title: A researcher's guide to mass spectrometry-based proteomics.
abstract: Mass spectrometry (MS) is widely recognized as a powerful analytical tool for molecular research. MS is used by researchers around the globe to identify, quantify, and characterize biomolecules like proteins from any number of biological conditions or sample types. As instrumentation has advanced, and with the coupling of liquid chromatography (LC) for high-throughput LC-MS/MS, a proteomics experiment measuring hundreds to thousands of proteins/protein groups is now commonplace. While expert practitioners who best understand the operation of LC-MS systems tend to have strong backgrounds in physics and engineering, consumers of proteomics data and technology are not exposed to the physio-chemical principles underlying the information they seek. Since articles and reviews tend not to focus on bridging this divide, our goal here is to span this gap and translate MS ion physics into language intuitive to the general reader active in basic or applied biomedical research. Here, we visually describe what happens to ions as they enter and move around inside a mass spectrometer. We describe basic MS principles, including electric current, ion optics, ion traps, quadrupole mass filters, and Orbitrap FT-analyzers.
authors.affiliation: Proteomics Center of Excellence, Northwestern University, Evanston, Illinois, USA.|Comprehensive Transplant Center, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA.
authors.forename: John P
authors.initials: JP
authors.lastname: Savaryn
authors.affiliation: Department of Molecular Biosciences, Northwestern University, Evanston, Illinois, USA.
authors.forename: Timothy K
authors.initials: TK
authors.lastname: Toby
authors.affiliation: Proteomics Center of Excellence, Northwestern University, Evanston, Illinois, USA. n-kelleher@northwestern.edu.|Department of Molecular Biosciences, Northwestern University, Evanston, Illinois, USA. n-kelleher@northwestern.edu.|Department of Chemistry, Northwestern University, Evanston, Illinois, USA. n-kelleher@northwestern.edu.
authors.forename: Neil L
authors.initials: NL
authors.lastname: Kelleher
mesh_terms: D002853:Chromatography, Liquid / Q000379:methods; D004867:Equipment Design; D005583:Fourier Analysis; D007477:Ions; D013058:Mass Spectrometry / Q000295:instrumentation* / Q000379:methods*; D040901:Proteomics / Q000295:instrumentation / Q000379:methods*; D053719:Tandem Mass Spectrometry / Q000295:instrumentation / Q000379:methods
chemical_list: D007477:Ions