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 2025: Tuesdays & Thursdays 12:001:30 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: Intro, Information Currencies | 04/03/2025 | Brian | 1.Intro.Information.Currencies | 1.NASA.EM.book
1.NASA.EM.graphic
1.NIST.SP.1247
| | | 2: Information Theory | 04/08/2025 | Brian | 2.Information.Theory | 2.Guardian.Fourier.Transforms
2.Guardian.Shannon
2.Sampling | | | 3: Evaluating Information | 04/10/2025 | Brian | 3.Evaluating.Information | 3.ejifcc.testing.pdf
3.Montparnasse.Accident.pdf | Problem Set 1 | | 4: Why Tech Dev? | 04/15/2025 | Mike | 4.WhyTechDev | 4.ScienceTechnology.Brooks
4.Annurev.Anchem.Hood | | | 5: Signal-to-noise | 04/17/2025 | Mike | 5.SignalNoiseBias | 5.Agilent.Signal-Noise
5.JCE.SN.Coor
5.JCE.ShotNoise.Mclain-Wright | | | 6: Quantitative Analysis 101 | 04/22/2025 | Mike | 6.Quant101.Calibration | 6.NIST.Calibration
6.LOB-LOD-LOQ.Armbruster
6.Shimadzu.TOF.Calibration | | | 7: Basics of Biomedical Separation | 04/24/2025 | Mike | 7.Separations | 7.Chrom.FigsMerit.Agilent
7.Laemmli-SDSPAGE
7.OFarrell.2DGel
7.CentrifugationSeparations | | | 8: Mass Spectrometry 1: Ionization and Mass Analyzers | 04/29/2025 | Mike | 8.MS.Ionization.Analyzers | 8.ElectrosprayReview
8.Quadrupole.JCE1986
8.IonTraps.March
8.MALDIReview.Hillenkampetal | | | 9: Mass Spectrometry 2: Intro to qualitative peptide and protein analysis | 05/01/2025 | Mike | 9.QualitativePeptideAnalysis | 9.ResidueMass.Table
9.HuntSpectraInterpretation
9.KinterAndSherman-Chapter4 | | | 10: Mass spectrometry 3: Quantitative Analysis | 05/06/2025 | Mike | 10.QuantitativeProteomics | 10.IsobaricMassTags.MCP
10.SWATH.MCP | | | 11: Proteomics: Alternatives to mass spectrometry | 05/08/2025 | Mike | 11.Non-MSBasedProteomics | 11.Alfaro.NatMeth.SingleMol
11.Gold.Aptamer.SomoScan
11.Rooney.MultiplexAssays.ClinChem.2025,/br>11.MacCoss.NatMeth.SingleMol | | | 12: Spatial and Single-cell Proteomics | 05/13/2025 | Mike | 12.SpatialProteomics | | | | 13: Light Sources | 05/15/2025 | Brian | 13.Light.Sources | 13.Laser.History
13.Lamps | | | 14: Multispectral imaging | 05/20/2025 | Brian | 14.Multispectral.Imaging | 14.Chroma.dichroics
14.Edmund.filters | | | 15: Fluorescent labels | 05/22/2025 | Brian | 15.Fluorescent.Labels | 15.Dyes
15.GFP.history | | | 16: Optical detection | 05/27/2025 | Brian | 16.Optical.detection | 16.FACS.detectors
16.Prime95B.sCMOS
16.Zeiss.PSF | Problem Set 4 | | 17: Objectives and PSFs | 05/29/2025 | Brian | 17.Objectives.PSFs | 17.Olympus.Decon
17.Photometrics.SDC | | | 18: Single Molecule Localization Microscopy | 06/03/2025 | Brian | 18.SMLM | | |