process is highly sensitive to a cell’s physiological state, glycans have been widely
established as robust molecular reporters of pathological conditions and, in particular, of the neoplastic transformation of human tissues. The aberrant expression of
cancer‐specific glycan antigens by neoplastic cells, which stems from a variety of
dysregulated mechanisms affecting the cellular glycosylation machinery, has been
linked to the majority of malignant features supporting tumor cell survival, proliferation, differentiation, immune evasion, and local or distant organ dissemination.
At the cellular level, TACAs drive malignant transformation by either disrupting the

homeostatic functions of tumor‐suppressive elements or by enhancing the onco-
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genic properties of proteins controlling cell adhesion, programmed cell death, mitogenic signaling, and extracellular communication. However, the mechanistic basis
underlying such alterations, as well as the functional impact that these may have on
tumor onset, development, and metastatic spread, warrant further investigation.
Indeed, several biosynthetic and structural features of glycans pose unique challenges to their compositional characterization, structural elucidation, carrier assignment, and functional study. The vast array of monosaccharide substrate donors and
transporters and the partial redundant and overlapping specificities depicted by GTs
and glycosidases exponentially increase the structural complexity of the human glycosylation landscape. Moreover, the nontemplate‐driven nature of glycosylation
greatly hinders the unequivocal analytical‐based structural elucidation of complex
glycan chains. In recent years, we have witnessed the exponential technological
development of cellular‐, imaging‐, and analytical‐based tools and platforms that
have been instrumental in the unprecedented association between a glycan structure and its function within complex biological systems. The rapidly expanding toolbox of gene editing technologies has allowed the generation of cellular and animal
models depicting cleaner and well‐defined glycosylation backgrounds in which the
study of glycan biosynthesis and function can be performed in the absence of confounding factors such as GT redundant and compensatory activity. Increasingly
complex imaging systems have prompted the comprehensive characterization of
glycan expression patterns and distribution across histologically defined regions, as
well as the identification and mapping of tumor‐relevant glycan–protein interactions at the single complex level, in tissue specimens from oncological patients. The
emerging glycan microarray technology has fueled the high‐throughput interrogation and dissection of the glycan‐binding specificities of disease‐relevant carbohydrate‐based molecular interactions actively underpinning numerous features of
malignant cells, including evasion to immune recognition and surveillance. The
MS‐based elucidation of the composition, 3D structure, and site of attachment of
cancer‐associated glycan antigens has the potential to revolutionize the structure‐
guided design and optimization of cancer therapeutics. In conclusion, glycans
undeniably represent a novel set of tools that will become indispensable in the field
of modern‐era precision oncology, either as robust molecular biomarkers bearing
diagnostic, prognostic, predictive, and stratifying value, or as promising targets for
the delivery of personalized anticancer therapeutic agents.
183
List ofAbbreviations
capillary electrophoresis CE
carcinoembryonic antigen CEA
Consortium for Functional Glycomics CFG
collision‐induced dissociation CID
concanavalin A ConA

184
CRISPR‐associated protein 9 CRISPR/Cas9
extracellular matrix ECM
epidermal growth factor receptor EGFR
electrospray ionization ESI
electron transfer dissociation ETD
formalin‐fixed paraffin‐embedded FFPE
N‐acetylgalactosamine GalNAc
glycan‐binding protein GBP
N‐acetylglucosamine GlcNAc
guide RNA gRNA
glycosyltransferase GT
higher energy collisional dissociation HCD
high‐performance liquid chromatography HPLC
hematoxylin/eosin H&E
Helicobacter pylori H. pylori
imaging mass spectrometry IMS
jacalin JAC
knock‐in KI
knock‐out KO
Lewis b Le
monoclonal antibody MAb
Maackia amurensis lectin MAL
matrix‐assisted laser desorption/ionization MALDI
2
MALDI‐(time‐of‐flight)
‐MS MALDI‐TOF/TOF‐MS
mass spectrometry MS
N‐acetylgalactosaminyltransferases ppGalNAcT
porous graphitized carbon PGC
proximity ligation assay PLA
peptide‐N‐glycosidase F PNGase F
nonhomologous end joining NHRJ
sialic acid Neu5Ac
open reading frame ORF
patient‐derived xenograft PDX
receptor tyrosine kinase RTK
sialyl Lewis a sLe
sialyl Lewis x sLe
Sambucus nigra agglutinin SNA
so lid‐phase hydrophilic interaction
liquid chromatography SPE‐HILIC
surface plasmon resonance SPR
sialyl Tn STn
tumor‐associated carbohydrate antigen TACA
tr anscription activator‐like effector
nucleases TALEN
b
a
x

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185
titanium dioxide TiO
2
tissue microarray TMA
Vicia villosa agglutinin
wheat germ agglutinin
Wisteria floribunda agglutinin
zinc‐finger nuclease
VVA
WGA
WFA
ZFN
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