BCMB3X92 Proteomics and Func Genomics Complete Course Notes (Distinction)

Description

These BCMB3X92 notes include my raw personal lecture notes, laboratory examples, and textbook summaries. I received a final mark of 80 (Distinction). Contents ---------- Course information +-- Contact +-- Lectures Miscellaneous +-- Amino acids and their structures Lecture 01 Lecture 02 +-- Systems biology +-- +-- Techniques/technolgies Lecture 03 +-- Sequence search +-- Sequence motifs +-- The big why? Lecture 04 +-- 2D gels +-- +-- 2D gel prep +-- +-- Charge dimension: IEF +-- +-- Mass dimension: Acrylamide +-- +-- Choosing a stain +-- +-- After running the gel +-- 2d-gel approaches +-- +-- Difference in-gel eelctrophoresis (DIGE) +-- +-- Radiolabelling +-- Summary Lecture 05 +-- Mass spectrometry +-- +-- Ionisation systems +-- +-- Mass analyser +-- +-- Detection +-- Interpreting the data +-- Time of flight +-- Summary Lecture 06 +-- Peptide mass fingerprinting (PMF) +-- Micro-reverse phase columns +-- Summary Lecture 07 +-- Quadrupole (Q) MS +-- Tandem MS +-- +-- Fragmentation +-- +-- Selective reaction monitoring (SRM) +-- Quadrupole time of flight +-- Summary Lecture 08 +-- Ion traps +-- Revisiting 2D gels +-- Shotgun proteomics +-- +-- Separating the peptides Lecture 09 +-- Protein identification with Shotgun +-- Protein quantification with Shotgun +-- +-- Relative quantification +-- +-- Absolute quantification Lecture 10 +-- Isobaric affinity tags +-- SILAC Lecture 11 +-- The SILAC mouse +-- +-- Summary +-- Other 'omes +-- +-- Stimulomes +-- +-- Regulomes +-- +-- Phenomes Lecture 12 +-- More 'omes +-- +-- Surfaceomes +-- +-- Secretomes Lecture 13 Lecture 14 +-- Post translational modifications (PTM) Lecture 15 +-- Phosphorylation +-- Phosphoproteomics +-- +-- 2D gels +-- +-- Characterisation of phosphopeptides +-- +-- Enrichment of phosphopeptides +-- MS$^3$ Lecture 16 Lecture 17 +-- Structure +-- +-- N-linked glycosylation +-- +-- O-linked glycosylation +-- Function +-- Analytical +-- +-- Characterisation of glycopeptides by MS +-- +-- Enrichment techniques +-- +-- Ion traps +-- +-- Information from spectra Lecture 18 Supplementary notes +-- Properties of glycobiology +-- Biosynthesis of N-glycans +-- +-- Processing +-- Mucin +-- Sialic acids +-- Major functions of glycosylation Lecture 19 +-- Redox proteomics and other PTMs +-- +-- Oxidation and oxidative stress +-- +-- Post-translational cleavage +-- +-- Deamidation Lecture 20 Lecture 21 +-- Proteoforms +-- Top-down proteomics +-- +-- Whole protein analysis Lecture 22 +-- Diagnostic proteomics +-- +-- Serum proteomics +-- Profiling using SELDI-TOF +-- MS tissue profiling / imaging +-- Summary Lecture 23 +-- Methods for validating proteomics results +-- +-- Western blotting +-- +-- Transcript levels +-- +-- Immunohistochemistry +-- +-- The human protein atlas +-- +-- Selective reaction monitoring (SRM) +-- +-- Metabolomics +-- Summary Lecture 24 +-- Metabolomics Lecture 25 +-- Protein-protein interactions (PPI) +-- Purification / enrichment +-- +-- Yeast 2-Hybrid +-- +-- Immunoprecipitation +-- +-- Native PAGE +-- +-- 2D Blue native and SDS-PAGE +-- +-- Tandem affinity purification (TAP) +-- Limitations of PPI investigations +-- Summary Lecture 26 +-- Exam