A comprehensive LFQ benchmark dataset on modern day acquisition strategies in proteomics.

In the last decade, a revolution in liquid chromatography-mass spectrometry (LC-MS) based proteomics was unfolded with the introduction of dozens of novel instruments that incorporate additional data dimensions through innovative acquisition methodologies, in turn inspiring specialized data analysis pipelines. Simultaneously, a growing number of proteomics datasets have been made publicly available through data repositories such as ProteomeXchange, Zenodo and Skyline Panorama. However, developing algorithms to mine this data and assessing the performance on different platforms is currently hampered by the lack of a single benchmark experimental design.

Ultra-fast proteomics with Scanning SWATH.

Accurate quantification of the proteome remains challenging for large sample series and longitudinal experiments. We report a data-independent acquisition method, Scanning SWATH, that accelerates mass spectrometric (MS) duty cycles, yielding quantitative proteomes in combination with short gradients and high-flow (800 µl min) chromatography. Exploiting a continuous movement of the precursor isolation window to assign precursor masses to tandem mass spectrometry (MS/MS) fragment traces, Scanning SWATH increases precursor identifications by ~70% compared to conventional data-independent acquisition (DIA) methods on 0.

A W-Geometry Ortho-TOF MS with High Resolution and Up to 100% Duty Cycle for MS/MS.

Orthogonal injection time-of-flight (orthoTOF) mass spectrometry (MS) is the most prevalent form of TOFMS, owing to its greater control over incoming ion energy, the ability to correct for aberrations in incoming ion velocity and position, and its ability to provide an entire mass spectrum within a single scan. However, the duty cycle of orthoTOFMS is low compared with scanning analyzers, which can have 100% duty cycle when measuring a single type of ion. Typical duty cycles for orthoTOFMS range from 1% to 30%, depending on instrument geometry.