Cole_Mass.spec Flashcards
what does mass spec measure?
mass, and plots as mass to charge ratio (m/z)
what three basic molecular properties can you interrogate with MS?
elemental composition, structure (through fragmentation patterns), and relative abundances
what are two ways you can ionize your sample?
MALDI (matrix assisted laser desorption and ionization) and ESI (electrospray ionization)
how does MALDI work
mix your sample with some matrix, dry it to a metal plate and shoot that plate with lasers. The laser ionizes molecules in the matrix, and then protons from the matrix are transferred onto your sample molecules. Once they are charged, they can fly
how does electrospray ionization work
you perform liquid chromatography, then produce ions from your liquid by applying a high voltage to create an ionized aerosol. sample undergoes solvent evaporation and ion release upon a coulombic explosion
what shit in your sample prep will mess with ionization and why (3)
inorganic acids (cause corrosion), detergents (suppress ionization), salts (form adducts with analytes)
how do you sort ions by charge (4)?
TOF (time of flight, ion drift time), resonant frequency, transient frequency, or ion mobility
how do detect ions? (2)
either by an electron amplifier, which works like a photomultiplier tube, or by a faraday cup, which sounds like a menstrual product but is actually instead something i don’t really understand
isotopic series
the series of peaks you can visualize at a high resolution which are representative of the isotopic variation for any given atom. Monoisotopic mass most accurate, but often people just report the weighted average of all peaks within the isotopic series
how does tandem MS work?
you perform topdown MS on a protein complex or solution of proteins, then you isolate out individual components of the solution and fragment them, then obtain a second spectra (sibling spectra) of that component
what types of macromolecules can you examine with tandem MS?
all of them, although lipids and carbs are much harder to resolve than proteins and nucleic acids
where do oligonucleotides fragment?
at the phosphate bridge bonds
where do peptides fragment?
at the peptide bond
what is preferred protein cleaving enzyme and why?
trypsin, regular cutter at 10-20 AA (arg and lys)
PMF
protein mass fingerprint, can ID 1-3 proteins by their m/z patterns, bottom up approach
useful to map out PTM sites
electron capture, or electron transfer, dissociation, they don’t knock off PTMs since their primary ions are c and z ions
how to calculate false discovery rate?
need to align your putative protein seqs against a decoy database as well as a real database, and your ratio of false hits to real database hits is FDR
what is a standard false discovery rate?
~1%
what are some protein features you can most easily interrogate with top down MS? (4)
number of proteoforms, ID of post translational mods, stochiometry of PTMs and proteoforms, cleavage sites
what are 4 applications of quantitative proteomics?
detect changes in protein levels, changes in protein mods, differences in subcellular localization, and kinetics
three basic ways to label proteins for quantitative MS?
chemical (a few diff types), enzymatic (O isotope labeling) and metabolic (SILAC)
what is main advantage to using label-free methods?
no addition steps to analysis
what are disadvantages to label-free methods?
you have to do one sample at a time, you have biological and technical variability to deal with
what are advantages to labeling methods
many samples at same time, cuts instrument run time per sample, and reduces technical variability
