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. 2019 Dec 9;9:18635. doi: 10.1038/s41598-019-54566-4

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© The Author(s) 2019

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

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Proteomics analysis of proteins from bone conditioned media. (A) Venn diagram of secreted proteins identified in Bone-CM1 versus Bone-CM2. Two independent batches of Bone-CM were subjected to LC-MS/MS analysis. Proteins were selected using 1% false discovery rate (FDR). We focused on the secreted proteins and obtained a total of 132 secreted proteins from the Bone-CM. We grouped the 132 secreted proteins into three major categories of extracellular matrix (ECM) proteins according to the Matrisome Project (http://matrisomeproject.mit.edu)¹⁵. We further curated our list of secreted proteins by searching against the matrisome atlas using the MatrisomeDB2.0 software^15,16. (B) Matrisome core proteins include ECM-glycoportiens, collagens and proteoglycans. (C) Matrisome-associated proteins include ECM-affiliated proteins and ECM regulators. (D) Other secreted factors include growth factors and other proteins. For a complete list of proteins identified in Bone-CM1 (n = 416) and Bone-CM2 (n = 244), see Supplemental Tables S1 and S2.