Increasing the rate at which we measure proteins increases the rate at which we can discover new biology and solve disease.

Koina is an open-source, online platform that simplifies access to machine learning models in proteomics, enabling easier integration into analysis tools and helping researchers adopt and reuse ML mod...

Dates 17-19 November 2025 To foster international participation, this course will be held online

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...

Multiplexing samples in mass spectrometry-based proteomics has long been accomplished by isotopologues of small molecules. These chemically-identical "mass tags" conjugate to peptides to encode sample...

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

YouTube video by Parallel Squared Technology Institute

ALT: a teddy bear is standing in front of a blue door

Advances in mass spectrometry (MS) instrumentation, including higher resolution, faster scan speeds, and improved sensitivity, have dramatically increased the data volume and complexity. The adoption of imaging and ion mobility further amplifies these challenges in proteomics, metabolomics, and lipidomics. Current open formats such as mzML and imzML struggle to keep pace due to large file sizes, slow data access, and limited metadata support. Vendor-specific formats offer faster access but lack interoperability and long-term archival guarantees. We here lay the groundwork for mzPeak, a next-generation community data format designed to address these challenges and support high-throughput, multidimensional MS workflows. By adopting a hybrid model that combines efficient binary storage for numerical data and both human- and machine-readable metadata storage, mzPeak will reduce file sizes, accelerate data access, and offer a scalable, adaptable solution for evolving MS technologies. For researchers, mzPeak will support complex workflows and regulatory compliance through faster access, improved metadata, and interoperability. For vendors, it offers a streamlined, open alternative to proprietary formats. mzPeak aims to become a cornerstone of MS data management, enabling sustainable, high-performance solutions for future data types and fostering collaboration across the mass spectrometry community.

YouTube video by Parallel Squared Technology Institute

Protein ubiquitination regulates cell biology through diverse avenues, from quality control-linked protein degradation to signaling functions such as modulating protein-protein interactions and enzyme...