IGF1R Peptide Selection for SRM Mass Spectrometry in FFPE Tissue
Find Innovative SolutionsGenerate Solutions
Solution Overview
Problem
Current methods for analyzing the Insulin-Like Growth Factor 1 Receptor (IGF1R) protein in formalin-fixed cancer tissue samples are inefficient due to the unsuitability of many peptide sequences for mass spectrometry-based assays, leading to difficulties in detecting and quantifying the protein accurately.
Innovation Solution
Development of a mass spectrometry-based Selected Reaction Monitoring (SRM)/Multiple Reaction Monitoring (MRM) assay using specific peptides derived from the IGF1R protein, which are identified through experimental determination to ionize well and survive sample preparation conditions, allowing for relative and absolute quantitation of the protein in complex lysate samples.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Reliability
If conventional mass spectrometry-based assays are used to analyze IGF1R protein in formalin-fixed cancer tissue, then the analysis can be performed on preserved tissue samples, but the peptide sequences are unsuitable for detection leading to inaccurate quantification
Solution Approach 1:
The IGF1R protein is segmented into specific peptide sequences that are optimized for mass spectrometry detection. The patent identifies and uses particular peptide regions (e.g., amino acid sequences with specific properties) that ionize efficiently and survive formalin fixation, thereby enabling reliable detection of the otherwise undetectable protein in fixed tissue samples.
Solution Approach 2:
The patent changes the parameters of peptide selection by identifying sequences with specific characteristics (ionization efficiency, resistance to formalin cross-linking) rather than using conventional peptides. This parameter change enables the peptides to withstand sample preparation conditions and be accurately detected by mass spectrometry, resolving the contradiction between detectability and reliability.
2Duration of action of stationary object
If formalin fixation is used to preserve cancer tissue samples, then long-term storage and analysis are enabled, but the fixation process makes peptide detection and quantification difficult
Solution Approach 1:
The patent performs preliminary identification of peptide sequences that are resistant to formalin fixation effects before actual analysis. By pre-selecting peptides that survive the fixation process and can be detected by mass spectrometry, the method enables both long-term sample storage and subsequent accurate detection, resolving the contradiction between storage stability and detectability.
3Adaptability or versatility
If standard mass spectrometry methods are used, then general protein analysis is possible, but specific IGF1R peptide sequences cannot be accurately detected or quantified
Solution Approach 1:
The patent applies local quality by selecting specific peptide sequences from the IGF1R protein that have optimized properties for mass spectrometry detection. Rather than attempting to detect all peptides equally, the method focuses on particular regions with high ionization efficiency and resistance to fixation, thereby achieving precise measurement of IGF1R levels while maintaining the versatility of mass spectrometry for general protein analysis.
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
Enables accurate and precise measurement of IGF1R protein levels in cancer tissue samples, providing diagnostic and therapeutic insights, and aiding in determining the appropriate treatment for patients by correlating protein expression with cancer stage and therapeutic response.
Implementation Method 1
mass spectrometry-based Selected Reaction Monitoring (SRM)/Multiple Reaction Monitoring (MRM) assay
Implementation Method 2
detecting and quantifying the amount of one or more modified or unmodified IGF-1R fragment peptides in a protein digest prepared from said biological sample using mass spectrometry
Data Source
AI summary
Peptides from the Insulin-Like Growth Factor 1 Receptor (IGF-1R) protein are provided that are particularly advantageous for quantifying the IGF-1 R protein directly in biological samples, such as samples fixed in formalin. The ionization characteristics of the peptides also are disclosed. The peptides may be used in Selected Reaction Monitoring (SRM) mass spectrometry methods, also referred to Multiple Reaction Monitoring (MRM) mass spectrometry methods. The samples are chemically preserved and fixed, such as 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. A protein sample may be prepared from the biological sample and the IGF-IR protein is quantitated by the method of SRM/MRM mass spectrometry by quantitating one or more of the described peptides. These peptides can be quantitated in either modified or unmodified form. An example of a modified form of an IGF-1 R peptide is phosphorylation of a tyrosine, threonine, serine, and/or other amino acid residues within the peptide sequence.