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-  I've got to start a new page of notes for day 2 or OneNote will definitely crash. Obviously there is a lot of unpublished data here I don't know if I can share or not, but some of this is out or preprinted. If you very very carefully controlled pH and reaction kinetics could you label all of one side of a peptide with TMT and all of the other side with dimethyl labels? Apparently, yes.Nikolai beat me to the question […]
- Publication date: 15 August 2026Source: Journal of Proteomics, Volume 330Author(s):
- Natural product synthesis by non-ribosomal peptide synthetases (NRPS) is greatly defined by the substrate selectivity of the adenylation (A) domains. Previous assays for specificity determination were mainly performed in vitro and were requiring protein purification. In this work, we developed – based on NRPS engineering – a novel in vivo assay suitable for high-throughput application named ASCR (A domain screening). Using the recently described XUT fusion sites, A domains and their upstream condensation domains were assembled as di-domains to characterized […]
- Multi-omics and spatial-omics technologies are exploding in use, producing increasingly complex datasets. Existing bioinformatics tools are developing rapidly but fail to fully enforce the FAIR principles, leaving the field vulnerable to escalating issues in computational reproducibility. Here, we introduce a reproducible-by-design paradigm represented in an omics data processing package, RomicsProcessor. At its core, the 'Romics_object', which is a self-contained digital artifact that encapsulates the full history of the data from the original data to the fully processed state, capturing the […]
- Publication date: Available online 13 July 2026Source: Journal of Chromatography AAuthor(s): Lingyu Dun, Jingjing Zhang, Kang Ji, Xu Zhang, Yanjun Jia, Longxia Wen, Fangdi Hu
- Journal of Mass Spectrometry, Volume 61, Issue 8, August 2026.
- Journal of Mass Spectrometry, Volume 61, Issue 8, August 2026.
- ABSTRACT Luxury food products such as olive oil, wine, and whisky are highly vulnerable to fraudulent practices. Their chemical complexity, fortunately, provides numerous potential adulteration markers, but unfortunately also necessitates the use of powerful, comprehensive profiling approaches involving detailed methods for sample cleanup and analysis. One technique capable of both targeted marker analysis and untargeted profiling is comprehensive two-dimensional gas chromatography coupled to high-resolution mass spectrometry (GCĂGC-HRMS). However, as with other chromatographic methods, this technique typically requires substantial sample preparation […]
- Protein phosphorylation regulates nearly every cellular process, yet most of the hundreds of thousands of human phosphosites remain functionally uncharacterized. Rather than prioritising phosphosites by conservation or structural features, here we use the abundance of an interaction partner as a readout of whether a phosphosite affects that interaction. This idea exploits the fact that subunits of stable complexes are often degraded when unbound. Here, we apply a nested linear regression model to pan-cancer data from 1,006 tumours, while controlling for […]
- The functional complexity inherent in microbiomes complicates analytical approaches aimed at defining phenotype. As proteins are the functional effectors of microbiome phenotypes, improving the performance of mass spectrometry-based metaproteomics is critical to achieving the functional characterization of these systems. Data-independent acquisition (DIA) improves protein coverage and reduces data missingness when compared to data-dependent acquisition (DDA) in metaproteomics. However, the application of DIA to complex microbial systems remains constrained by analytical throughput and computational scalability. Here, we optimized LCMS/MS acquisition parameters […]
- Through deuterium isotope labeling, we demonstrate a dual-coupled degradation mechanism in Sodium-based Prussian blue analogs (NaPBA) cathodes involving âcrystalline water-induced distortion accumulation coupled with defect-triggered electrolyte decompositionâ. The In(OTf)3 additive exhibits synergistic cation/anion effects that simultaneously immobilize crystalline water and passivate [Fe(CN)6]4â vacancy defects. This dual action mitigates structural distortion while suppressing electrolyte decomposition side reactions. Consequently, the In(OTf)3-containing NaPBA||Na cell achieves 80.63% capacity retention after 1000 cycles. ABSTRACT Sodium-based Prussian blue analogues (NaPBA) are promising cathodes for sodium-ion batteries […]
- Early maturation of host antimicrobial peptide defences is associated with hostâpathogen coexistence
- Cellular redox homeostasis plays a critical role in regulating protein function, including chaperone activity, through reversible oxidation of cysteine and methionine residues. Previously, we found that budding yeast cells experiencing redox imbalance due to inactivated thioredoxin reductase ( trr1{triangleup}) activate the heat shock response and induce hyperaccumulation of the small heat shock protein/sequestrase Hsp42 with misfolded proteins. Building on that finding, this study identified cysteine 127 (C127) within Hsp42 as a redox-active residue that becomes oxidized in trr1{triangleup} cells, upon […]
- Dried blood spots (DBS) are well-established microsamples used in clinical testing and newborn screening. However, their use in deep proteomics is hindered by highly abundant blood proteins and inefficient protein recovery from filter paper matrices. The non-targeted analysis of non-specifically DBS-absorbed proteins (NANDA) workflow partially overcomes the impact of abundant blood proteins and has enabled the identification of over 5,000 proteins from DBS samples. Nonetheless, residual abundant proteins, including hemoglobin and fibrinogen, constrain deep proteomic analysis. Therefore, this study aimed […]
- Publication date: 1 January 2027Source: Talanta, Volume 311Author(s): Mengyao Tang, Yunfeng Zhang, Zhendong Hua, Wei Jia, Na Wang, Boyu Huang, Haixing Wang, Cuimei Liu
-  The world's first conference on Single Cell Proteomics is back – today! for it's 9th year. That doesn't seem possible, but I counted twice. I can't wait. The line up is amazing. Is it too late to register digitally? Probably! But you should have already, silly. If you do miss it, most of the talks every year end up curated and up on YouTube! I watch the old ones on my lunch breaks all the time. Got a backup tablet in my […]
- The membrane-associated periodic skeleton (MPS) is a submembrane lattice composed of actin rings and spectrin tetramers that repeats every 190 nm along axons and maintains mechanical stability. Loss of the MPS precedes axon fragmentation during degeneration, but during axon regrowth after injury the extent and timing of MPS reformation are not clear. We used stimulated emission depletion (STED) microscopy to track {beta}II-spectrin periodicity in regenerating axons from mouse cortical neurons, human iPSC-derived cortical neurons, and human iPSC-derived motor neurons following […]
-  A couple days ago I found out about the iSCMS BMSS joint meeting in London in October. I was like "who is organizing this and how can I help?" So now I am! If you are at BMSS, you can put your name into a literal hat. Hopefully a fancy London hat! And get interviewed in front of a live audience for an episode of THE Proteomics Show.Is it cold enough in October there for me to dress up like Tom Baker […]
- Capillary electrophoresis-mass spectrometry (CE-MS) offers unique analytical advantages for polar metabolite profiling but has remained underutilized in metabolomics relative to liquid chromatography-MS (LC-MS), in part due to challenges in managing migration time drift during data analysis. Here we introduce the use of indexed migration time (iMT) for easily managing this aspect of CE-MS data for metabolomics. Migration time indexing using a panel of stable isotope-labeled (SIL) amino acid reference standards, stored as an iRT database in Skyline, outperformed both uncorrected […]
- Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease whose diagnosis often remains delayed. Skeletal muscle is increasingly recognized as an early contributor to ALS pathology. Using lipid imaging mass spectrometry (LIMS) in Tibialis anterior muscle from hSOD1G93A mice across disease stages, we identified fiber-type-specific and sex-dependent lipid remodeling. Lipid alterations were detected at the presymptomatic stage, preceding motor neuron loss and clinical symptoms. LIMS distinguished fast-twitch oxidative-glycolytic (type IIA) and glycolytic (type IIB/IIX) fibers and revealed their differential vulnerability […]
- Publication date: Available online 12 July 2026Source: Journal of ProteomicsAuthor(s): S. Wislet, C. Le Goff, Massonet Ph, S. Hody, J.L. Croisier, V. Dâorio, J.F. Kaux, G. Mazzucchelli, R. Cloots
- Publication date: Available online 11 July 2026Source: Journal of ProteomicsAuthor(s): Dirk Winkelhardt, Julia P. Schessner, Sven Berres, Alireza Nameni, Armin Soleymaniniya, Ayla SchrĂśder, Caroline Jachmann, Douwe Schulte, Georg Wallmann, Henry Webel, Johannes Rainer, Katerina Nastou, Laurent Gatto, Magnus Palmblad, Maike Weber, Omar Shouman, Pavel Sinitcyn, Ralf Gabriels, Robbe Devreese, Tim Van Den Bossche
- With the rapid development of mass spectrometry-based proteomics, the volume of phosphoproteomic data has increased substantially. However, accurate localization of phosphorylation sites and standardized statistical validation remain critical analytical bottlenecks. To address the lack of standardized cross-algorithm evaluation, we introduce onsite, a unified and open-source Python framework. onsite integrates an alanine-decoy strategy to estimate the false localization rate (FLR) across three algorithms: AScore, PhosphoRS, and pyLucXor. This modular architecture efficiently processes large-scale datasets and enables global FLR calculation. Benchmarking on […]
- Heterozygous de novo missense mutations in the EEF1A2 gene encoding translation elongation factor eEF1A2 result in neurodevelopmental disorders, typically characterised by early onset epilepsy and intellectual disability (ID). The E122K mutation is the most commonly reported missense mutation and is amongst the more severe in terms of epilepsy and ID. Here we made use of a recently developed mouse model which recapitulates the E122K mutation to examine how mutations in EEF1A2 might disrupt neuronal gene expression. Primary neurons from mutant […]
- ABSTRACT Loureirin D is a bioactive dihydrochalcone isolated from Dracaena resin with very high therapeutic value. A sensitive and high-throughput ultra-performance liquid chromatographyâmass spectrometry (UPLCâMS/MS) method was developed for the quantitative analysis of loureirin D in rat plasma with only 50âÎźL of sample per assay. Sample extraction was protein precipitation using acetonitrile, and isoscoparin was used as internal standard (IS). Separation was achieved on the BEH C18 column with a gradient mobile phase of 0.1% (v/v) aqueous formic acid and […]