How ‘Pippi’ works as a team member in a protein analysis laboratory in Denmark - Automate your complex and variable protocols for protein analyses

Proteins are the most versatile and manifold macromolecules in nature. Our knowledge about proteins, their biological functions, therapeutic effects or potential technical usage is accumulating rapidly. We are fascinated by these ‘sensitive lab pets’ because the insights will promote the emergence of new technologies in material science and/or biomedicine. And this ultimately motivates us to work hard for any finding we can make about these amazingly versatile macromolecules.

But everybody who handles proteins or peptides in the lab knows: The sample preparation procedures are very laborious and challenging. Aside of all scientific pioneering spirit it is crucial to produce high quality and – even more importantly – reproducible results to prove somebody’s findings. This is the most important argument for laboratories to acquire automated liquid handlers. Did you ever think about automating your wet lab procedures?

Alphalyse®, a contract research organization in Denmark and the USA, did so. The laboratory team at Alphalyse deals with a large variety of sample types (biosimilars, antibodies, peptides, vaccines, etc.), and copes with a lot of different analysis workflows such as host cell protein analysis and cutting-edge mass spectrometry techniques. One year ago, they acquired their lovingly called ‘Pippi’ (named so after the character by Astrid Lindgren), a reliable and robust automated liquid handler (epMotion® 5075vt).

“For us the automation of routine procedures is important because we can now run long procedures overnight, saving us a substantial amount of time. This both reduces our turn-around time on the actual project and frees up time, which we now spend on more variable manual tasks. In addition, complex procedures can be run reproducibly by different persons, ensuring a stable quality. Finally, manual pipetting – possibly damaging the hand, arm and shoulder - is reduced, creating a better work environment.“ Anette Resmussen



The epMotion 5075vt exhibits an integrated vacuum manifold, which supports many different filter plate formats, as well as a Eppendorf ThermoMixer® position where enzymatic digestion of proteins can be performed fully automatically.

The team at Alphalyse performs a variety of different protein sample preparation methods where Pippi, their liquid handler, is involved with:

Characterization of proteins – sequencing, disulfide bridges, glycosylations, etc.

At Alphalyse the liquid handling platform epMotion 5075vt (Pippi) performs a complete workflow starting from soluble protein, to digestion and protein purification. Their in-house protocol employs two different SPE filter plates, which can be processed on Pippi´s vacuum manifold. Protein digestion is performed on the integrated ThermoMixer position (4-90 °C, up to 2,000 rpm for up to 24 hours), while samples are automatically transported by a gripper. The integrated vacuum manifold is mounted together and dissembled fully automatically.


Throughout the complete process of up to 8 hours there are just two times that somebody needs to rearrange the labware on the liquid handler deck. This protocol can be performed with 1 to 96 samples, which allows for a high flexibility daily freeing up time for other methods that still need manual processing.

In-gel digestion of proteins

The preparation of proteins that have been separated in an SDS-PAGE is a standard method for “protein people”, and so at Alphalyse. Their in-house protocol starts with tiny pieces of gel material, which contain the desired proteins, in a 96 well microtiter plate. The whole process starts with dehydrating, reducing, and alkylating the gel material, followed by protein digestion using specific proteases. The digestion reaction is terminated by adding TFA. Pippi even takes over the loading of the mass spectrometry plate (MTP AnchorChip™ 384), which requires an experienced and steady hand if performed manually.

epMotion® 5075t – Vacuum functionallity

Aside of being a great asset to the laboratory team at Alphalyse, Pippi is also a resource friendly worker. The epBlue™ software of the epMotion allows for tips to be re-stored and re-used when the same liquid is transferred. This considerably reduces the plastic waste associated with sample preparation, while the accuracy and precision of the liquid transfer is not impaired.
Secondly, the platform can be programmed in a way so that every single well of a filter plate can be used in independent sample processing runs. Thus, even if it requires a bit of exercise and concentration to tell the system, which specific wells are the ones for today´s run, the epMotion 5075v handles the expensive filter plates with 100 % efficiency.

Alphalyse® is a registered trademark of Alphalyse A/S, Odense, Denmark. MTP AnchorChip™ is a trademark of Bruker, USA. Eppendorf Thermomixer® and epMotion® are registered trademarks of Eppendorf AG, Germany. epBlue TM is a trademark of Eppendorf AG, Germany.