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Pathway-Informed Discovery and Targeted Proteomic Workflows Using Mass Spectrometry.

Caroline S Chu1, Christine A Miller2, Andy Gieschen2

  • 1Agilent Technologies, Inc., 5301 Stevens Creek Blvd, Santa Clara, CA, 95051, USA. caroline_chu@agilent.com.

Methods in Molecular Biology (Clifton, N.J.)
|February 12, 2017
PubMed
Summary
This summary is machine-generated.

This study presents a comprehensive proteomics workflow, integrating discovery and targeted approaches for biological insights. It enhances protein quantitation and pathway analysis for biomarker discovery and gene-metabolite correlations.

Keywords:
Data-dependent acquisitionInformaticsMass spectrometryProtein quantitationProteinsProteomicsQQQQTOFQuadrupoleTime-of-flight

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Area of Science:

  • Proteomics and Mass Spectrometry
  • Multi-omics Integration
  • Biological Pathway Analysis

Background:

  • Advancements in mass spectrometry (MS) and data analysis software drive new biological discovery strategies.
  • Proteomics has expanded from protein identification to integrated multi-omics projects, linking proteins to genes and metabolites.
  • Biological pathway information facilitates targeted protein quantitation for monitoring expression changes and biomarker discovery.

Purpose of the Study:

  • To describe a complete proteomics workflow from discovery to targeted quantitation.
  • To demonstrate the utility of integrated multi-omics data and pathway analysis.
  • To highlight the application of targeted proteomics for biomarker discovery and robust sample analysis.

Main Methods:

  • Discovery proteomics using quadrupole Time-of-Flight (Q-TOF) MS with data-dependent acquisition.
  • Protein database searching and statistical analysis of identified protein abundances.
  • Targeted proteomics using triple quadrupole (QQQ) MS with peptide-based assays for quantitation.

Main Results:

  • A workflow integrating discovery proteomics (Q-TOF) with targeted proteomics (QQQ) was established.
  • Pathway analysis of discovery data informed the selection of protein targets for targeted assays.
  • Peptide-based QQQ assays enabled sensitive, selective, and robust quantitation of large sample batches.

Conclusions:

  • The described workflow enables comprehensive biological discovery and biomarker identification.
  • Integrating discovery and targeted proteomics with pathway analysis provides deeper biological insights.
  • Peptide-based targeted assays are effective for robust quantitative analysis in biological pathway studies.