Answers to HW Questions

Questions that are more specific to MS:1.11. How is product ion scanning superior to single quadrupole analysis of aprotein mixture for the purpose of identifying or quantifying a given componentof a complex biological sample?In the product ion scan, one can screen the mixture for the mass of the component ofinterest in Q1, fragment it in Q2 and then scan for the fingerprint of the fragmentationproducts in Q3. This is powerful if you know what you are looking for! Even if Q1admits some interfering species, the fingerprint in Q3 is likely to be interpretable.1.12. Given the exact structure of a small molecule, say, CO, and the mass spectrumcomprising just the monocation, CO+, how many peaks do you expect to find inthe MS of this molecule? Assume you can measure within about 100:1 signal tonoise ratio. If more than one, then with what relative intensities?It’s kind of a weak question, I admit – but the idea is that CO + should show up in fourplaces corresponding to 12 C 16 O + , 13 C 16 O + , 12 C 18 O + and 13 C 18 O + . The abundance of13 C is about 1%, so this one should be seen at SNR=100. But 18 O is rarer and theisotopomers with 18 O would not normally be observed unless the sample wereenriched in 18 O. One to two peaks should be observed for CO + .1.13. Apply the same reasoning to the analysis of a 5 kDa protein (not in detail, justdiscuss the general idea).The basic idea then is this – the 5 kDa peak will have many sidebands comprisingsmall and variable amounts of 13 C and 2 H. So, for example, if the resolving power ofan instrument is 10,000 at 5kDa, then while it is conceivable that one might resolvethe centers of the distributions formed by two different proteins of nominal mass5000 Da and a 4,998 Da proteins, their individual isotoper masses will not beresolved. Take home message: Proteins will produce isotopic distributions aroundtheir nominal masses that are normally unresolved. Even if an instrument has theresolving power to distinguish two proteins, they actual resolution may be difficult tothese distribution functions.