More mass spectrometry booksreviewed by T. Nelson
Wiley, 2016, 350 pages
Reviewed by T. Nelson
ydrogen-deuterium exchange mass spectrometry, or HX for short, is a new technique for studying the structure or function of a protein and for identifying epitopes involved in ligand binding and protein-protein interactions. Although it's not terribly difficult for someone with lots of protein mass spec experience, there are many pitfalls that can be missed when looking at review papers and such.
That's why a book like this was badly needed. To my knowledge, this is the first one ever published on this subject. Many of the authors of these 18 chapters are well known experts. A beginner will benefit from their experience and from becoming familiar with the potential problems, of which there are many.
In HX, you mix your protein with D2O to replace the hydrogens with deuteriums. Then you remove the D2O and add water, chop the protein into small peptides, and throw it on the mass spectrometer. This tells you where the deuterium is on the protein; if some part of the protein is exposed on the surface, the deuterium will be replaced by hydrogen faster.
One problem is H/D scrambling in collision-induced dissociation, or CID (you can probably see by now why we use all those acronyms). CID causes H and D to be scrambled in MS/MS spectra, greatly limiting the resolution. New ionization types, notably electron capture dissociation (ECD) and electron transfer dissociation (ETD) will help (if you can afford them).
Still, the multi-author format means there's a certain amount of repetition. HX is just a technique, but there are few nitty-gritty details: no pictures of the equipment, no detailed algorithms, and not much statistical analysis. There are also no step-by-step protocols, no comparisons of different techniques or different instruments, mass spec settings, or columns, and no background on interpreting spectra for anyone unfamiliar with that.
This makes sense: someone just starting out with protein mass spec has a big enough learning curve already. This book will get you oriented to the new technique, maybe give you an idea of what you could use it for, and point you to the software you'll need. Take my word for it: you don't want to calculate these things by hand.
It's pretty biophysics-oriented, so there are lots of discussions of kinetics and some structural biochemistry. Mostly you'll find specific examples of how the technique was used in the authors' own experiments. So, while this book will be interesting to those (like me) who are planning to use the technique, my advice to the general reader is: stay away. Stay far, far away.
jul 01, 2017; edited jul 04, 2017
Wiley, 2016, 466 pages
Reviewed by T. Nelson
ipidomics is the latest ‘omics’ to stagger in from the cold. It still lags behind genomics and proteomics because, compared to proteins and DNA molecules, lipids are a pain in the butt to analyze: they stick to everything, they clog up your instrument, they autoxidize, and there are no common derivatization methods. Worst of all, unlike proteins and DNA, it's still tough to unambiguously identify a lipid molecule.
That's why the chapter on fragmentation libraries in this new book by Xianlin Han is particularly welcome. These software-based techniques, such as LipidBlast, are still incomplete, which means you still need to have a standard to make a solid identification. But they're improving, and at least it means that lipid chemists now nave an omics and a database of their very own.
The boiling points of many lipids are too high for GC, so Han uses LCMS and infusion mass spec exclusively. He has chapters on fragmentation patterns for glycerophospholipids, sphingolipids, glycerolipids, and fatty acids, but only a short paragraph on sterols.
There are also chapters on instrumentation—triple quads like the TSQ are the most popular, he says, but Orbitraps are probably the best to use—and he has a chapter on ionization, which is exclusively focused on electrospray ionization (ESI).
This is a very useful book, with many good references to the literature. It assumes that the researcher is familiar with mass spectrometry, but it would've been nice if Dr Han had a few suggestions about what to do with those frickin' bureaucrats. They're making me crazy.
Lipidomics is one field where the bureaucrats hone their expertise. In my lab they've developed the annoying habit of squirreling away our solvents in weird places so that doing an experiment becomes an exercise in hide-and-seek. They told us not to use chloroform, so we switched to MTBE; then they decided that MTBE is even worse, and they locked up all our MTBE in explosion-proof boxes and forbade us to use it.
Then there my co-workers. We use a pure teflon squirt bottle to avoid leaching of organics. One day one guy came along and dumped out our ultra-pure water and used our $400 squirt bottle to bail out the dirty, rusty water from an old waterbath.
Oh, what, have I started ranting again?
Ahem. This book will be essential to newcomers as well as experienced scientists studying lipids. At the moment, it's by far the best book in the field. Han also co-wrote the classic text Lipid Analysis: Isolation, Separation, Identification and Lipidomic Analysis with W.W. Christie, which also discusses gas chromatography along with classical lipid techniques. Hopefully there will be a second edition of this book that will discuss derivatization, non-ESI ion sources like APCI/APPI, analysis of unstable signaling molecules like lipid peroxides and hydroperoxides, and simple but obnoxious ones like cholesterol and waxes.
sep 24, 2017