Reviews & Perspectives
Data Management of Sensitive Human Proteomics Data: Current Practices, Recommendations, and Perspectives for the FutureIn Brief Availability of proteomics data in the public domain has become the norm, as it has been the case in genomics and transcriptomics for many years. Analogously to sequencing data, there are increasing ethical issues and legal requirements related to sensitive human clinical proteomics data. We review the current state of the art and make concrete recommendations to address these issues in the proteomics field, which are summarized in four different areas.
An Introduction to Advanced Targeted Acquisition MethodsIn Brief The analytical power of targeted proteomics depends on how efficiently the mass spectrometer detects target peptides. A number of “smart” acquisition approaches have been developed that enable more targets per run and improve analytical performance such as sensitivity, specificity, and quantitative accuracy. This review provides an introduction to these methods and highlights their inherent strengths and weaknesses.
Recent Advances in Analytical Approaches for Glycan and Glycopeptide QuantitationIn Brief Recent years have seen an explosion in novel strategies for quantitative glycomics and glycoproteomics. Whether through metabolic incorporation of stable isotopes, deposition of custom isotopic labels, or high-throughput isobaric chemical tags, these numerous novel strategies provide ease of access to glycomic and glycoproteomic investigation. This review highlights the recent innovations in labeling methods, label-free strategies, acquisition modes, and bioinformatic tools for glycan and glycopeptide quantitation, while providing critical evaluations and technical considerations to enable effective analysis.
The Role of Data-Independent Acquisition for GlycoproteomicsIn Brief As a highly abundant and diverse post-translational modification, protein glycosylation is challenging to characterize in various approaches including MS. In MS-based proteomics, data-independent acquisition (DIA) has been advanced rapidly and showed outstanding analytical performances. DIA now started to be applied in different facets of glycoproteomics, including deglycosylated and intact N-linked and O-linked glycopeptides, and screening of oxonium ions. We summarized current applications of DIA in glycoproteomics and discussed its limitations and perspectives.