Proteomics articles from across Nature Portfolio

Reicher, Reiniš et al. report a method for multicolour tagging using genome-scale intron-targeting sgRNA libraries that, in combination with computer vision, enables the systematic detection of protein localization changes.

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.

Papillary thyroid cancers (PTC) generally have good prognosis, but their recurrence rate remains high. Here, the authors use proteogenomics and metabolomics to identify molecular features in PTC tumours and determine PTC subtypes that are associated with prognosis and potential targeted therapies.

Here the authors characterise the impact of phosphorylation site mutations in intrinsically disordered regions (IDRs) on protein-protein interactions, highlighting the critical role of phosphorylation of IDRs in health and disease.

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.

The rate of ATP production and the total mass of enzymes were quantified for both glycolysis and mitochondrial respiration to determine the proteome efficiency of these pathways. Per unit of enzyme mass, mitochondrial respiration generates energy faster than glycolysis and is thus more proteome efficient. Despite being less proteome efficient, constitutive glycolysis comes with the benefit of rendering cells robust to hypoxia.

Chemically reactive metabolites such as formaldehyde are often toxic and are proposed to react promiscuously with biomolecules. New work shows that some reactive sites on proteins are uniquely sensitive to formaldehyde, leading to functionally important regulation of protein and cell functions.

Selecting omic biomarkers using both their effect size and their differential status significance (i.e., selecting the “volcano-plot outer spray”) has long been equally biologically relevant and statistically troublesome. However, recent proposals are paving the way to resolving this dilemma.

The grant deadline approaches but budget details are still missing. Experienced budget-makers share how they manage budgets and the ‘boom–bust’ cycle.