Open AccessEvaluation and Refinement of Sample Preparation Methods for Extracellular Matrix Proteome Coverage
Author(s) -
Maxwell C. McCabe,
Lauren R. Schmitt,
Ryan C. Hill,
Monika Dzieciątkowska,
Mark Maslanka,
Willeke F. Daamen,
Toin H. Van Kuppevelt,
Danique J. Hof,
Kirk C. Hansen
Publication year - 2021
Publication title -
molecular and cellular proteomics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 2.757
H-Index - 187
eISSN - 1535-9484
pISSN - 1535-9476
DOI - 10.1016/j.mcpro.2021.100079
Subject(s) - extracellular matrix , decellularization , proteome , chemistry , matrix (chemical analysis) , sample preparation , extraction (chemistry) , computational biology , computer science , biological system , chromatography , biochemistry , biology
The extracellular matrix is a key component of tissues, yet it is underrepresented in proteomic datasets. Identification and evaluation of proteins in the extracellular matrix (ECM) has proved challenging due to the insolubility of many ECM proteins in traditional protein extraction buffers. Here we separate the decellularization and ECM extraction steps of several prominent methods for evaluation under real-world conditions. The results are used to optimize a two-fraction ECM extraction method. Approximately one dozen additional parameters are tested, and recommendations for analysis based on overall ECM coverage or specific ECM classes are given. Compared with a standard in-solution digest, the optimized method yielded a fourfold improvement in unique ECM peptide identifications.
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