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Optimization for Peptide Sample Preparation for Urine Peptidomics.

Tara K Sigdel1, Carrie D Nicora2, Wei-Jun Qian2

  • 1Department of Surgery, University of California San Francisco, San Francisco, CA, USA. tara.sigdel@ucsf.edu.

Methods in Molecular Biology (Clifton, N.J.)
|April 7, 2018
PubMed
Summary
This summary is machine-generated.

A modified solid-phase extraction (mSPE) method improves urine sample preparation for high-throughput peptidomics. This novel approach enhances peptide identification and analysis sensitivity using liquid chromatography-mass spectrometry (LC-MS).

Keywords:
BiomarkerBiomarker discoveryPeptidomicsProteomicsTransplantationUrine

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Area of Science:

  • Biochemistry
  • Analytical Chemistry
  • Nephrology

Background:

  • Analysis of endogenous peptides in biofluids offers insights into disease mechanisms and disease biomarker discovery.
  • Urine peptidomics is attractive for renal disease research due to noninvasive sample collection and abundant peptides.
  • Standard urine peptidomics faces challenges in sample preparation, leading to background interference and reduced peptide identification.

Purpose of the Study:

  • To develop and evaluate a modified solid-phase extraction (mSPE) method for improved urine sample preparation in peptidomics.
  • To enhance peptide yield, analysis sensitivity, and efficiency compared to standard SPE methods for LC-MS-based peptidomics.

Main Methods:

  • A novel adaptation of standard solid-phase extraction (SPE) to a modified SPE (mSPE) approach was developed.
  • The mSPE method was applied to urine sample preparation for liquid chromatography-mass spectrometry (LC-MS)-based peptidomics.
  • Performance metrics including time, cost, column clogging, peptide yield, quality, and identification number were compared.

Main Results:

  • The mSPE method demonstrated significantly improved efficiencies for urine peptide sample preparation.
  • mSPE resulted in higher peptide yield, better peptide quality, and an increased number of identified peptides compared to standard SPE.
  • The optimized sample cleanup via mSPE provided improved experimental inference from confidently identified peptides.

Conclusions:

  • The modified SPE (mSPE) method is superior to the conventional SPE method for urine peptide sample preparation.
  • mSPE enhances the reliability and depth of LC-MS-based peptidomics analysis of urine.
  • This improved methodology facilitates more effective investigation into the pathogenesis of renal disease using urine peptidomics.