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10 reasons why you should choose mass spectrometry to study your molecule of interest

Posted by Jean-Philippe Couture, Ph.D. on September 7, 2016

Why should I use mass spectrometry in my research project?

It is no secret that mass spectrometry can be very intimidating for new users. For a lot of biologists and physicians, MS represents a shadow of a memory, in a distant undergraduate class. We all heard the terms TOF or MALDI-TOF, and remember that it means Time-of-flight and something-something-laser(!)-Time-of-flight, but for the majority of us, that's about it. We think that the mass spectrometer spits out thousands of numbers in a spreadsheet, and that if you are not sitting with the scientists who performed the analysis, you won't be able to get anything meaningful out of this mess. Also, it costs money. A lot of money.

Well.. that is not totally wrong! Here's what you got right :

  • TOF does mean Time-of-flight
  • The MS does spit out thousands of numbers
  • These numbers need to be decoded by experts to mean something

Now, the aim of this post is not to keep you away from mass spectrometry! It is rather to get you to consider it from a new angle, by stating a list of advantages that MS has over other molecular biology/medicine tools. So here are 9 reasons why you should choose mass spectrometry to study your molecule of interest!

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1. Mass spectrometry is sensible and precise

This one is pretty self explanatory. If your thinking quantification of your molecule of interest, MS should be one of the first thing to pop to your head. Coupled to liquid chromatography (LC), LC-MS can deliver highly precise quantification. Also, when performed by experts, it is highly reproducible and accurate over several orders of magnitude (of course, this is molecule-dependant!).

2. It multiplexes molecule analysis

Tired of studying only one molecule? Why not multiplex your analysis? Using MRM or SWATH, LC-MS/MS can accuratly quantify 10s, 100s or 1000s molecules at the time! Some very interesting example are amino acid analysis where 33 amino acids are analyzed in 15 minutes and pesticide screening where 100s of pesticides can be quantified in one run. Even more impressive, with the advance of next generation mass spectrometry using SWATH, more than 20 000 peptides can be profiled in less than 2h. This represents close to 4000 proteins, or 33 proteins per minutes. I bet your good old western blot can't beat that!

What about samples multiplexing? MS can do that too! Using an isobaric tag that reacts with amine groups (like iTRAQ), one can multiplex up to 8 samples, while maintaining molecule multiplexing capacity. All these features can save you a lot of MS time!

3. It can handle a lot of samples

Some of us fear robots, other put their ability to repeat the same task over and over again to good use. Automatisation of LC-MS/MS analysis indeed enables scientists to process hundreds, if not thousands of samples in a row without even being in the lab. Have you tried doing that much Western Blot to quantify one protein? That's what I thought!

4. It is highly customizable

Since mass spectrometers can work both in directed and non-directed fashion as well as in positive or negative mode, there are almost not molecule it can not detect. Thus, even if you work with a synthetic drug, a modified protein or a hard to solubilize lipid, MS can help you to quantify it. In addition, optimizing the preparation methods and chromatographic conditions can help to enhance even more the sensitivity of the MS for your molecule of interest.

5. It can perform shotgun experiments (omics)

The different omics fields gained a lot in popularity in the last decades. There are no better way than these techniques to profile a sample or to verify the effects of a treatment on a living organism. When coupled to appropriate bioinformatic programs, omics can generate incredible amounts of useful data that can lead to very important findings. With mass spectrometry, one can perform proteomics, lipidomics and/or metabolomics experiments and lift their research projects to new heights. 

6. It is not limited by the existence of kits or affinity tools to study your molecule of interest

How often do you hear people complaning about the poor quality or the lack of an antibody? I sure complained a lot myself, back in my lab days. The same problems could also apply to most post-translational modifications or proteins on alternate reading frame. However, the power of mass spectrometry can help to overcome these problems. As long as you know the sequence of the protein you want to study, you will probably be able to see it by MS. In addition, as stated earlier, the optimization of the preparation method can help a lot to increase sensitivity. 

7. It has the power to see things you would have missed with other techniques

Mass spectrometers are really, really powerful machines. They have the speed, resolution and sequencing depth to analyze your samples in details. One of the most amazing aspect of mass spects (I'm kind of a poet!), is that they can be dialed according to what you need to know from your sample. For example, they can be very precise while looking at only one thing. However, they can also be very broad in their analysis to have a larger idea of what's going on. Whatever you need to look at, MS has the power to do it.

8. Combine with sample preparation to get amazing results

With the right preparation techniques (see our blog post on sample preparation), you can enrich your sample for a specific type of molecules. For example, you could concentrate phosphorylated proteins by using titanium oxyde magnetic beads. This would allow you not only to verify if your protein of interest is phosphorylated, but also to see every phosphorylated residue on your protein. This kind of test can be very useful to study cell signaling events. Of note, this can be used with any post-translational modification that can be targeted by an affinity purification method. If you are studying smaller molecules, mass spectrometry could help you to detect, identify and quantify the different metabolites of your drug of interest. 

9. and 10.  It can save you time and money!

I know I said 10 reasons, but reasons 9 and 10 really come together, since time is money. Everyone want to complete their milestones efficiently, as fast as possible and with the best results possible. Well, this is essentially what LC-MS/MS does. Yes, mass spectrometry can be a costly technique and this fact alone does scare investigators. However, they may be missing the larger picture. If you try to compare a task undertaken by LC-MS or by conventional scientific approach (taking into account, the material, the human ressources and the time), the robustness, power, and reproducibility of MS to rapidly lead to tangible results greatly outperforms conventionnal approaches. All in all, one well conducted MS experiment will not cost more than numerous tries with conventional molecular biology techniques. And if you opt for omics experiment, it will yield a heck of a lot of data, on which you can feed for months!

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We listed here some of the reasons that could get you to turn to MS for a future experiment. While avoiding MS to do the experiment in your own lab can be what seems to be the easiest option, remember that the power of mass spectrometry can give a huge boost to your research projects, if designed and done properly. Whether you want publications, develop IPs or commercialize better produts, LC-MS can be a game changer when added to your current lab tools. In addition, the use of omics experiments can most certainly accelerate the understanding of your research model and also lead to several new research projects! Let's hope this post realigned your thoughts on the matter closer to what we feel is the reality!

Topics: Sample preparation, Mass spectrometry

Written by Jean-Philippe Couture, Ph.D.

Jean-Philippe Couture
Jean-Philippe is an Application Specialist in charge of Customer Experience at PhenoSwitch Bioscience.
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