Automate Your Sample Prep with the Biomek Workstation and Protein Preparation Kits

Sep 15, 2015 | Blogs, Life Science Research, Proteomics | 0 comments

Frankly, who has the time? With so many samples to prepare, day after day, week after week, month after month, there’s time for little else. And those repetitive tasks of pipetting over and over again, just keep, well, repeating.

It’s time to automate your sample prep! In this technical note, see how researchers reduce day-to-day variability resulting from manual, time-consuming, and multi-step protocols such as the protein denaturation, reduction, alkylation and digestion steps which precede LC/MS analysis.  Here, the researchers use a Biomek NXP Span-8 Workstation and protein preparation kits with ready-to-use reagents to automate the entire workflow. Then, they tested the automated workflow for their quantitative proteomics studies.

First, the reproducibility of the digestion protocol alone was tested. As shown in the technical note, very high reproducibility was obtained, with about 90% of peptides monitored by LC/MS having digestion reproducibility below 10% CVs. Next, the digestion protocol was transferred to the Biomek NXP Span-8 Workstation. Many of the proteotypic peptides analyzed showed very high reproducibility with %CVs ~ 2-3%. As expected, for both the manual and automated protocol some peptides showed higher variability than others from the same protein, reflecting inherent digestion heterogeneity. When developing assays for peptide/protein quantitation, it’s important to assess the variability in digestion reproducibility in order to choose the highest performing peptides. Automation of this step can greatly simplify the assessment.

Finally, the researchers tested the reproducibility across different labs and workstations, and across multiple days. The results show very similar cumulative reproducibility curves with more than 80% of peptides monitored having CVs below 10%, demonstrating that the automation method and protocol were very robust and transferable.

To learn more, download the full technical note and see how the Biomek Workstation with optimized protein preparation kits can help you save time while providing reproducible sample preparation today.

Now, what will you do with all that free time?

ProteinPilot phosphopeptide library and DIA-NN

I have prepared a spectral library for a phosphopeptide enriched sample and I am generating my SWATH samples from similarly enriched samples. The problem is that when I use DIA-NN for the retention time alignment and quant, it doesn’t recognise the terminology of the spectral library annotated by ProteinPilot. DIA-NN recognises Unimod:21 for phosphorylation, but PP uses phospho(Tyr) etc. Other than changing the data dictionary to get around the mismatch, anyone have any suggestions for how I might resolve this? Thank you, Roz

Current proteomics software compatibility for ZenoTOF 7600 system

Below is a summary of various other software packages that are useful for processing proteomics data from the ZenoTOF 7600 system.  Note this list is not comprehensive and only covers the tools we have lightly tested to date. Acquisition Type Software Files needed...

Sequential processing of multiple data-files in ProteinPilot

I would like to use ProteinPilot 5.0.2 to process data-sets containing 16 wiff files acquired from fractionated peptides on a 6600 TripleTOF. A Precision T7910 workstation struggles to process four files in parallel and I would like to be able to queue sequential processing of individual files overnight. I currently use the ‘LC ‘ tab to load and process individual data-files but this leads to parallel processing. Is it possible to generate 16 .group files sequentially?

Posted by



Submit a Comment