Sequencing Ion PGM libraries using Ion Proton

[MissDNA]

Has anyone sucessfully sequenced 200 bp libraries originally constructed for Ion PGM, using Ion Proton.

We have been told by tech support that it was possible and should work well but our experience so far has been proven disastrous.

After some tests we know for a fact we don't have any instrument nor reagents problem. When we sequenced the same libraries in the PGM we got median lengths around 170 bp and in the PGM around 75 bp. The amount of reads with low quality and polyclonals is very big.

I am not convinced Proton chemistry can handle 200 bp PGM libraries.

[MissDNA]

I got an answer from tech support:

PGM libraries are not compatible with available Proton chemistry due to their size. Proton libraries may have only up to 270 bp.

Size is critical for sequencing with Proton and even a 10bp difference can cause severe problems.

Imagine 60 pb!

[albert liu]

running 60 pool Ampliseq libraries for PGM on one Proton

HI MissDNA:

Just did two run of pooled samples on Proton.
With new Proton Seq 200 v3 kit, we run with 60 pool of ampliseq on one PI v2 chip.
The result was very similar to PGM run.
We did comparison before with early proton reagent ( PI chip and proton 200 kit ) which did not match PGM's perfromace.