Tuesday, June 27, 2017

CHarge Ordered Parallel Ion aNalysis (CHOPIN)

They started making hybrid mass spectrometers so that one box could have more capabilities than any single instrument alone. A few years ago, a new type of hybrid instrument was produced that has a quadrupole an ion trap and a Kingdon trap system. In the simplest use of the experiment for proteomics, the high resolution trap acquires MS1 peptide signals while the low resolution trap simultaneously acquires fragmentation data from ions isolated via the quadrupole and fragmented either by CID in the ion trap of by HCD on the ion's way to the trap.

With all these capabilities, could there be a better way? These authors seem to think so!

What is it? A really complicated instrument method that further prioritizes the capabilities of each fragmentation type, mass analyzer, and instrument parallelization.

Honestly, I looked at this for a couple hours last night and I'm still not sure I understand where the extra time is coming from, but I do understand that over the course of one cycle they are able to gain 7 extra MS/MS scans. I also understand that this is an instrument method that I could just copy from their Supplemental info and give it a try!

I highly recommend checking out the RAW files at PRIDE here.  They evaluated this method on an offline fractionated cancer cell line with both the standard method and with CHOPIN. In both cases, these are really nice datasets.

I respect the amount of work that they put into optimizing this instrument method. However, the highlight of this beautiful paper for me might be the use of the Elastase enzyme in conjunction with trypsin to get the absolute deepest proteome coverge!


  1. Dear Ben,

    I would like to add that this method was developped using the 2.0 tune for Lumos instrument.

    The precursor selection using the least intense ion for fragmentation is not anymore available starting fron the tune 2.1.

    Best regards,

  2. Hi Ben,
    thanks for mentioning the paper...glad that you like it! The extra MSMS scans come from acquiring simultaneously MSMS in the Orbi and the ion trap...if there are enough precursors, this is very beneficial.
    It is correct that the "least intense" priority has vanished in 2.1, but you can still do this by just adding another decision into the method, basically generating intensity bins to pick from.