Lecture
This lecture covers the challenges in quantifying proteins using mass spectrometry, including the impact of ionization efficiency on peak intensity and the complexities in measuring analyte abundance. It also discusses techniques like label-free quantification, SILAC, and TMT for comparing peptide levels between samples. The lecture delves into the principles of spectral counting, AQUA peptides for absolute quantification, and the use of Super SILAC mix as an internal standard. Additionally, it explores the role of UniprotKB in providing functional information on proteins and the process of MS/MS ion search using peak lists. The importance of mass tolerances, enzyme selection, and accurate database searching is emphasized.