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Gen575

Gen 575: Fundamentals of Biomedical Instrumentation

Course description

An introduction to the fundamentals of instrumentation commonly used in biomedical research settings including mass spectrometers, optical microscopes, and DNA sequencers. Emphasis on a practical understanding of the physical and chemical properties that underlie operation and sources of uncertainty, noise, and error.

Instructional staff

Michael MacCoss, PhD
Brian Beliveau, PhD

Meeting times and locations

Spring Quarter 2026: Tuesdays & Thursdays 12:00–1:30 pm, Foege S-110

Prerequisites

Background in molecular and cellular biology, chemistry, genetics, biochemistry, engineering, or related discipline and experience with quantitative problem solving.

Course materials

There is no one textbook that can effectively cover the information presented in this course. To supplement the lecture content, the instructors will assign supplemental readings from reviews, historical papers, and/or free online sources.

Course requirements

Late homework will be accepted, but penalized. Specifically, each assignment is worth 100 points, from which 10 points will be deducted for each day (or fraction thereof) that you turn it in late. The maximum deduction for being late is 60 points (even if you are more than 6 days late).

Students may miss lectures without suffering a penalty to their participation grade provided that their absence is cleared with an instructor. While we realize it may not always be possile to do this in advance (eg, becauese of illness or emergency), but we please ask when possible that we be given >1 week notice. 5% will be deducted from the class participation grade for each uncleared absence.

Course grade

Participation: 60%
Problem sets: 40% (4, worth 10% each).

Course format

Each 80-minute class will be divided between lecture content about an instrumentation topic, discussion, and problem solving exercises related to the lecture topic.

Lecture Topic Date Instructor Slides Readings Assignments
1: Why Tech Dev? 03/31/2026 Mike 1.WhyTechDev 1.ScienceTechnology.Brooks 1.Annurev.Anchem.Hood
2: Signal-to-noise 04/02/2026 Mike 2.SignalNoiseBias 2.Agilent.Signal-Noise 2.JCE.SN.Coor 2.JCE.ShotNoise.Mclain-Wright 2.UsingShotNoise.EstimatingDetectorGain
3: Quantitative Analysis 101 04/07/2026 Mike 3.Quant101.Calibration 3.NIST.Calibration 3.LOB-LOD-LOQ.Armbruster 3.Shimadzu.TOF.Calibration
4: Basics of Biomedical Separation 04/09/2026 Mike 4.Separations 4.Chrom.FigsMerit.Agilent 4.Laemmli-SDSPAGE 4.OFarrell.2DGel 4.CentrifugationSeparations 4.UltraCentrifugation.Mendes.extra 4.ZonalCentrifuge.Anderson.extra
5: Mass Spectrometry 1: Ionization and Mass Analyzers 04/14/2026 Mike 5.MS.Ionization.Analyzers 5.ElectrosprayReview 5.Quadrupole.JCE1986 5.IonTraps.March 5.MALDIReview.Hillenkamp_et_al
6: Mass Spectrometry 2: Intro to qualitative peptide and protein analysis 04/16/2026 Mike 6.QualitativePeptideAnalysis 6.ResidueMass.Table 6.HuntSpectraInterpretation 6.Interpretation_of_MS2_Spectra 6.JPR.Pino2020 6.KinterAndSherman-Chapter4
7: Intro, Information Currencies 04/21/2026 Brian 7.Intro.Information.Currencies 7.NASA.EM.book 7.NASA.EM.graphic 7.NIST.SP.1247 7.photoelectric.effect
8: Information Theory 04/28/2026 Brian 8.Information.Theory 8.Guardian.Fourier.Transforms 8.Guardian.Shannon 8.Sampling
9: Evaluating Information 04/30/2026 Brian 9.Evaluating.Information 9.ejifcc.testing 9.Montparnasse.Accident Problem Set 1
10: Light Sources 05/05/2026 Brian 10.Light.Sources 10.Laser.History 10.Lamps
11: Multispectral imaging 05/07/2026 Brian 11.Multispectral.Imaging 11.Chroma.dichroics 11.Edmund.filters
12: Fluorescent labels 05/12/2026 Brian 12.Fluorescent.Labels 12.Dyes 12.GFP.history
13: Optical detection 05/14/2026 Brian 13.Optical.detection 13.FACS.detectors 13.Prime95B.sCMOS 13.Zeiss.PSF Problem Set 4
14: Mass spectrometry 3: Quantitative Analysis 05/19/2026 Mike 14.QuantitativeProteomics 14.IsobaricMassTags.MCP 14.SWATH.MCP
15: Proteomics: Alternatives to mass spectrometry 05/21/2026 Mike 15.Non-MSBasedProteomics 15.Alfaro.NatMeth.SingleMol 15.Gold.Aptamer.SomoScan 15.Rooney.MultiplexAssays.ClinChem.2025 15.MacCoss.NatMeth.SingleMol
16: Spatial and Single-cell Proteomics 05/26/2026 Mike 16.SpatialProteomics
17: Objectives and PSFs 05/28/2026 Brian 17.Objectives.PSFs 17.Olympus.Decon 17.Photometrics.SDC
18: Single Molecule Localization Microscopy 06/02/2026 Brian 18.SMLM 18.Glaser.eLife.2024

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