Project PXD005521

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Biomedical Dataset
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Proteomic characterization of stem cell-derived extracellular matrices


We characterized and compared the proteomic composition of ECM produced in vitro by bone marrow-derived MSC, adipose-derived MSC and neonatal fibroblasts isolated from different donors, employing a multidimensional proteomic approach coupled with label-based quantitative proteomics. Each cell-derived ECM displayed a specific and unique matrisome signature, yet they all shared a common set of proteins. We evaluated the biological response of cells cultured on the different matrices and compared them to cells on standard TCPS. The matrices lead to differential proliferation and gene expression profiles between the cell types and as compared to TCPS, indicating that the cell-derived ECM influence each cell type in a unique manner.

Sample Processing Protocol

The ECM was mechanically detached from the 75 cm2-cell culture flask using a cell scraper in 2 ml of HBSS +/+, centrifuged at 16,000x g for 5 min, washed with 1 ml of HBSS +/+, centrifuged, and dried in a Speed-Vac (Savant) for 15 min. The ECM pellet was resuspended and reduced in a solution of 8 M urea, 100 mM ammonium bicarbonate, and 10 mM dithiothreitol at pH 8 under agitation at 37°C for 2 h. After cooling, cysteines were alkylated by adding iodoacetamide at a final concentration of 25 mM for 30 min. The ECM sample was then diluted to 2 M urea, 100 mM ammonium bicarbonate (pH 8), and deglycosylated with PNGaseF (2000 U, New England BioLabs, Ipswich, MA) for 2 h under agitation at 37°C, followed by digestion with Lys-C (Wako Chemicals USA, Richmond, VA), at a ratio of 1:100 enzyme:substrate, under agitation at 37°C for 2 h. Final digestion was done using trypsin (Sequencing Grade, Promega, Madison, WI), at a ratio of 1:50 enzyme:substrate, under agitation at 37°C overnight, followed by a second aliquot of trypsin, at a ratio of 1:100 enzyme:substrate, and an additional 2 h of incubation. Digests were acidified and desalted using 30mg HLB Oasis Cartridges (Waters Corp., Milford, MA) eluted with 50% acetonitrile with 0.1% trifluoroacetic acid (TFA), followed by concentration in a Speed-Vac.

Data Processing Protocol

Each sample was separated by reverse phase HPLC using an EASY-nLC1000 liquid chromatograph (Thermo Fisher Scientific, Waltham, MA) over a 140-minute gradient before nanoelectrospray using a Q Exactive mass spectrometer (Thermo Fisher Scientific). The mass spectrometer was operated in a data-dependent mode. The parameters for the full scan MS were: resolution of 70,000 across 350-2000 m/z; AGC 3e6; and maximum IT 50 ms. The full MS scan was followed by MS/MS for the top 10 precursor ions in each cycle with a NCE of 28 (unlabeled samples) or 32 (labeled samples) and dynamic exclusion of 30 s. Raw mass spectral data files (.raw) were searched using Proteome Discoverer (Thermo Fisher Scientific) and Mascot version 2.4.1 (Matrix Science) using the SwissProt Homo sapiens database containing 20,199 entries. Mascot search parameters were: 10 ppm mass tolerance for precursor ions; 0.8 Da for fragment ion mass tolerance; 2 missed cleavages of trypsin; fixed modification were carbamidomethylation of cysteines and for the quantitative experiments: TMT 6plex modification of lysines and peptide N-termini; variable modifications were oxidized methionines, deamidation of asparagines, pyro-glutamic acid modification at N-terminal glutamines; and hydroxylation of prolines and lysines.


Amanda Del Rosario, Janssen Pharmaceuticals
Amanda Del Rosario, Massachusetts Institute of Technology ( lab head )

Submission Date


Publication Date



Not available


Q Exactive


Not available



Experiment Type

Shotgun proteomics

Assay count



Publication pending


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Showing 1 - 10 of 11 results
# Accession Title Proteins Peptides Unique Peptides Spectra Identified Spectra View in Reactome
1 72944 150219_122_HR_BM001.mzid 559 29068 4240 23007 0
2 72945 150219_122_HR_BM002_2.mzid 896 19968 5345 22619 0
3 72953 150219_122_HR_BM003_2.mzid 531 22356 3577 22500 0
4 72954 150611_147_HR_TMT_15.mzid 246 11802 2226 19338 0
5 72951 160115_214_HR_7plex_TMT_2.mzid 249 30197 2074 20539 0
6 72952 160209_214_HR_7plex_TMT_techrep2.mzid 365 19429 3311 26951 0
7 72950 160217_147_HR_TMT_techrep.mzid 281 13909 2491 20274 0
8 72948 160217_225_HR_6plex_TMT.mzid 218 15844 1994 18660 0
9 72949 160217_225_HR_6plex_TMT_techrep.mzid 237 15766 2000 18862 0
10 72946 160218_224_HR_3plex_TMT.mzid 216 11446 1684 17141 0