Mass Spectrometry Instrumentation in Proteomics

Abstract Mass spectrometry has evolved into a crucial technology for the field of proteomics, enabling the comprehensive study of proteins in biological systems. Innovative developments have yielded flexible and versatile mass spectrometric tools, including quadrupole time‐of‐flight, linear ion trap, Orbitrap and ion mobility instruments. Together they offer various and complementary capabilities in terms of ionisation, sensitivity, speed, resolution, mass accuracy, dynamic range and methods of fragmentation. Mass spectrometers can acquire qualitative and quantitative information on a large scale to study protein expression, protein interactions and modifications, in complexes, organelles, cells and tissues. The currently available technological platforms and approaches offer a wide selection for proteomics experiments from low to high throughput, from shotgun discovery to targeted validation. In terms of desired outcome, cost and time, choosing between available instrumentation and methodologies is key to find the best analytical strategy suiting a particular proteomics experiment. Key Concepts: The basic elements of a mass spectrometer are an ionisation source, mass analyser and detector. Mass spectrometers central to proteomics‐based research are mostly ‘hybrid’ instruments combining the capabilities of different types of mass analysers. Key properties of MS instruments for proteomics are sensitivity, speed, resolution, mass accuracy, dynamic range and methods of fragmentation. Bottom‐up LC–MS‐based shotgun approaches have become the dominant form of analysing complex samples in various proteomics approaches Mass spectrometry is a crucial tool in proteomics research, but proper experimental design and sample preparation remains key; garbage in–garbage out. The choice for a particular instrument is dependant on the chosen workflow, ranging from low throughput to shotgun discovery and targeted validation strategies.