A nucleic acid MS/MS search engine!!!!

Do you guys know how most labs check the accuracy of their PCR products?

By running gels....

It looks super precise -- until you realize that 100 base pairs is like 40kDa. You can get higher resolution (longer) gels, of course -- and there are other capillary based technologies -- but these things just generate an average mass. They don't tell you if something is wrong.

If only we had a NUCLEIC ACID SEARCH ENGINE!  We could use mass spectrometry to get a precise mass -- and sequence things! But that's more futurist mumbling, right?

Starting with BioPharma Finder 2.0 -- nucleotide deconvolution is a feature -- I was thrilled to find it and to see support in some other software as well. That's a good sign -- but a Nucleic Acid Search Engine is a critical next step.

If you'd asked me yesterday -- I'd guess 3-5 years and we'd see one...fortunately, I'm wrong a lot!

Consider how old-fashioned mass measurements are of amplified and often purified nucleotide sequences.

This group jumps a light year ahead and looks at how REAL RNA SEQUENCES are not only aligned -- but modified in an epigenetic sense.

Using HCD OT fragmentation of transfer RNA from people, they find they can monitor at least 20 different modifications -- effectively blowing open the doors on an entirely new way of studying epigenetics -- and maybe opening a completely new field for mass spectrometry!?!?!

I'm not sure the importance of this preprint can be overstated. This could revolutionize molecular biology and our understandings of the control between transcription and translation. And the method is straight-forward -- and the software is available for download here. Right now.