Hi,

I'd say that if you're planning to run a targeted proteomics approach, so knowing what proteins/peptides you're aiming for, the triplequad will be the best (most sensitive) option for quantitative purposes.

In case you're trying to map as many proteins in your samples as possible (untargeted) however, the ion trap might be favorable.

Hope this helps!

Different acquisition principles for different purposes. You are asking HRMS or TQ MS and this query can only be solved after clarifying the purpose. For a relative label-free quantification IT-TOF can also be used but you need to consider about the proteins (peptides) in terms of abundance. QQQ is sensitive enough to absolute quantification at trace amounts of several proteins on the other hand IT-TOF can enable to distinguish of major proteins (by exact mass of the corresponding peptides) by a relative quantitation approach. Even if IT configuration can enhance the sensitivity of the traditional TOF, they cannot respond as QQQ when the sensitivity is the bottleneck. I can strongly suggest QQQ if the signature peptides of the proteins are known otherwise you nearly have to own an HRMS equipped with mass filters such as Orbitrap or TOF...

Besides Shimadzu, Bruker TIMS TOFs (trapped ion mobility) are the new generation of highly sensitive TOF and should also be evaluated.

Thank you so much for the input mr. İsmail Emir Akyildiz and mr. Eef . May I further ask whether qTOF and qTRAP is sensitive enough (comparable to QqQ) to do relative quantification?