Instrumental Analysis PART 2

What are the 2 reasons you would use Mass Spectrometry?

1. I know the structure I’m looking for so I use this and look for it in my data

2. I have no clue what’s in my sample so I use MS to figure it out

Mass Spectrometry

molecular ion or protonated molecule generated and undergo fragmentations in gas (produce more ions)

• 1st step of production of gas-phase ions of the analyte

• some ions are more or less (break apart more) stable

all ions separated in mass spectrometry and detected by their abundance (based on MASS and CHARGE)

Ion

charged molecule/atom; charge imbalance through addition or subtraction

• we have electric fields in instruments and the molecules will be affected by it (forms ions)

• required for manipulation with electrical or magnetic fields

Formal Charge Formula

Formal Charge = (Valence e-) - (Covalent Bonds) - (Lone Pair e-)

Total Charge of an Ion Equation

q = ze

• e = 1.6 × 10^-19 C (electron charge)

• z = number of charges

• C = Columbs (unit of electron charge)

Electron Ionization

molecule bombarded with e- beam heating the molecule

• neutral initially and then e- beam heating the molecule = form molecular ion

Molecular Ion

[M]+.

positive radical ion, formed in EI, by removal of an electron from a molecule

Cation

[M]+/+.

Positively charged ion

Anion

[M]-/-z

Negatively charged ion

Protonated Molecule

[M+H]+

Positive ion, formed by the addition of a proton

Adduct Ion

[M+Na]+ or [M+Cl]-

Any ion formed by the addition of an ionizing species to a molecule

Multiple Charged Ion

[M+nH]^n+

Product formed by adding multiple protons, typically to a peptide or protein, during ESI

Mass-to-Charge Ratio (m/z)

what separates ions in mass spectrometer

• m = relative mass

• z = charge number

• unitless

Characteristic/Distinct Peaks

most intense peaks- what you look for to identify a molecule

(ex. the 3 characteristic ions for cocaine)

Isotopes

elements specified by number of protons in nucleus

• atomic number = Z

• Z is given as subscript before element symbol

• isotopes of the same element differ in the number of neutrons (N) by the mass number (A)

• A is superscript before element symbol

Nominal Mass

mass of the predominant isotope of each element rounded to the nearest integer value that corresponds to the mass number

Monoisotopic Mass

calculated by using the exact mass of the most abundant isotope for each element

Chromatogram

graph from instrument

Chromatograph

instrument

Mass Spectrum

plot of ion abundance vs. m/z

• y-axis = number of ions, ion counts, or relative intensity

• x-axis = represents m/z

• probability density function of ions in the sample

• don’t select low abundance fragments (want the MOST INTENSE peaks to analyze the sample)

Column Bleeding

when stationary phase start degrading and leaving the column

• happens with use (if very sudden = damage to column)

• cause background ions

• In GC-MS, there is a way to do a background subtraction OR you can do another thing

Base Peak

most abundant peak in mass spectrum

• related to the stability of the ion

• mass spectra are often displayed in relative ion intensity or abundance by normalization to the base peak

• everything else will be calculated relative to m/z of that peak

• look at ratios of compounds (must accept 20% tolerance range of ion-ratio in methodology)

Fragment Ions

observed at smaller m/z values that the molecular ion

• ions sequentially fragment

• no mass gain

• no fragment will contain a larger number of atoms than the molecular ion