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. Author manuscript; available in PMC: 2013 Feb 1.
Published in final edited form as: Circ Cardiovasc Genet. 2012 Feb 1;5(1):o1–o7. doi: 10.1161/CIRCGENETICS.110.957803

Table 1.

Strengths And Limitations Of Proteomic Approaches for Evaluation of ECM

  1. 2-DE gel analysis
    • Strengths: established technology; separates intact proteins; provides MW and pI information; can detect post-translational modifications
    • Limitations: number of proteins resolved per gel is limited; multiple proteins can co-migrate in a single spot
  2. MS-based methods approaches
    • Strengths: can be label-based or label-free; capacity for high throughput; more extensive proteome coverage than 2-DE gels by several orders of magnitude
    • Limitations: needs sophisticated instrumentation and software to acquire and process data
  3. Protein arrays
    • Strengths: allows evaluation of a large number of similar samples in high throughput manner
    • Limitations: can only be used for specified protein targets; ECM is not included in many of the currently available commercial arrays
  4. Fractionation approaches
    • Strengths: focuses on cell type or organelle of interest; enrichment for ECM is possible; this approach can be coupled with any of the above approaches
    • Limitations: analysis dependent on purity of the preparation

Abbreviations: 2-DE, two dimensional electrophoresis; ECM, extraceullar matrix; MW, molecular weight; pI, isoelectric point