Also a big thank you to ‪@vadim-demichev.bsky.social‬‬ for the DIA-NN support to enable multi-column searching!

SynchroSep-MS: Parallel LC Separations for Multiplexed Proteomics Achieving high throughput remains a challenge in MS-based proteomics for large-scale applications. We introduce SynchroSep-MS, a novel method for parallelized, label-free proteome analysis that leverages the rapid acquisition speed of modern mass spectrometers. This approach employs multiple liquid chromatography columns, each with an independent sample, simultaneously introduced into a single mass spectrometer inlet. A precisely controlled retention time offset between sample injections creates distinct elution profiles, facilitating unambiguous analyte assignment. We modified the DIA-NN workflow to effectively process these unique parallelized data, accounting for retention time offsets. Using a dual-column setup with mouse brain peptides, SynchroSep-MS detected approximately 16,700 unique protein groups, nearly doubling the peptide information obtained from a conventional single proteome analysis. The method demonstrated excellent precision and reproducibility (median protein %RSDs less than 4%) and high quantitative linearity (median R2 greater than 0.96) with minimal matrix interference. SynchroSep-MS represents a new paradigm for data collection and the first example of label-free multiplexed proteome analysis via parallel LC separations, offering a direct strategy to accelerate throughput for demanding applications such as large-scale clinical cohorts and single-cell analyses without compromising peak capacity or causing ionization suppression.

Check out our new manuscript on parallel LC separations! Super cool how the very high scan rates of modern MS systems coupled with DIA can allow us to run several samples at the same time with little loss in depth. Congrats to Noah and the team. #JASMS pubs.acs.org/doi/10.1021/...

Plasma Proteomics With Professor Joshua Coon Explore plasma proteomics innovations tackling the dynamic range challenge, revealing biomarkers and advancing personalized medicine with Professor Joshua Coon.

Sharing a recent interview in Technology Networks discussing the past, present and future of plasma proteomics.

High-flow LC separations for faster throughput quantitative proteomics

Read more: https://www.ncqbcs.com/high-flow-lc-separations-for-faster-throughput-quantitative-proteomics/

Significant improvements in multi-omics analysis

Read more: https://www.ncqbcs.com/significant-improvements-in-multi-omics-analysis/

Discoveries in deep proteome sequencing

Read more: https://www.ncqbcs.com/discoveries-in-deep-proteome-sequencing/

Achieving deep analysis of the human proteome in less than an hour

Read more: https://www.ncqbcs.com/achieving-deep-analysis-of-the-human-proteome-in-less-than-an-hour/

Comprehensive quantification of lipids using high-throughput MS with isobaric labelling

Read more: https://www.ncqbcs.com/comprehensive-quantification-of-lipids-using-high-throughput-ms-with-isobaric-labelling/

Achieving deep analysis of the human proteome in less than an hour

Read more: https://www.ncqbcs.com/new-plasma-protocol-for-lc-ms-ms/

Discoveries in deep proteome sequencing

Read more: https://www.ncqbcs.com/study-reveals-the-protein-machinery-central-to-coq-trafficking-in-yeast/

Comprehensive quantification of lipids using high-throughput MS with isobaric labelling

Read more: https://www.ncqbcs.com/ms-analyses-profiles-neuropeptides-to-understand-their-role-in-biology/

The Coon lab will have several presentations and posters at @asms.org in Baltimore, just a few short weeks away!

The One Hour Human Proteome In BriefWe present deep analysis of the human proteome in less than 1 h. The Orbitrap Astral mass spectrometer, alongside advances in sample preparation, method development, and data processing, is ushering in a new era of proteomics where a harmony of throughput, depth, and sensitivity are enable studies of unprecedented impact. We contextualize these results within the landscape of human proteomics. Comparisons with previous instrumentation in interrogating gene knockouts demonstrate the potential of proteomics to elevate biological investigation in years to come.

New publication by Serrano et al. describes deep analysis of the human proteome in less than 1 hour! This paper describes the process and how it takes advantage of the new Orbitrap Astral mass spec high acquisition speeds. www.mcponline.org/article/S153...