Mass spectrometry articles from across Nature Portfolio

The spatial mapping of proteins can give important functional insights. Here, Zhu et al. develop a cross-linking mass spectrometry-based spatial proteomics method that does not require protein engineering, affords sub-organelle resolution, and elucidates both protein locations and membrane topologies.

The molecular heterogeneity of glycosylated biotherapeutics often complicates analysis by intact mass spectrometry. Here, the authors propose a simplified procedure for characterization that employs proton transfer charge reduction. Integration with glycomic and glycopeptide datasets can further provide glycoform-level information.

Mass spectrometry-based quantitative chemoproteomics is widely used for the identification of protein targets as well as modified residues, however, sample preparation and data analysis remain tedious. Here, the authors develop silane-based cleavable linkers functionalized tandem mass tags as click-compatible isobaric tags, introducing the isobaric label earlier in sample preparation, achieving decreased sample preparation time, with high coverage and high-accuracy quantification.

Thirty-four years ago, Curry and Rumelhart described a neural network-based approach to annotate tandem mass spectra. Their ideas foreshadowed several important developments in computational mass spectrometry over the past decade, but many of the challenges they discuss remain relevant today.

The integrated stress response affects cell survival or death under stress conditions, and depends on the activity of the eukaryotic translation initiation factor eIF2B. New research identifies a protein helix that modulates this response by controlling the structural states of eIF2B.

Although light-driven conversion of carbon dioxide receives widespread attention, it is also criticized due to the challenge of discerning true product formation from that of impurities. Now, significantly advanced guidelines for proper product identification have been developed, so we can better trust in what we see.

We developed OxoScan-MS, a mass spectrometric acquisition technology for high-throughput quantification of glycopeptides. When applied to plasma of patients with COVID-19, OxoScan-MS revealed differential glycosylation in disease-relevant proteins. This approach offers potential for large-scale applications, moving beyond traditional protein abundance measurements to explore glycosylated protein biomarkers.

We identified a comprehensive targetome for glycolytic metabolites in cancer cells using a novel target discovery approach — target responsive accessibility profiling (TRAP). The targetome revealed diverse regulatory modalities for glycolytic metabolites that include engaging with metabolic enzymes, influencing transcriptional outputs and modulating post-translational modification levels, thereby elucidating how glycolytic metabolites function as signaling molecules.