Low molecular weight protein enrichment on mesoporous silica thin films for biomarker discovery

Jia Fan, James W. Gallagher, Hung Jen Wu, Matthew G. Landry, Jason Sakamoto, Mauro Ferrari, Ye Hu

Research output: Contribution to journalArticle

11 Citations (Scopus)

Abstract

The identification of circulating biomarkers holds great potential for non invasive approaches in early diagnosis and prognosis, as well as for the monitoring of therapeutic efficiency.The circulating low molecular weight proteome (LMWP) composed of small proteins shed from tissues and cells or peptide fragments derived from the proteolytic degradation of larger proteins, has been associated with the pathological condition in patients and likely reflects the state of disease. Despite these potential clinical applications, the use of Mass Spectrometry (MS) to profile the LMWP from biological fluids has proven to be very challenging due to the large dynamic range of protein and peptide concentrations in serum. Without sample pre-treatment, some of the more highly abundant proteins obscure the detection of low-abundance species in serum/plasma. Current proteomic-based approaches, such as two-dimensional polyacrylamide gel-electrophoresis (2D-PAGE) and shotgun proteomics methods are labor-intensive, low throughput and offer limited suitability for clinical applications. Therefore, a more effective strategy is needed to isolate LMWP from blood and allow the high throughput screening of clinical samples. Here, we present a fast, efficient and reliable multi-fractionation system based on mesoporous silica chips to specifically target and enrich LMWP. Mesoporous silica (MPS) thin films with tunable features at the nanoscale were fabricated using the triblock copolymer template pathway. Using different polymer templates and polymer concentrations in the precursor solution, various pore size distributions, pore structures, connectivity and surface properties were determined and applied for selective recovery of low mass proteins. The selective parsing of the enriched peptides into different subclasses according to their physicochemical properties will enhance the efficiency of recovery and detection of low abundance species. In combination with mass spectrometry and statistic analysis, we demonstrated the correlation between the nanophase characteristics of the mesoporous silica thin films and the specificity and efficacy of low mass proteome harvesting. The results presented herein reveal the potential of the nanotechnology-based technology to provide a powerful alternative to conventional methods for LMWP harvesting from complex biological fluids. Because of the ability to tune the material properties, the capability for low-cost production, the simplicity and rapidity of sample collection, and the greatly reduced sample requirements for analysis, this novel nanotechnology will substantially impact the field of proteomic biomarker research and clinical proteomic assessment.

Original languageEnglish (US)
Article numbere3876
JournalJournal of Visualized Experiments
Issue number62
DOIs
StatePublished - Apr 17 2012
Externally publishedYes

Fingerprint

Biomarkers
Proteome
Silicon Dioxide
Molecular Weight
Molecular weight
Silica
Proteins
Thin films
Proteomics
Nanotechnology
Electrophoresis, Gel, Two-Dimensional
Mass spectrometry
Mass Spectrometry
Polymers
Peptides
Throughput
Recovery
Peptide Fragments
Fluids
Surface Properties

Keywords

  • Bioengineering
  • Early diagnostics
  • Issue 62
  • Low molecular weight proteomics
  • MALDI-TOF mass spectrometry
  • Nanoporous silica chip
  • Peptidomics
  • Proteomics

ASJC Scopus subject areas

  • Neuroscience(all)
  • Chemical Engineering(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Immunology and Microbiology(all)

Cite this

Low molecular weight protein enrichment on mesoporous silica thin films for biomarker discovery. / Fan, Jia; Gallagher, James W.; Wu, Hung Jen; Landry, Matthew G.; Sakamoto, Jason; Ferrari, Mauro; Hu, Ye.

In: Journal of Visualized Experiments, No. 62, e3876, 17.04.2012.

Research output: Contribution to journalArticle

Fan, Jia ; Gallagher, James W. ; Wu, Hung Jen ; Landry, Matthew G. ; Sakamoto, Jason ; Ferrari, Mauro ; Hu, Ye. / Low molecular weight protein enrichment on mesoporous silica thin films for biomarker discovery. In: Journal of Visualized Experiments. 2012 ; No. 62.
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