Opentrons

Smile! Protein and peptide sample preparation automated

Application for high throughput proteomic sample preparation for LC-MS analysis using liquid-handling platforms from Opentrons

The challenge:

Plasma samples contain proteins spanning an enormous range of concentrations, making it challenging to generate reliable, comprehensive data. Manual preparation introduces variability between operators and across batches, compromising reproducibility. In addition, manual bead-based workflows are labor-intensive and time-consuming, limiting throughput and scalability.

The solution:

Automating plasma proteomics with Opentrons® brings consistency and reliability to every step of the magnetic-bead workflow, from enrichment through lysis and digestion. The platform ensures controlled liquid handling and uniform processing conditions, and when paired with a positive pressure device such as the Tecan Resolvex® A200 for peptide cleanup, it enables a rapid and streamlined end-to-end procedure. This setup reduces hands-on time from hours to minutes without compromising the depth of protein and peptide identification achieved with manual preparation.

^*Opentrons^{is a registered Trademark of a third party}^*Tecan^{is a registered Trademark of a third party}

Apply! Simple, streamlined workflows

1. Adding samples

Samples should be in liquid form such as plasma or serum.

2. Kit setup

Set up the PreOmics consumables on the Opentrons deck.

3. Sample preparation

Run pre-defined protocols in consultation with your automation specialist.

4. Peptide Clean-up

Perform the peptide cleanup using a positive-pressure system, such as Tecan Resolvex A200, or use a centrifuge.

5. MS analysis

Analyze samples by LC-MS.

6. Data processing

Process data to see improved peptide identities.

Results

**Figure 1:** Proteome depth and cross-contamination assessment of ENRICH-iST on the OT-2 platform. Number of identified (A) peptides and (B) proteins across LC blank, manual blank, OT-2 blank, manual plasma, and OT-2 plasma samples.

**Figure 2:** Reproducibility of manual versus OT-2–based ENRICH-iST processing. Distribution of (A) peptide-level and (B) protein-level coefficients of variation (% CV) across replicate plasma samples processed manually or on the OT-2.

‍More detailed explanations about these results can be found in the Opentrons® TechNote.

DOWNLOAD NOW

PreOmics^®'

Opentrons

values

Smile

Confident in Sample Quality

Automated workflows maintain equivalent proteome depth to manual preparation
No detectable carryover or cross‑contamination across wells, confirmed by blank‑run analysis
Improved reproducibility with lower peptide and protein CVs compared to manual workflows

‍

Relax

Stress-Free, High-Throughput Workflow

Automation on the Opentrons platforms reduces hands‑on time from ~3 hours to ~10 minutes
Scalable format supports 8–96 samples through programmable magnetic‑bead handling and liquid transfers
Standardized processing minimizes operator‑dependent variability and ensures consistent execution

Realize

Achieve Research Goals Faster

Automated workflow enables reliable, scalable plasma proteomics for large cohorts and multi-site studies
High sensitivity preserved: approx. 10,000 peptides and 1,300 proteins identified per plasma sample
A robust solution supporting biomarker discovery and translational research with consistent performance across replicates

PepSep® Columns & Emitters

Request quote

Cart

Request a quote

Opentrons

Request quote

Instrument

Application for high throughput proteomic sample preparation for LC-MS analysis using liquid-handling platforms from Opentrons

Opentrons

Request quote

Instrument

Application for high throughput proteomic sample preparation for LC-MS analysis using liquid-handling platforms from Opentrons

Opentrons

Request quote

Instrument

Application for high throughput proteomic sample preparation for LC-MS analysis using liquid-handling platforms from Opentrons

PepSep® Classics* – Performance Meets Simplicity

Versatile columns for standard and advanced proteomics workflows.

50 cm × 75 µm × 1.5 µm → Spectral Library Generation | Art.-Nr. 1895846
25 cm × 75 µm × 1.5 µm → Sensitivity | Art.-Nr. 1893484
25 cm × 150 µm × 1.5 µm → Versatility | Art.-Nr. 1893476
15 cm × 150 µm × 1.5 µm → Throughput | Art.-Nr. 1893474
8 cm × 150 µm × 1.5 µm → Speed | Art.-Nr. 1893470

* additional column dimensions available. The full list of dimensions can be found in the brochure

PepSep® Advanced – Next Level Sensitivity

For the highest performance and maximum peptide coverage.

25 cm × 75 µm × 1.5 µm → New gold standard | Art.-Nr. 1919826

CaptiveSpray 2 Emitters

Plug-and-play emitters for hassle-free CaptiveSpray setup. Two variants, separate from columns for easy replacement and longer LC-MS system life with peak performance (Pack of 2 pieces).