SRM/MRM Assay for Mesothelin Protein Quantification in FFPE Samples

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Solution Overview

Problem

Current cancer treatments, including traditional chemotherapeutic agents and targeted therapies, often fail to selectively kill cancer cells, as they also affect rapidly dividing normal cells, and there is a need for more precise methods to determine the effectiveness of therapies based on cancer biomarker levels.

Innovation Solution

A mass spectrometry-based Selected Reaction Monitoring (SRM/MRM) assay is developed to quantify the Mesothelin protein (MSLN) in formalin-fixed tissues, enabling precise measurement of MSLN protein levels for improved diagnostic and therapeutic decision-making, using specific peptides and internal standards for relative and absolute quantitation.

Engineering Contradictions & Design Principles

VSEngineering Contradiction Analysis

1Reliability

If traditional chemotherapeutic agents are used to kill rapidly dividing cells, then cancer cells are killed, but normal rapidly dividing cells are also killed

Engineering Contradiction:

Improveselectivity of cancer cell killingVSAvoiddamage to normal cells

Core Design Contradiction:

ReliabilityVSObject-affected harmful factors

Solution Approach 1:

The patent changes the detection parameter from general cell division markers to specific protein expression levels (MSLN, CA125, HE4) to identify cancer cells more selectively, allowing differentiation between cancer and normal cells based on protein expression profiles rather than just division rate

Inventive Principle:

Principle #35Parameter changes

Solution Approach 2:

The patent replaces the mechanical/cellular approach of targeting dividing cells with a biochemical detection system using mass spectrometry to measure specific protein markers, enabling identification and targeting of cancer cells through their unique protein expression signature

Inventive Principle:

Principle #28Mechanics substitution (Replace mechanical system)

2Reliability

If targeted therapies are used to attack cancer-specific proteins, then selectivity is improved, but the complexity of determining which patients will benefit increases

Engineering Contradiction:

Improveselectivity of cancer cell targetingVSAvoidcomplexity of patient selection process

Core Design Contradiction:

ReliabilityVSDevice complexity

Solution Approach 1:

The patent creates a universal mass spectrometry-based assay platform that can simultaneously detect multiple cancer biomarkers (MSLN, CA125, HE4) in a single test, making the system multi-functional and applicable to different cancer types and therapeutic decisions without requiring separate tests for each marker

Inventive Principle:

Principle #6Universality (Multi-functionality)

Solution Approach 2:

The patent measures absolute protein concentrations rather than relative presence/absence, providing quantitative data that simplifies patient stratification by giving clear numerical thresholds for predicting therapeutic response

Inventive Principle:

Principle #35Parameter changes

3Measurement precision

If mass spectrometry is used to quantify MSLN protein levels, then measurement precision is improved, but the difficulty of detecting and measuring increases

Engineering Contradiction:

Improveprecision of MSLN quantificationVSAvoiddifficulty of MSLN detection

Core Design Contradiction:

Measurement precisionVSDifficulty of detecting and measuring

Solution Approach 1:

The patent performs preliminary sample preparation steps including formalin-fixed tissue processing and protein extraction to convert complex tissue samples into digestible protein extracts, making the subsequent mass spectrometry measurement feasible and accurate

Inventive Principle:

Principle #10Preliminary action

Solution Approach 2:

The patent uses specific peptide fragments of MSLN as intermediary targets instead of measuring the entire protein directly, allowing mass spectrometry to detect and quantify MSLN levels with high precision through these intermediate peptide markers

Inventive Principle:

Principle #24Intermediary (Mediator)

Applied Scientific Principles

This section explains which scientific principles are used to turn an abstract innovation direction into a practical engineering solution.

Function Achieved in This Case

This method provides accurate and precise quantification of MSLN protein levels, aiding in cancer diagnosis, prognosis, and personalized treatment strategies by correlating protein expression with therapeutic agent effectiveness, thereby enhancing treatment outcomes.

Implementation Method 1

detecting and/or quantifying the amount of a MSLN fragment peptide in a protein digest prepared from said biological sample using mass spectrometry

Methodology Applied

Scientific EffectMass spectrometry:

Data Source

PatentEP3295180B1SRM/MRM assay for the mesothelin (MSLN) protein

Publication Date: 2020.07.22 ONCOPLEX DIAGNOSTICS INC

AI summary

The current disclosure provides methods for quantifying the MSLN protein directly in biological samples, including samples that have been fixed in formalin by Selected Reaction Monitoring/Multiple Reaction Monitoring (SRM/MRM) mass spectrometry. Samples that can be assayed include tissues and cells treated with formaldehyde containing agents/fixatives including formalin-fixed tissue/cells, formalin-fixed/paraffin embedded (FFPE) tissue/cells, FFPE tissue blocks and cells from those blocks, and tissue culture cells that have been formalin fixed and or paraffin embedded. Methods to prepare a protein sample from such a biological sample are provided and MSLN protein is quantitated by SRM/MRM mass spectrometry by quantitating in the protein sample at least one or more of the peptides described.