A spiked human proteomic dataset from human osteogenic differentiated BMSCs and ASCs for use as a spectral library, for modelling pathways as well as protein mapping

Abstract

This article describes a mass spectrometry data set generated from osteogenic differentiated bone marrow stromal cells (BMSCs) and adipose tissue derived stromal cells (ASCs) of a 24-year old healthy donor. Before osteogenic differentiation and performing mass spectrometric measurements cells have been characterized as mesenchymal stromal cells via FACS-analysis positive for CD90 and CD105 and negative for CD14, CD34, CD45 and CD11b and tri-lineage differentiation. After osteogenic differentiation, both cell types were homogenized and then fractionated by SDS gel electrophoresis, resulting in 12 fractions. The proteins underwent an in-gel digestion, spiked with iRT peptides and analysed by nanoHPLC-ESI-MS/MS, resulting in 24 data files. The data files generated from the described workflow are hosted in the public repository ProteomeXchange with identifier PXD015026. The presented data set can be used as a spectral library for analysis of key proteins in the context of osteogenic differentiation of mesenchymal stromal cells for regenerative applications. Moreover, these data can be used to perform comparative proteomic analysis of different mesenchymal stromal cells or stem cells upon osteogenic differentiation. In addition, these data can also be used to determine the optimal settings for measuring proteins and peptides of interest.

Systems biology analysis of osteogenic differentiation behavior by canine mesenchymal stem cells derived from bone marrow and dental pulp

“…Recent studies using omics-based systems biology approach have thoroughly dissected the osteogenic differentiation behavior of BM-MSCs and DPSCs from human resources suggesting the correlated and uncorrelated characteristics upon an in vitro induction model 10,11 . These data efficiently demonstrated the potential osteogenic regulating pathways referring the potential application of cells in further in vivo models [12][13][14] . Thusly, this kind of information is crucial for progressive development of cMSC-based bone tissue engineering (BTE) in veterinary practice.…”

Comparative proteomic analysis of osteogenic differentiated human adipose tissue and bone marrow‐derived stromal cells

“…ASC and BMSC isolation was performed following modified standard protocols as described in our data article on the generation of the spectral library for this project 25‐29 . In brief, adipose tissue was rinsed with pre‐warmed (37°C) PBS (PAN Biotech, Germany).…”

“…Cell isolation, expansion and osteogenic differentiation were performed as described above. The methods for the creation of the spectral library are described elsewhere 29 …”

“…ASC and BMSC isolation was performed following modified standard protocols as described in our data article on the generation of the spectral library for this project. [25][26][27][28][29] In brief, adipose tissue was rinsed with pre-warmed (37°C) PBS (PAN Biotech, Germany). Blood vessels and connective tissue were carefully detached and discarded, before the tissue was minced.…”

“…The methods for the creation of the spectral library are described elsewhere. 29 Patient specific samples-The patient samples were prepared in the same way as the samples for the spectral library, followed by protein concentration determination by Bradford assay. These samples were used for data-independent acquisition (DIA)-based mass spectrometry as well as for Western blot analysis.…”