Mass Spectrometry and Proteomics - Frequently Asked Questions

Mass Spectrometry and Proteomics - FAQs

1 - Is it really unlimited use?

Yes - mostly.  There is no specific limit on how many samples you can run other than those imposed by sample capacity of the instrumentation and how many other users need time. You cannot run your samples in preference or to the exclusion of anyone else.  You have to share. However if the machine is free you can use it non-stop.  We want the machines running 24/7.  They cost almost the same if they are working or not so we may as well run them as much as possible. 

2 - Are there any hidden costs?

Generally No.  We cover the cost of all system solvents, columns and general mass spectrometry consumables such as sample vials.  We even provide trypsin and buffers for small volume users.  We will only charge for the above if you start working on a massive scale.  We also do not cover the cost of expensive reagents like SILAC, iTRAQ or TMT labels.  However our Dimethyl Labelling reagents are free. 

3 - Can I submit just a few samples instead of the membership?

Yes.  But we do not normally work that way.  We usually find that one or two samples inevitably turn into 4 or 5 samples when controls are added and then another 5 samples when a repetition of the result is required.  By that time you may as well have paid the 3 month cost and done as many controls and repeats as you like.

4 - I would prefer if you just did it all for me and sent me the result.  Can you do that?

No.  This is not how we work.  There are plenty of other proteomic and mass spectrometry facilities around that can do this sort of thing.

5 - How hard is it to process my gel spots?

Its not hard at all.  If you can run an SDS-PAGE gel you can process a gel spot.  If it was hard we would not have 70 people doing it.  We have the mass spectrometry setup ready to go so all you need to do is put the sample in the queue.  If you want to know how the machine works then we can explain but most people do not care. They just want the gel result.  We have an online system that lets you search and analyse your data from anywhere. There is no need to return to the MSPF to do the data analysis.

6 - What kind of samples can I analyse?

We are principally a proteomics facility so any protein mass spectrometry experiment you can think of, we are here to help:

  • Gel spots,
  • Phosphorylation,
  • Ubiquitination,
  • Comparison of all proteins in a sample,
  • SILAC,
  • iTRAQ,
  • TMT,
  • Dimethylation,
  • TAILS,
  • Quantitation,
  • Immunoprecipitation of protein complexes,
  • Disulfide arrangements,
  • Post-translational modifications. 

We also run an instrument for the chemists so they can test their synthetic products – did I get the synthesis right?  If you are working with, or want to look at metabolites like amino acids, lipids sugars, etc. then you should contact the laboratory next door to us Metabolomics Australia

7 - Can I test recombinant proteins?

Yes. We have a dedicated mass spectrometer set up for the analysis of intact proteins.  It is accurate to about 0.5 Daltons on a 50,000 Da protein. This instrument is able to spot a single disulfide bond in a recombinant protein. So, not only can you check that you expressed the correct protein, you can also get structural information that would never be seen on an SDS-PAGE gel. Not only that; its faster than running a gel. It take about 15 minutes to analyse one intact protein. If you want to know how the machine works, then we can explain, but most people just want the result. So we can show you how to open a pre-made method and load a sample then press the "go" button. Simple!

8 - Can I test chemical synthesis?

Yes. We have a dedicated mass spectrometer for the chemistry groups to test their synthetic products. Mass accuracy is good to about 2 decimal places. If you want to know how the machine works then we can explain, but most people just want the result. So we can show you how to open a pre-made method and load a sample then press the "go" button. Simple!

9 - Do non-University of Melbourne academics receive the same access?

Yes. The only difference is that external academics pay about 20% more for the same thing – which is still an absurdly low price.

10 - Can industry groups use this facility?

Yes. Industry groups are welcome and we have a number of current industry clients.  The cost for industry groups is approximately 150% more than the University of Melbourne rate. This is still an absurdly low price for access to millions of dollars’ worth of mass spectrometry hardware and expertise. For more details contact us.

11 - Can you teach our students?

Yes. This is our primary purpose. Our staff are often part of PhD committees and we often co-supervise students.

12 - We need some proteomic work as part of a grant proposal.  Can you help?

Yes. Our staff are involved in many projects and we are often included as AIs or CIs on grant proposals. We can help with grant writing where required.

13 - How do we analyse our data?

This depends on your samples. For many samples such as gel spots, or trypsin digests of protein complexes we have an online search application that allows you to access and search your data from anywhere in the world. There is no need to return to the lab to do the analysis. For the more complicated work we have computer hot desks in the office area and we teach you how to do the analysis – at any time you can ask questions and get the help you need to get the work done.

14 - Do you do mass spectrometry imaging?

No. There are other groups specialising in this area and at the present time we do not have the resources to do this kind of work.