Methods for electrode cleaning for Echo MS systems

Jun 3, 2025 | Blogs, Echo® MS+ system, Pharma | 0 comments

Read Time: 2 min

Depending on the samples that you are running on the system, it is possible for the Echo MS electrode to become dirty or occluded over time. Below are two different cleaning strategies that will be helpful for you to maintain your system and keep your electrodes running well.

Quick cleaning protocol

This protocol is easy to perform between running your sample plates.

From the Maintenance menu of the Echo MS direct control, select OPI Port Access then Lift to provide access to the top of the OPI port.
Disconnect electrode by loosening the finger tight red nut and pulling straight up
Place the OPI port end of the electrode into solvent. With the MS system still active, the draw created from the GS1 flow will draw solvent through the OPI into the MS source, turn Spray voltage to 0.
Wash with Milli-Q water for 1 min
Wash with 20% Acetonitrile with 0.1 M Formic Acid (0.4% FA) for 20 min
- Drawing speed is about 450 µL/min based on the consumption of 20% Acetonitrile with 0.1 M FA
Wash with Milli-Q water for 1 min
Reattach the electrode to the system and tighten the red nut finger tight.
Restart the mobile phase flow and check the Maximum Supported Flow (MSF)

Intensive cleaning protocol

This protocol is an offline protocol that can be used periodically for a more intensive wash of the electrode or to recover electrodes that are suffering from reduced flow rates.

Connect the OPI electrode to a small union (1/16 to 1/32) , IDEX Part # P-881 )

Place the electrode end of the capillary in a waste vessel capable of holding 200 mL or more
Flow at least 200 ml of 50% methanol through the electrode at a flow rate of 5 – 8 mL/min using an HPLC pump
Test on Echo MS system for droplet linearity, reproducibility, and peak shape
If storing the recovered electrode flush with 100% methanol before storing.

Some electrodes may not be able to be recovered but we have had good success with this method.

Why middle‑down and subunit MS analyses powered by EAD are transforming biopharmaceutical characterization

As an analytical strategy, middle-down mass spectrometry (MS) workflows characterize biotherapeutic proteins by analyzing large, digested protein fragments or defined subunits, rather than fully intact proteins (top-down) or digested peptides (bottom-up). A middle-down strategy combines the strengths of top-down and bottom-up approaches by delivering high sequence coverage and structural specificity while maintaining relatively simple sample preparation. In practice, middle-down analysis enables accurate mass measurement, rapid sequence confirmation, and localization of key post-translational modifications (PTMs) on protein subunits that are directly relevant to product quality.

Why electron-activated dissociation (EAD) improves sequence variant analysis in biopharma LC/MS workflows

In biopharmaceutical development, sequence variants (SV) are considered an inherent risk of producing complex proteins in living systems. Sequence variants are unintended changes to the amino acid sequence of a biotherapeutic and can be caused by errors in transcription or translation in the host cell, or cell culture and process conditions. Detailed analysis of SVs is important in process and product development to ensure the drug’s safety and efficacy. Even low‑level sequence variants can have significant implications for product quality, safety, and efficacy, making their accurate detection and characterization a critical requirement across development, process optimization, and regulatory submission.

How NFD improves impurity detection and peak integration in CE SDS workflows

CE‑SDS remains a cornerstone assay for characterizing fragmentation, aggregation, and product‑related impurities in therapeutic proteins. UV detection has been the long‑standing standard. However, it frequently struggles with baseline noise, limited sensitivity for minor fragments, and subjective integration.

Posted by

John Gibbons

Trained and working in Organic Synthesis I started using mass spectrometry to aid in my synthesis work. As my interest in mass spectrometry grew, I change roles several times within the pharmaceutical industry to be able to focus on its use and applications. I joined SCIEX in 2006, initially as a demo chemist, then with R&D, primarily focused on Analyst, and eventually SCIEX OS software development. More recently I switched to technical product management for Echo MS systems.

0 Comments