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Proteomic Profile of EPS-Urine through FASP Digestion and Data-Independent Analysis
Published on: May 8, 2021
Quantitative urinary proteome analysis for biomarker evaluation in chronic kidney disease
Justyna Jantos-Siwy1, Eric Schiffer, Korbinian Brand
1Mosaiques Diagnostics & Therapeutics, Hannover, Germany.
Journal of Proteome Research
|November 18, 2008
Summary
For chronic kidney disease (CKD) biomarker discovery, relative quantification using endogenous peptides is sufficient for determining urinary polypeptide levels. Absolute quantification with labeled standards offers no additional benefit for clinical applicability.
Area of Science:
- Proteomics
- Clinical Chemistry
- Biomarker Discovery
Background:
- Clinical applicability of proteomic methods is limited by the inability to directly quantify proteins/peptides from mass spectrometry (MS) spectra.
- Accurate quantification of urinary biomarkers is crucial for diagnosing and monitoring chronic kidney disease (CKD).
Purpose of the Study:
- To compare absolute and relative quantification strategies for urinary polypeptides in CKD.
- To evaluate the clinical utility of different calibration methods in capillary electrophoresis coupled with mass spectrometry (CE-MS).
Main Methods:
- Compared signal intensity calibration using urinary creatinine or stable isotope-labeled synthetic analogues (absolute quantification).
- Utilized ion counting with abundant collagen fragments as endogenous references for relative quantification.
- Applied CE-MS for the analysis of urinary polypeptides in CKD patients.
Main Results:
- Relative quantification based on ion counts of endogenous "housekeeping" peptides adequately determined urinary polypeptide levels.
- Absolute quantification using exogenous stable isotope-labeled peptide standards provided no significant additional benefit over relative methods.
- The study demonstrates the sufficiency of relative quantification for CKD biomarker assessment.
Conclusions:
- Relative quantification is a sufficient and practical method for assessing urinary polypeptide levels in CKD.
- Absolute quantification methods do not offer added value for the clinical application of CE-MS in CKD biomarker studies.
- Simplified quantification strategies enhance the clinical applicability of proteomic techniques.
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