From mass to compound iden3ty

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Melvin Simmons
5 years ago
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Mass Spectrometry Analy&cal tool measuring

organic molecules For a 40 kda protein, there is a

1 Mass Spectrometry Analy&cal tool measuring molecular weight of molecules in chemistry, biology and pharmacology Only picomolar concentra&ons required Within 5 ppm for small organic molecules For a 40 kda protein, there is a 4Da error MS can detect amino acid subs&tu&ons, posttransla&onal modifica&ons

2 From mass to compound iden3ty MS iden&fies a mass, but does not tell you what the compound is. Many molecules will have the same mass Interpreta&on of fragmenta&on paierns may help if you choose from a small set Proteins: with a fixed human genome, it may be possible

3 Physics behind MS An ion moves in a magne&c field A neutral molecule CAN NOT BE measured with MS Magne&c field bends the trajectories according to the ra&o m/q

4 Electric (E) and Magne3c (B) Fields Field = Force on a probe charge q=1 Current (I) flowing through a wire produces a magne&c field, B [tesla] E Coulomb = C q r source 2

5 Lorenz Force When charged molecules move in electric and magne&c fields In electric fields they accelerate. F el = qe In magne&c fields their trajectories bend F mg = qvb F = q( E + v B) ( m / q) a = E + v B

6 Radius of ion trajectory The a force is perpendicular to V it causes circular mo&on with accelera&on v 2 /R If magne&c field B is perpendicular to V, then ma = qv B mv R 2 = m R = q qvb v B

7 Mass-to-charge ra3o m/q, or m/e, or m/z, z is the electronic charge of a molecular ion or fragment. If z=+1,m = m/z Mass: isotopes are detected. E.g. 12 C, 13 C, 79 Br : 81 Br, intensity 1:1 and 35 Cl : 37 Cl, intensity 3:1 Charge: in an electron impact mass spectrometer, a high energy beam of electrons displaces an electron from the organic molecule to form a radical ca3on known as the molecular ion. If the molecular ion is too unstable then it can fragment to give other smaller ions.

8 Spectrum of 2-chloropropane Loss of Cl gives the main peak.

Separa3on of mixtures Chromotography, (greek, color- wri&ng) Chromatography exploits par&&on between a mobile phase and a sta&onary phase to separate the components in a mixture.

9 Separa3on of mixtures Chromotography, (greek, color- wri&ng) Chromatography exploits par&&on between a mobile phase and a sta&onary phase to separate the components in a mixture. Molecules interact with the sta&onary phase based on charge, rela&ve solubility or adsorp&on Gas, thin layer, paper, Column (liquid) ion-exchange (charge) size-exclusion (size) Affinity FPLC (proteins) and HPLC (pressure) Mikhail Semenovich Tsvet, , a Russian botanist. He used liquid - adsorp&on column chromatography Thin layer chromatography is used to separate components of chlorophyll

Chromatography terms Prepara3ve chromatography is used to nondestruc&vely purify sufficient quan&&es of a substance for further use, rather than analysis. Large HPLC columns.

10 Chromatography terms Prepara3ve chromatography is used to nondestruc&vely purify sufficient quan&&es of a substance for further use, rather than analysis. Large HPLC columns. Analy3cal chromatography is used to determine the iden&ty and concentra&on of molecules in a mixture. Quan&ta&ve. Mid-size HPLC columns LC of LCMS. Small HPLC columns. The analyte is the substance which is to be purified A chromatogram is the visual output of the chromatograph. Different peaks -> different molecules The mobile phase is the analyte and solvent mixture which travels through the sta&onary phase The reten3on 3me is the characteris&c &me it takes for a par&cular molecule to pass through the system Sta3onary phase: Examples include the silica layer, or columns

11 HPLC High-performance (high pressure) LC

12 Shopping in Factory outlets The elu&on &me depends on the number and dura&on of stops

A d. Par$cle size and the rate of dissolu$on. Consider the surface of the fixed amount of compound as the func$on of linear microcrystal

A d. Par$cle size and the rate of dissolu$on. Consider the surface of the fixed amount of compound as the func$on of linear microcrystal Par$cle size and the rate of dissolu$on Consider the surface of the fixed amount of compound as the func$on of linear microcrystal size, d, and the total volume V For non-cubic shapes, calculate the Area