#FragPipe with #MSFragger Open and Labile PTM searches plus the Diagnostic Ion Mining module help to unravel novel RNA adducts in RNA-protein crosslinking studies: "Mass Spectrometric Evidence for the Under-represented RNA–Protein Cross-Links" | ACS Omega pubs.acs.org/doi/full/10.10…

Major reduction of memory usage by future DIA-NN versions. Current development version searching 20 million phosphopeptides:

PTMD 2.0: an updated database of disease-associated post-translational modifications academic.oup.com/nar/advance-ar… --- #proteomics #prot-paper

Decoding the impact of neighboring amino acid on ESI-MS intensity output through deep learning sciencedirect.com/science/articl… --- #proteomics #prot-paper

Hey #TeamMassSpec! I am hiring a technician whose main responsibilities will be implementing bottom up proteomics and targeted metabolomics workflows. We are looking for BS or MS, and pay with experience. We currently have an eclipse and a brand new Exploris 120 en route… 1/2

The coolest visual representation of a Fourier transform. 😲 [bit.ly/3uCu4a9]

Covalent Labeling Automated Data Analysis Platform for High Throughput in R (coADAPTr): A Proteome-Wide Data Analysis Platform for Covalent Labeling Experiments pubs.acs.org/doi/10.1021/ja… --- #proteomics #prot-paper

ProteusAI: An Open-Source and User-Friendly Platform for Machine Learning-Guided Protein Design and Engineering biorxiv.org/content/10.110… --- #proteomics #prot-preprint

Release News: V90 of #Reactome is live! 🥂 🎉 We have new and updated topics and pathways in this release, including Cellular response to stimuli, Disease, Gene Expression, Metabolism, and Metabolism of Proteins, which you can read about at this link: reactome.org/about/news/261…

Online Now: Spatial oncology: Translating contextual biology to the clinic dlvr.it/TDyf57

PIRATE: Plundering AlphaFold Predictions to Automate Protein Engineering biorxiv.org/content/10.110… --- #proteomics #prot-preprint

Metaproteomics beyond databases: addressing the challenges and potentials of de novo sequencing chemrxiv.org/engage/chemrxi… --- #proteomics #prot-preprint

PhD programs that can be finished in 3 years are always awesome.. And the project being proteomics method development must be the cherry on the top..

Sitetack: A Deep Learning Model that Improves PTM Prediction by Using Known PTMs • Introducing Sitetack, a deep learning model that enhances the prediction of post-translational modification (PTM) sites by utilizing known PTM locations in the sequence. • Sitetack uses a novel

Kanpig: K-mer analysis of long-read alignment pileups for structural variant genotyping biorxiv.org/content/10.110…

Bio2Token: All-atom tokenization of any biomolecular structure with Mamba Flagship Pioneering • This paper introduces “Bio2Token”, a method that tokenizes biomolecular structures at an all-atom level using Mamba. Unlike many current approaches that rely on coarse-grained

Second up is Jesper V. Olsen telling us about turnover at the single cell but he starts by reminding us of the massive differences in dynamic range and abundance between proteins and RNA. Hundreds of mRNAs Vs hundreds of millions for proteins. #iSCMS2024

Apparently, a 1000 spectra per second de novo peptide sequencing tool, novor.cloud, enabled those diverse antibody sequence mapping generated from those plethora of protease digestions...

🔓 #OpenAccess + Most Read in the past 30 days: "A Rapid One-Pot Workflow for Sensitive Microscale Phosphoproteomics" go.acs.org/bqp