Intact glycopeptide identification has long been known as a key and challenging barrier to the comprehensive and accurate understanding the role of glycosylation in an organism. Intact glycopeptide analysis is a blossoming field that has received increasing attention in recent years. Mass spectrometry (MS)-based strategies and relative software tools are major drivers that have greatly facilitated the analysis of intact glycopeptides, particularly intact N-glycopeptides. This manuscript provides a systematic review of the intact glycopeptide identification process using mass spectrometry data generated in shotgun proteomic experiments, which typically focus on N-glycopeptide analysis. Particular attention is paid to the software tools that have been recently developed in the last decade for the interpretation and quality control of glycopeptide spectra acquired using different MS strategies. The review also provides information about the characteristics and applications of these software tools, discusses their advantages and disadvantages, and concludes with a discussion of outstanding tools.

A new, simplified method for the synthesis of dialkylphenacylsulfonium salt cationic photoinitiators has been developed. This novel method was successfully used for the preparation of dialkylphenacylsulfonium salts bearing a wide variation in the length and structure of the alkyl chains as well as the light absorbing aryl ketone chromophores and the anions. Modification of the lengths of the alkyl chains permits the design of compatible photoinitiators for highly nonpolar monomers and oligomers such as epoxy functional silicones, epoxidized polybutadiene and vegetable oils. This article describes the synthesis and characterization of these photoinitiators.

A study of the photoinitiated and thermally initiated cationic polymerizations of several monomer systems using dialkylphenacylsulfonium salt (DPS) photoinitiators bearing different alkyl chains and anions has been conducted. DPS compounds are capable of photoinitiating the cationic polymerization of a wide variety of epoxy and vinyl ether monomers directly on irradiation with UV light or by using visible light irradiation in the presence of photosensitizers. Kinetic studies show that DPS photoinitiators compare favorably with respect to their reactivity to diaryliodonium and triarylsulfonium salt photoinitiators in the polymerization of epoxides. The photopolymerizations of vinyl and 1-propenyl ethers display a marked induction period consistent with termination of the growing chains by reaction with the photogenerated ylides. Preliminary studies have demonstrated that DPS can also be employed as thermal initiators for the cationic ring-opening polymerization of epoxides at moderate temperatures.

Large-scale profiling of intact glycopeptides is critical but challenging in glycoproteomics. Data independent acquisition (DIA) is an emerging technology with deep proteome coverage and accurate quantitative capability in proteomics studies, but is still in the early stage of development in the field of glycoproteomics. We propose GproDIA, a framework for the proteome-wide characterization of intact glycopeptides from DIA data with comprehensive statistical control by a 2-dimentional false discovery rate approach and a glycoform inference algorithm, enabling accurate identification of intact glycopeptides using wide isolation windows. We further utilize a semi-empirical spectrum prediction strategy to expand the coverage of spectral libraries of glycopeptides. We benchmark our method for N-glycopeptide profiling on DIA data of yeast and human serum samples, demonstrating that DIA with GproDIA outperforms the data-dependent acquisition-based methods for glycoproteomics in terms of capacity and data completeness of identification, as well as accuracy and precision of quantification. We expect that this work can provide a powerful tool for glycoproteomic studies.

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