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Related Experiment Video

Updated: Jul 14, 2026

Simultaneous Affinity Enrichment of Two Post-Translational Modifications for Quantification and Site Localization
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Simultaneous Affinity Enrichment of Two Post-Translational Modifications for Quantification and Site Localization

Published on: February 27, 2020

Laboratory methods to improve SELDI peak detection and quantitation.

Dominique Rollin1, Toni Whistler, Suzanne D Vernon

  • 1Chronic Viral Diseases Branch, Division of Viral and Rickettsial Diseases, Centers for Disease Control and Prevention, 1600 Clifton Rd, MS-G41 Atlanta, Georgia 30333, USA. DRollin@cdc.gov

Proteome Science
|July 4, 2007
PubMed
Summary

Optimizing experimental parameters for surface-enhanced laser desorption-ionization time-of-flight mass spectrometry (SELDI-TOF MS) significantly improves biomarker discovery reproducibility. These methods enhance peak detection and reduce variability in protein profiling.

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Area of Science:

  • Biomarker discovery
  • Proteomics
  • Mass spectrometry

Background:

  • Surface-enhanced laser desorption-ionization time-of-flight mass spectrometry (SELDI-TOF MS) is a key technique for identifying potential biomarkers.
  • Reproducibility challenges in SELDI-TOF MS hinder the validation of identified candidate biomarkers.
  • Technical parameters significantly impact the reliability of peak detection in SELDI-TOF MS.

Purpose of the Study:

  • To enhance the reproducibility of peak detection in SELDI-TOF MS.
  • To identify and mitigate factors contributing to variability in protein profiling experiments.
  • To optimize experimental protocols for more reliable biomarker discovery.

Main Methods:

  • SELDI-TOF mass spectrometry was conducted using Ciphergen Biosystems equipment and ProteinChip System.

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PTR-ToF-MS Coupled with an Automated Sampling System and Tailored Data Analysis for Food Studies: Bioprocess Monitoring, Screening and Nose-space Analysis
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PTR-ToF-MS Coupled with an Automated Sampling System and Tailored Data Analysis for Food Studies: Bioprocess Monitoring, Screening and Nose-space Analysis

Published on: May 11, 2017

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Last Updated: Jul 14, 2026

Simultaneous Affinity Enrichment of Two Post-Translational Modifications for Quantification and Site Localization
12:11

Simultaneous Affinity Enrichment of Two Post-Translational Modifications for Quantification and Site Localization

Published on: February 27, 2020

PTR-ToF-MS Coupled with an Automated Sampling System and Tailored Data Analysis for Food Studies: Bioprocess Monitoring, Screening and Nose-space Analysis
08:43

PTR-ToF-MS Coupled with an Automated Sampling System and Tailored Data Analysis for Food Studies: Bioprocess Monitoring, Screening and Nose-space Analysis

Published on: May 11, 2017

  • Pooled serum from 10 donors was fractionated and applied to different ProteinChips over one month.
  • Peak detection variance was measured using Ciphergen Express software after optimizing spot protocols and instrument settings.

    • Main Results:

    • Optimization of spot protocols (laser intensity, detector sensitivity) reduced peak detection variance.
    • Optimal instrument settings, regular calibration, and controlled sample handling nearly doubled detected peaks.
    • Intensity variance was significantly decreased through protocol and instrument optimization.

    Conclusions:

    • The study successfully assessed and reduced variation in fractionated sera processed over a month.
    • Implemented optimizations demonstrably decreased variance and increased the number of detected peaks.
    • Improved reproducibility in SELDI-TOF MS supports more reliable biomarker discovery and validation.