Peptide and Protein Bioanalysis

A Quantification Workflow Designed for Large Molecules

Waters Peptide and Protein Bioanalysis solutions accelerate your project timelines, increase productivity, and shorten the gap between delivery of samples to your lab and the results required to make business decisions.

We deliver a complete solution, on a familiar LC/MS/MS platform, positioning your lab to approach the quantification of peptides and proteins with confidence.

Overview

Solution Overview

The Challenge:

Simplified, bioanalytical method development applicable to a wide range of peptides/proteins.
Accuracy, precision, and sensitivity equal to a ligand-binding assay, but with shorter development time.
High throughput, leading to faster quantification of samples from PK studies or clinical trials.
Peptide and protein bionanalysis on an existing, familiar platform.

The Waters Solution:

Integration. We combine industry-standard LC/MS/MS technology, software tools that automate entire steps of the sample preparation and peptide/protein quantification process, and highly-specific protein/peptide separation columns—delivering a total bioanalysis solution.
Enhanced and accelerated results. Our solution meets or exceeds the traditional ligand-binding assay development approach—but months in assay development now become weeks or even days.
Single platform. Small molecule and multiple analyte peptide/protein bioanalysis can be accomplished on the same platform.

Critical for Peptide and Protein Bioanalysis: Sample Preparation

One challenge in peptide and protein bioanalysis is the complexity of the plasma proteome and the fact that many biotherapeutics are present at concentrations many orders of magnitude lower than the most abundant, endogenous plasma proteins. This makes the need for appropriate sample preparation paramount. Typical steps in these workflows include cleanup at the protein level using techniques such as affinity purification or depletion plates, and post-digest peptide-level cleanup options such as SPE. This figure demonstrates the differences and incremental benefits achieved through several approaches to sample preparation using a therapeutic monoclonal antibody in human plasma.

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Comparison of sample preparation options for protein quantification

SPE-LC/MS/MS Assay Workflow

Preparing the sample
The key to a selective methodology is through the use of Oasis SPE µelution plates. The orthogonality of Oasis particles and modifications allow a simple yet flexible method of analyte extraction. The µelution plates mean that precious analyte can easily be concentrated and labile peptides undergo the minimum of sample manipulation for high recovery and sensitivity.

Chromatographic separation of the analyte
ACQUITY UPLC Peptide Separation Technology (PST) Columns provides the pore size required for larger molecules for accurate and precise retention characteristics – sharp, narrow UPLC peaks for accurate and precise quantitation.

Detecting the analyte with MS/MS
Using the Xevo TQ-S tandem quadrupole mass spectrometer, a mass range of m/z 2000 on the first and second quadrupole allows the analyst to select the best charge state of the peptide to monitor for a high level of flexibility and simplicity of method development. IntelliStart streamlines the process by selecting the best precursor and product ions, even when the product ion has a higher m/z than the precursor ion.

Combine the market-leading sensitivity of Xevo TQ-S with the selectivity and efficiency of Oasis and ACQUITY UPLC, and developing effective methods for peptide bioanalysis is significantly simplified.

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