Sanchez-Garcia et al. report that systemic hypoxia-induced epigenetic reprogramming of neutrophil progenitors in the bone marrow reduces their effector function to limit lung tissue damage.

α/β-hydrolase domain-containing protein 11 (ABHD11) is a mitochondrial hydrolase, and its expression in CD4 + T-cells has been linked to remission status in rheumatoid arthritis. Here the authors repo...

Here, we will offer a tutorial for how to build instrument-specific spectral library predictions for PSMtag modified peptides using DIA-NN 2.3.0. This will allow users to do more accurate proteome-wid...

ALT: a spongebob squarepants scene with a mailbox and a flower

Walmsley and colleagues report that systemic hypoxia induces persistent loss of histone H3K4me3 marks and epigenetic reprogramming in neutrophil progenitors, resulting in long-term impairment of subse...

Nature Immunology - Walmsley and colleagues report that systemic hypoxia induces persistent loss of histone H3K4me3 marks and epigenetic reprogramming in neutrophil progenitors, resulting in...

In this Review, the authors describe and discuss hypoxia-associated extracellular matrix mechanisms of neutrophil recruitment, polarization and immunosuppression, how these lead to immunotherapy resis...

Joel Mokyr, Philippe Aghion and Peter Howitt share economics prize for work that underlines the importance of investing in research and development.

Mass spectrometry instrumentation continues to evolve rapidly, yet quantifying these advances beyond conventional peptide and protein detections remains challenging. Here, we evaluate a modified Orbit...

Myelin damage in multiple sclerosis can be detected up to 7 years before symptoms, with early immune pathway activation and a 21-protein panel showing promise for presymptomatic diagnosis.

Accurate and comprehensive peptide spectrum annotation is a crucial step to interpreting mass spectrometry-based proteomics data. While peak assignment in peptide fragmentation spectra is central to a broad range of proteomics applications, current tools tend to be specialized to a specific task. Here, we present a more comprehensive interactive graphical tool (Annotator), along with the underlying codebase written in Rust (rustyms). Annotator enables unified spectrum annotation for bottom-up, middle-down, top-down, cross-linked, and glycopeptide fragmentation mass spectra from all fragmentation methods, including all ion types: a/b/c, x/y/z, d/v/w, and immonium ions. The Annotator integrates all known post-translational modifications from common databases and additionally allows for the definition of custom fragmentation models and modifications. Modifications allow for diagnostic fragment ions, site-specific neutral losses, and multiple breakage sites for cross-linkers. The underlying library used for the theoretical fragmentation and matching is based on the unified peptidoform notation ProForma 2.0 and is made available as a Rust library with Python bindings. This enables spectrum annotation in an interactive, graphical interface of diverse and complex peptidoforms across the broad range of mass spectrometry-based proteomics applications.

Since no one asked for it (and ASMS ignored me)!  THE Proteomics Show will record live at International HUPO on Monday, November 10th. Mai...