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Proteomics2017; 17(13-14); 1700018; doi: 10.1002/pmic.201700018

Comparison between chaotropic and detergent-based sample preparation workflow in tendon for mass spectrometry analysis.

Abstract: Exploring the tendon proteome is a challenging but important task for understanding the mechanisms of physiological/pathological processes during ageing and disease and for the development of new treatments. Several extraction methods have been utilised for tendon mass spectrometry, however different extraction methods have not been simultaneously compared. In the present study we compared protein extraction in tendon with two chaotropic agents, guanidine hydrochloride (GnHCl) and urea, a detergent, RapiGest™, and their combinations for shotgun mass spectrometry. An initial proteomic analysis was performed following urea, GnHCl, and RapiGest™ extraction of equine superficial digital flexor tendon (SDFT) tissue. Subsequently, another proteomic analysis was performed following extraction with GnHCl, Rapigest™, and their combinations. Between the two chaotropic agents, GnHCl extracted more proteins, whilst a greater number of proteins were solely identified after Rapigest™ extraction. Protein extraction with a combination of GnHCl followed by RapiGest™ on the insoluble pellet demonstrated, after label-free quantification, increased abundance of identified collagen proteins and low sample to sample variability. In contrast, GnHCl extraction on its own showed increased abundance of identified proteoglycans and cellular proteins. Therefore, the selection of protein extraction method for tendon tissue for mass spectrometry analysis should reflect the focus of the study.
© 2017 The Authors. Proteomics Published by WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
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Publication Date: 2017-06-22 PubMed ID: 28547889PubMed Central: PMC5575552DOI: 10.1002/pmic.201700018Google Scholar: Lookup
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  • Comparative Study
  • Journal Article

Summary

This research summary has been generated with artificial intelligence and may contain errors and omissions. Refer to the original study to confirm details provided. Submit correction.

This research paper compares the effectiveness of different protein extraction methods used in mass spectrometry analysis of tendons with the aim of better understanding physiological and pathological processes. The results indicate that the method chosen should depend on the specifics of the study being conducted.

Summary of Methods

  • The research compared the protein extraction in tendon samples using two chaotropic agents, guanidine hydrochloride (GnHCl) and urea, alongside a detergent, RapiGest™.
  • They first performed a proteomic analysis after extraction with urea, GnHCl, and RapiGest™ from equine superficial digital flexor tendon (SDFT) tissue.
  • Following this, they carried out a further proteomic analysis using GnHCl, Rapigest™, and combinations of the two.

Key Findings

  • Of the two chaotropic agents tested, GnHCl was found to extract more proteins. Meanwhile, a greater number of proteins were only identifiable after extraction with RapiGest™.
  • Protein extraction through a combination of GnHCl and subsequent use of RapiGest™ on the insoluble pellet led to an increase in the abundance of identified collagen proteins and reduced sample variability.
  • Conversely, using GnHCl alone led to a greater abundance of identified proteoglycans and cellular proteins.

Implications of Results

  • These findings indicate that the technique employed for protein extraction in tendon tissue analysis via mass spectrometry needs to be chosen based on the specifics of the study at hand.
  • The better a technique suits the specific proteins of interest within the analysis, the more effective the extraction, identification and analysis process will be.

Limitations and Future Research

  • This study provides the foundation for further research in this area, as there are potential improvements and additions that could be tested, such as comparing chaotropic agents against other detergents.
  • The methodology could also be refined in future studies, for instance by exploring different combinations of extraction techniques.

Cite This Article

APA
Ashraf Kharaz Y, Zamboulis D, Sanders K, Comerford E, Clegg P, Peffers M. (2017). Comparison between chaotropic and detergent-based sample preparation workflow in tendon for mass spectrometry analysis. Proteomics, 17(13-14), 1700018. https://doi.org/10.1002/pmic.201700018

Publication

Proteomics
ISSN: 1615-9861
NlmUniqueID: 101092707
Country: Germany
Language: English
Volume: 17
Issue: 13-14
PII: 1700018

Researcher Affiliations

Ashraf Kharaz, Yalda
  • Department of Musculoskeletal Biology, Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool, UK.
Zamboulis, Danae
  • Department of Musculoskeletal Biology, Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool, UK.
Sanders, Karen
  • Department of Musculoskeletal Biology, Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool, UK.
Comerford, Eithne
  • Department of Musculoskeletal Biology, Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool, UK.
Clegg, Peter
  • Department of Musculoskeletal Biology, Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool, UK.
  • The MRC-Arthritis Research UK Centre for Integrated research into Musculoskeletal Ageing (CIMA), Liverpool, UK.
Peffers, Mandy
  • Department of Musculoskeletal Biology, Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool, UK.
  • The MRC-Arthritis Research UK Centre for Integrated research into Musculoskeletal Ageing (CIMA), Liverpool, UK.

MeSH Terms

  • Animals
  • Detergents / chemistry
  • Guanidine / chemistry
  • Horses
  • Proteins / analysis
  • Proteins / isolation & purification
  • Proteins / metabolism
  • Proteomics / methods
  • Tandem Mass Spectrometry / methods
  • Tendons / metabolism
  • Urea / chemistry
  • Workflow

Grant Funding

  • Wellcome Trust
  • MR/K006312/1 / Medical Research Council
  • MR/P020941/1 / Medical Research Council

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