Hi everybody.
We are looking for a Mass spectrometer with high resolution to indentify very low abundant proteins in a complex matrix, and able to perform and accurately quantitation of target peptides.
I have experiencience in target proteomics using a triple quadrupole in MRM mode, however this is not a good option to shotgun proteomics. We need to be able to carry out both approaches using the same mass spectrometer.
Please, any suggestion are welcome, I have read something about Q-Exactive Orbitrap, which can do accurtly both approaches.
Thank you very much.
Dear Elias Hurtado-Gaitán,
May i direct you to this valuable, free on-line resource https://planetorbitrap.com? Planet Obribtrap is a user forum managed by Thermo, where you may find all the info on individual instrument models and their applications including actual application notes, and user forums. The site does require registration as a user, but again, this costs nothing.
In my personal opinion, an LC-MS/MS platform based on recent Q-Exactive model is an excellent choice for shotgun proteomics. Note emphasis on "recent"! Quantitative ability of any MS-based measurement will strongly depend on your experimental design and software used for analysis of obtained MS data. I, personally, prefer PEAKS Studio over Thermo quantitative packages, although it works best for protein quantification identified by minimum 3-5 peptides rather than individual peptides. If individual peptide quantification is needed, then open source Skyline software does a nice job, but it helps to learn how it works before making measurements in order to understand the data treatment/normalization options and general principle, which will influence your experiment design.
Hope this helps, and best wishes in your research!
Elena
Yes, although new versions like orbitrap fusion have long been launched. I personally have a very satisfactory experience with this awesome machine. Try to perform an initially step to separate the highly abundant proteins, if possible, since they mask the low abundant ones. The machine is quite sensitive anyway.
Yes, it is a very good choice. Unfortunately, still very expensive...
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