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( A ) Schematic representation of the workflow for MS-based proteomic analysis of protein extracts from human ICM and donor patient myocardial tissue. Soluble proteins are depleted in the first <t>LiCl</t> <t>extraction</t> (LiCl) followed by solubilization of “insoluble” ECM proteins by extraction with buffer containing the photocleavable surfactant, Azo. ( B ) CVs of protein intensities across extracts from failing ICM and nonfailing donor tissues. The median CV of protein intensities was below 5% for extracts from both groups, indicating high quantitative reproducibility. CVs were calculated by (SD/mean intensity) × 100% for each quantified value in each replicate. ( C ) Upset plot and bar graph (inset) showing more than 6,000 unique protein identifications overall, as well as the degree of overlap between groups. ( D and E ) Simplified depiction of major categories of ECM proteins (per MatrisomeDB, ref. ) ( D ) and breakdown of the number of proteins in each category identified in this study ( E ). The inner circle shows the total number of proteins in each category while the outer circle indicates those that were identified herein. Black segments correspond to proteins present in MatrisomeDB that were not identified in human ICM and donor myocardial tissue.
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( A ) Schematic representation of the workflow for MS-based proteomic analysis of protein extracts from human ICM and donor patient myocardial tissue. Soluble proteins are depleted in the first <t>LiCl</t> <t>extraction</t> (LiCl) followed by solubilization of “insoluble” ECM proteins by extraction with buffer containing the photocleavable surfactant, Azo. ( B ) CVs of protein intensities across extracts from failing ICM and nonfailing donor tissues. The median CV of protein intensities was below 5% for extracts from both groups, indicating high quantitative reproducibility. CVs were calculated by (SD/mean intensity) × 100% for each quantified value in each replicate. ( C ) Upset plot and bar graph (inset) showing more than 6,000 unique protein identifications overall, as well as the degree of overlap between groups. ( D and E ) Simplified depiction of major categories of ECM proteins (per MatrisomeDB, ref. ) ( D ) and breakdown of the number of proteins in each category identified in this study ( E ). The inner circle shows the total number of proteins in each category while the outer circle indicates those that were identified herein. Black segments correspond to proteins present in MatrisomeDB that were not identified in human ICM and donor myocardial tissue.
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( A ) Schematic representation of the workflow for MS-based proteomic analysis of protein extracts from human ICM and donor patient myocardial tissue. Soluble proteins are depleted in the first LiCl extraction (LiCl) followed by solubilization of “insoluble” ECM proteins by extraction with buffer containing the photocleavable surfactant, Azo. ( B ) CVs of protein intensities across extracts from failing ICM and nonfailing donor tissues. The median CV of protein intensities was below 5% for extracts from both groups, indicating high quantitative reproducibility. CVs were calculated by (SD/mean intensity) × 100% for each quantified value in each replicate. ( C ) Upset plot and bar graph (inset) showing more than 6,000 unique protein identifications overall, as well as the degree of overlap between groups. ( D and E ) Simplified depiction of major categories of ECM proteins (per MatrisomeDB, ref. ) ( D ) and breakdown of the number of proteins in each category identified in this study ( E ). The inner circle shows the total number of proteins in each category while the outer circle indicates those that were identified herein. Black segments correspond to proteins present in MatrisomeDB that were not identified in human ICM and donor myocardial tissue.

Journal: JCI Insight

Article Title: Extracellular matrix alterations in chronic ischemic cardiomyopathy revealed by quantitative proteomics

doi: 10.1172/jci.insight.196933

Figure Lengend Snippet: ( A ) Schematic representation of the workflow for MS-based proteomic analysis of protein extracts from human ICM and donor patient myocardial tissue. Soluble proteins are depleted in the first LiCl extraction (LiCl) followed by solubilization of “insoluble” ECM proteins by extraction with buffer containing the photocleavable surfactant, Azo. ( B ) CVs of protein intensities across extracts from failing ICM and nonfailing donor tissues. The median CV of protein intensities was below 5% for extracts from both groups, indicating high quantitative reproducibility. CVs were calculated by (SD/mean intensity) × 100% for each quantified value in each replicate. ( C ) Upset plot and bar graph (inset) showing more than 6,000 unique protein identifications overall, as well as the degree of overlap between groups. ( D and E ) Simplified depiction of major categories of ECM proteins (per MatrisomeDB, ref. ) ( D ) and breakdown of the number of proteins in each category identified in this study ( E ). The inner circle shows the total number of proteins in each category while the outer circle indicates those that were identified herein. Black segments correspond to proteins present in MatrisomeDB that were not identified in human ICM and donor myocardial tissue.

Article Snippet: Pellets were homogenized in 20 volumes (~300 μL) of LiCl extraction buffer (3 M LiCl, 1 mM TCEP, 10 mM EDTA, and 1× Halt Protease Inhibitor Cocktail from Thermo Fisher Scientific) using a handheld Teflon homogenizer (Bel-Art).

Techniques: Extraction