Smile! Protein and peptide sample preparation automated

Application for high throughput proteomic sample preparation for LC-MS analyses using iST and SP3

The challenge:

How do you automate sample preparation of very dirty samples or where harsh denaturation reagents are needed? Typically these samples cause issues with proteomic sample preparation as the reagents can adversely impact digestion and subsequent LC-MS analyses.

The solution:

Use the combined advantages of SP3 and iST! Together, PreOmics and Tecan® have developed an automated LC-MS sample preparation workflow, combining the ability to wash and digest samples when bound to the SP3 beads and then do the clean-up step. This application meets the demands of efficient, robust proteomics sample preparation for difficult samples for LC-MS analysis with the bonus that an automated workflow helps labs decrease the hands-on time and produce high quality samples for LC-MS analysis!
“Tecan” is a registered Trademark of a third party

Relax! SP3-iST compatible workflows

Adding samples
Samples should be liquid, homogenates or a soft pellet.
SP3-iST kit set up
Prepare the SP3 beads and the DIGEST and add all reagents to the Tecan instruments.
Sample preparation
Wash, lyse and digest samples while bound to SP3 beads on the Tecan Freedom EVO®.
Sample clean-up
Samples are automatically transferred to the clean-up plate and processed on the Tecan Resolvex® A200.
MS and data analysis
Analyse samples by
LC-MS and process the data.


Table 1: Comparison of nanoLC-MS results for the SP3-iST automated and manual protocols.

Additional data can be found in the Tecan® SP3-iST application note. The numbers of PSMs and IDs for both peptides and proteins were very consistent for all samples, regardless of protein input, as well as between the manual and the automated protocols. Approximately 27,370 peptides and 2,960 proteins were identified in all samples, in agreement with the expected performance of the nanoLC-MS measurements conducted. This demonstrates the high efficiency, quality and robustness of the automated SP3-iST workflow for the entire range of tested input amounts (15-50 μg).

PreOmics SP3-iST Values


Improved sample quality

Working range: 1-100 µg
Good consistency between manual and automated workflows
Excellent missed cleavage rate


Challenging sample preparation automated

Benefit from combined SP3 and iST technology
Set up and walk away, hands-free LC-MS sample preparation
Fully flexible, process 1 to 96 samples


Cleaner peptides ready for analysis

Standardized workflow with high data reproducibility
Dual clean up step removes hydrophilic and hydrophobic contaminants
Achieve ready-to-measure peptides


Applying the science
Find out more about the wide range of applications and sample
types to which PreOmics technology has been successfully applied