Reviews & Perspectives
Deciphering Spatial Protein–Protein Interactions in Brain Using Proximity LabelingIn Brief PL has emerged as a powerful tool to identify proteomes in distinct cell types in brain as well as proteomes and protein–protein interaction networks in structures difficult to isolate, such as the synaptic cleft, axonal projections, or astrocyte–neuron junctions. Here, we review recent advances in PL methods and their application to neurobiology.
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.
Are There Indeed Spliced Peptides in the Immunopeptidome?In Brief Peptide splicing was suggested to significantly contribute ligands to the immunopeptidome. This article argues that peptide splicing is at most very rare, even if it happens at all. Considerations against peptide splicing are based on bioinformatics calculations related to the analysis of the LC-MS/MS data, and on the abundance of water in the cells, which should compete effectively with the transpeptidation reaction, needed for peptide splicing.
Recent Advances in Software Tools for More Generic and Precise Intact Glycopeptide AnalysisIn Brief This article provides a systematic review of the most recent MS-based strategies and corresponding software tools for the analysis of intact glycopeptides, particularly intact N-glycopeptides, reported in the last decade, including the process of identifying N-glycopeptides from MS data, the existing methods of MS data acquisition and interpretation, the quality control methods, the display of results, and the software applications.
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.
Calculating Glycoprotein Similarities From Mass Spectrometric DataIn Brief To understand the roles of glycoproteins in biological processes, it is necessary to quantify the changes that occur to glycosylation at individual sites and to the whole molecule. That glycoprotein glycosylation is inherently heterogeneous means that the distribution of glycoforms at each glycosite must be quantified in order to inform calculation of molecular similarities. We review analytical and statistical methods for determining glycoprotein molecular similarities from glycoproteomics data.