I have a somewhat strange discussion to start! A reviewer has asked that we include references for the first time each proteomic mass-spec technique we cover in a review was used. I've been trying to find a good historical review, but it's proving harder than I thought. It's also not easy to draw a line as to where one approach becomes another; for example, the Reviewer suggests that Desiderio 1996 was the first use of targeted proteomics, but of course it doesn't fit into what we would call SRM/PRM today.
So, in your opinion, what would be the first use of these techniques?
Label free quantitation
SRM
PRM
DIA/SWATH (presumably Aebersold)
Isobaric labelling plus and minus fractionation?
Or alternatively, do you have a comprehensive historical review to recommend? Thanks!
Hello Becky,
Sorry to learn about yet another pity state of peer-review. Below, I try to help the cause by providing some affirmative/ confirming references of the terms you must have mentioned in the Review:
Basically, the Reviewer wants you/ someone like me, to do a literature search for his papers/ grants or wants really to serve the proteomics research community! HUPO website should have it all- or who knows the reviewer is Rudi himself! : )
But then I did dig up some of these stuffs and could find some:
[1] LFQ/Spectral Counting first time USE is 2004: https://www.sciencedirect.com/science/article/pii/S0168170215300617
As per this: https://pubs.rsc.org/en/content/articlelanding/2014/an/c4an00463a#!divAbstract there are some other time lines.
[2] SRM FIRST time is here: Picotti, P., Bodenmiller, B., Mueller, L.N., Domon, B. & Aebersold, R. Full dynamic range proteome analysis of S. cerevisiae by targeted proteomics. Cell 138, 795–806 (2009). First demonstration of the capability of SRM to detect and quantify proteins over the whole range of cellular concentrations in S. cerevisiae. as per https://www.nature.com/articles/nmeth.2015
[3] Isopbaric labelling should be attributed to: Gygi SP, Rist B, Gerber SA, Turecek F, Gelb MH, Aebersold R (October 1999). "Quantitative analysis of complex protein mixtures using isotope-coded affinity tags". Nature Biotechnology. 17 (10): 994–9. hus Aebersold himself too. Also validated: https://sciex.com/community/blogs/mass-spectrometry-and-life-sciences-blogs/the-history-of-isotopic-labels-for-quantitative-proteomics as ICAT technology. ITRAQ is 2004. TMT is 2003.
[4] For fractionation approaches, I would consult Mostovenko, E., et al. (2013) “Comparison of peptide and protein fractionation methods in proteomics“, EuPA Open Proteomics, 1 (pp. 30–7), doi: 10.1016/j.euprot.2013.09.001. and see what he/she has to tell about the evolution of these methods (I believed it started with TMT???!!!). Possibly dates back to Gilar, M., Olivova, P., Daly, A. E., and Gebler, J. C. (2005) Two-dimensional separation of peptides using RP-RP-HPLC system with different pH in first and second separation dimensions. J. Sep. Sci. 28, 1694–1703 ; Toll, H., Oberacher, H., Swart, R., and Huber, C. G.(2005) Separation detection, and identification of peptides by ion-pair reversed-phase high-performance liquid chromatography-electrospray ionization mass spectrometry at high and low pH. J. Chromatogr. A 1079, 274–286; Gauci, S., Helbig, A. O., Slijper, M., Krijgsveld, J., Heck, A. J., and Mohammed, S.(2009) Lys-N and trypsin cover complementary parts of the phosphoproteome in a refined SCX-based approach. Anal. Chem. 81, 4493–4501 and Ducret, A., Van Oostveen, I., Eng, J. K., Yates, J. R., 3rd., and Aebersold, R.
(1998) High throughput protein characterization by automated reverse-phase chromatography/electrospray tandem mass spectrometry. Protein Sci. 7, 706–719 etc.
[5] PRM is here: Peterson, A.C. et al. Parallel reaction monitoring for high resolution and high mass accuracy quantitative, targeted proteomics. Mol. Cell. Proteomics published online (3 August 2012).
[6] DIA/SWATH: Röst, H.L., Rosenberger, G., Navarro, P., Gillet, L., Miladinović, S.M., Schubert, O.T., Wolski, W., Collins, B.C., Malmström, J., Malmström, L. and Aebersold, R., 2014. OpenSWATH enables automated, targeted analysis of data-independent acquisition MS data. Nature biotechnology, 32(3), p.219. and definitely Rudi !!
[7] In my review, I did also put a summary figure (but no historical descriptions in the text): https://onlinelibrary.wiley.com/doi/abs/10.1002/elps.201700401 So I only attach the figure for your reference.
I would put the above to the reviewers, and see if they disagree or have more accurate information.
Thanks,
Biswa
Wow, thanks so much Biswapriya! I spent all of today looking at this and I'm happy to say that we agree on all of the ones where I felt I'd probably got it right! I will check out the others tomorrow and compare with what I found. Thank you again - this is extremely helpful!
I took a better look at this this morning Biswapriya. I totally missed the PRM one, I had a different paper from a few months later. So that's great! I think there is a slightly earlier paper from the exact same group for DIA:
Gillet, L. C.; Navarro, P.; Tate, S.; Röst, H.; Selevsek, N.; Reiter, L.; Bonner, R.; Aebersold, R. Targeted Data Extraction of the MS/MS Spectra Generated by Data-independent Acquisition: A New Concept for Consistent and Accurate Proteome Analysis. Mol. Cell. Proteomics 2012, 11, O111.016717, doi:10.1074/mcp.O111.016717.
The one I'm really uncertain about is label free - the difficult there is obviously defining when generic LC-MS/MS became "label free." I think I'm going to stick with the 2003 Nature review by Mann and Aebersold and leave it at that :)
Once again, thanks so much for your help - it's really good to know that someone else came to similar conclusions from a literature search.
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