Reviews & Perspectives
Scaling Up Single-Cell Proteomics
In Brief Single-cell proteomics will drive the next wave of single-cell biology. This requires broad adoption of existing methods, the application of rigorous quality control standards, and the continuous advancement of the technology. The advancement will be driven by numerous innovations, including highly parallelized analysis, and will increase the throughput, quantitative accuracy, and the accessibility of the single-cell proteomics.An Introduction to Advanced Targeted Acquisition Methods
In 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.The Role of Data-Independent Acquisition for Glycoproteomics
In 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.Chromatin Proteomics to Study Epigenetics — Challenges and Opportunities
In Brief MS-based analysis of chromatin has emerged as a powerful tool to identify proteins associated with gene regulation. Total chromatin isolated from cells can be directly analyzed using MS, further fractionated into transcriptionally active and inactive chromatin, enriched for specific compartment or regions, and potentially used for single-locus isolation. This review highlights recent advances and discusses current challenges that should be addressed to further advance the field of chromatin proteomics.A Pragmatic Guide to Enrichment Strategies for Mass Spectrometry–Based Glycoproteomics
In Brief Interest in mass spectrometry–based glycoproteomics analysis is increasing because of recent advances in instrumentation and data analysis tools. Such studies can provide a wealth of information across a wide spectrum of glycan classes and biological systems. However, many studies require the choice of an enrichment strategy for glycosylated species prior to analysis to obtain the maximum amount of analytical information. Here, common enrichment strategies are reviewed with strengths and weaknesses, and the practical considerations for various methods are discussed.
