The fragmentation patterns of deprotonated sialylated oligosaccharides and glycans from fetuin obtained upon collisionally induced dissociation (CID) and 193 nm ultraviolet photodissociation (UVPD) in a linear ion trap are presented. UVPD produced a more extensive series of cross-ring cleavage ions, such as A- and X-type ions, and dual-cleavage internal ions, including A/Y and X/B fragment ions. In addition, UVPD generated unique fragment ions which arise from site-specific cleavage of the triol substituent of the sialic acid residue. In contrast, CID produced more conventional glycosidic cleavages and relatively few A-type ions. UVPD of doubly deprotonated sialylated oligosaccharides produced mostly singly deprotonated fragment ions, whereas the product ions in the CID spectra were overwhelmingly doubly charged ions, an outcome attributed to the more extensive cleavages of sialic acid residues upon UVPD and products from electron photodetachment. The larger array of product ions, including those arising from extensive cross-ring cleavages and dual-cleavage ions, generated by 193 nm UVPD relative to CID gives greater confidence for identification of glycans. Several key site-specific cleavages by UVPD, such as ones involving the sialic acid moieties, provide evidence of glycan composition.

O -glycopeptides are often acidic owing to the frequent occurrence of acidic saccharides in the glycan, rendering traditional proteomic workflows that rely on positive mode tandem mass spectrometry (MS/MS) less effective. In this report, we demonstrate the utility of negative mode ultraviolet photodissociation (UVPD) MS for the characterization of acidic O-linked glycopeptide anions. This method was evaluated for a series of singly- and multiply-deprotonated glycopeptides from the model glycoprotein kappa casein, resulting in production of both peptide and glycan product ions that afforded 100% sequence coverage of the peptide and glycan moieties from a single MS/MS event. The most abundant and frequent peptide sequence ions were a/x-type products, which, importantly, were found to retain the labile glycan modifications. The glycan-specific ions mainly arose from glycosidic bond cleavages (B, Y, C, and Z ions) in addition to some less common cross-ring cleavages. Based on the UVPD fragmentation patterns, an automated database searching strategy (based on the MassMatrix algorithm) was designed that is specific for the analysis of glycopeptide anions by UVPD. This algorithm was used to identify glycopeptides from mixtures of glycosylated and non-glycosylated peptides, sequence both glycan and peptide moieties simultaneously, and pinpoint the correct site(s) of glycosylation. This methodology was applied to uncover novel site-specificity of the O-linked glycosylated OmpA/MotB from the “superbug” A. baumannii to help aid in the elucidation of the functional role that protein glycosylation plays in pathogenesis.

The catalytic mechanism of the hydrogen-mediated coupling of acetylene to carbonyl compounds and imines has been examined using three techniques: (a) ESI-MS and ESI-CAD-MS analyses, (b) computational modeling, and (c) experiments wherein putative reactive intermediates are diverted to alternative reaction products. ESI-MS analysis of reaction mixtures from the hydrogen-mediated reductive coupling of acetylene to α-ketoesters or N-benzenesulfonyl aldimines corroborate a catalytic mechanism involving C=X (X = O, NSO 2 Ph) insertion into a cationic rhodacyclopentadiene obtained by way of acetylene oxidative dimerization with subsequent Brønsted acid cocatalyzed hydrogenolysis of the resulting oxa-or azarhodacycloheptadiene. Hydrogenation of 1,6-diynes in the presence of α-ketoesters provides analogous coupling products. ESI mass spectrometric analysis again corroborates a catalytic mechanism involving carbonyl insertion into a cationic rhodacyclopentadiene. For all ESI-MS experiments, the structural assignments of ions are supported by multi-stage collisional activated dissociation (CAD) ESI-MS analyses. Further support for the proposed catalytic mechanism derives from experiments aimed at the interception of putative reactive intermediates and their diversion to alternate reaction products. For example, rhodium catalyzed coupling of acetylene to aldehyde in the absence of hydrogen or Brønsted acid cocatalyst provides the corresponding (Z)-butadienyl ketone, which arises from β-hydride elimination of the proposed oxarhodacycloheptadiene intermediate, as corroborated by isotopic labeling. Additionally, the putative rhodacyclopentadiene intermediate obtained from the oxidative coupling of acetylene is diverted to the product of reductive [2+2+2] cycloaddition when N-p-toluenesulfonyldehydroalanine ethyl ester is used as the coupling partner. The mechanism of this transformation also is corroborated by isotopic labeling. Computer model studies based on density functional theory (DFT) support the proposed mechanism and identify Brønsted acid cocatalyst assisted hydrogenolysis to be the most difficult step. The collective studies provide new insight into the reactivity of cationic rhodacyclopentadienes, which should facilitate the design of related rhodium catalyzed C-C couplings.*

A comparison of the fragmentation pathways of both protonated and deprotonated O-linked glycopeptides from fetuin and κ-casein obtained upon collision induced dissociation (CID) and 193 nm ultraviolet photodissociation (UVPD) in a linear ion trap is presented. A strategy using non-specific pronase digestion, zwitterionic hydrophilic interaction liquid chromatography (ZIC-HILIC) solid phase extraction (SPE) enrichment, and nano-liquid chromatography (nano-LC) is employed. UVPD of deprotonated glycopeptides generally produced the greatest array of fragment ions, thus affording the most diagnostic information about both glycan structure and peptide sequence. In addition, UVPD generated unique fragment ion such as Y-type ions arising from cleavage at the N-terminus of proline. CID and UVPD of protonated glycopeptides produced fragment ions solely from glycan cleavages.

Conjugation of antibody has expanded its applications in therapeutics and diagnostics, and various methods have been developed based on chemical or enzymatic reactions. However, the majority of them have focused on synthetic molecules such as small molecules, nucleic acids, or synthetic materials, but site-specific conjugation of antibody with protein cargo has rarely been demonstrated. In this Communication, we report a PEptide-DIrected Photo-cross-linking (PEDIP) reaction for site-specific conjugation of IgG with protein using an Fc-binding peptide and a photoreactive amino acid analogue, and demonstrate this method by developing an immunotoxin composed of a Her2-targeting IgG (trastuzumab) and an engineered Pseudomonas exotoxin A (PE24). The ADP-ribosylation of eukaryotic elongation factor-2 by the bacterial toxin inhibits the ribosomal translation of protein, and the trastuzumab-PE24 conjugate exhibited the cytotoxicity toward Her2-overexpressing cell lines. The PEDIP reaction can also be applied for many other types of cargo with slight modifications of the method.

The impact of the conversion of carboxylates in peptides to basic or fixed charge sites on the outcome of electron transfer dissociation (ETD) is evaluated with respect to ETD efficiency and the number of diagnostic sequence ions. Four reagents, including benzylamine (BA), 1-benzylpiperazine (BZP), carboxymethyl trimethylammonium chloride hydrazide (GT), and (2-aminoethyl)trimethylammonium chloride hydrochloride (AETMA), were used for the carboxylate derivatization, with the first two replacing the acidic carboxylate groups with basic functionalities and the latter two introducing fixed charge sites. The ETD efficiencies and Xcorr scores were compared for both nonderivatized and derivatized tryptic and Glu-C peptides from cytochrome c. Derivatization of the carboxylate increases the average charge states, the number of fragment ions, and the dissociation efficiencies of peptides, especially for the fixed charge reagent, AETMA.

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