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An open-source platform for data-independent acquisition proteomics adapts predicted libraries to experimental settings.

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.

Bacterial phage infection and subsequent lysis are traditionally considered mechanisms of bacterial mortality and viral propagation; additionally, emerging evidence indicates that they may also contri...

Retinol binding protein 4 (RBP4), the circulating carrier of retinol, complexes with transthyretin (TTR) and is a potential biomarker of cardiometabolic disease. However, RBP4 quantitation relies on i...

Journal of the American Society for Mass SpectrometryDOI: 10.1021/jasms.5c00236

Dhungel et al. report an alternate receptor for AAV (AAVR2, carboxypeptidase D), which is distinct from the multi-serotype AAV receptor (AAVR). This study provides insights into AAV biology and clinic...

Current applications of mass-spectrometry-based proteomics range from single-cell to body fluid analysis, each presenting very different demands regarding sensitivity or sample throughput. Additionall...

PROTEOMICS, EarlyView.

I'm looking for your experience on doing proteomics on FFPE samples of tissues. Could you share protocols you use and tips and tricks? Thank...

We built and characterised a mass spectrometer capable of performing CID (both beam type and resonant type), UVPD, EID and ECD in an automated fashion during an LCMS type experiment. We exploited this...