PXD012460

PXD012460 is an original dataset announced via ProteomeXchange.

Title	In depth quantification of extracellular matrix proteins from human pancreas
Description	Extracellular matrix (ECM) is an important component of the pancreatic microenvironment which regulates β cell proliferation, differentiation and insulin secretion. Protocols have recently been developed for the decellularization of the human pancreas to generate functional scaffolds and hydrogels. In this work, we characterized human pancreatic ECM composition before and after decellularization using isobaric dimethylated leucine (DiLeu) labeling for relative quantification of ECM proteins. A novel correction factor was employed in the study to eliminate the bias introduced during sample preparation. In comparison to the commonly employed proteomic approaches (urea and FASP), a recently developed surfactant and chaotropic agent assisted sequential extraction/on pellet digestion (SCAD) protocol was proven to be a superior strategy for ECM protein extraction of human pancreatic ECM matrix. The quantitative proteomic results revealed the preservation of matrisome proteins while most of the cellular proteins were removed. This method was compared with a well-established label-free quantification (LFQ) approach which rendered similar expressions of different categories of proteins (collagens, ECM glycoproteins, proteoglycans, etc.). The distinct expression of ECM proteins was quantified comparing adult and fetal pancreas ECM, shedding light on the correlation between matrix composition and post-natal β cell maturation. Despite the distinct profiles of different subcategories in the native pancreas, the distribution of matrisome protein exhibited similar trends after the decellularization process. Our method generates the largest dataset of matrisome proteins from a single tissue type. These results provide valuable insight into the possibilities of constructing a bioengineered pancreas. It also facilitates an understanding of the significant roles that matrisome proteins play in post-natal  cell maturation.
HostingRepository	PRIDE
AnnounceDate	2019-06-17
AnnouncementXML	Submission_2019-06-17_05:54:06.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Fengfei Ma
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	4-hydroxy-L-proline; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2019-01-22 03:08:00	ID requested
⏵ 1	2019-06-17 05:54:07	announced

Ma F, Tremmel DM, Li Z, Lietz CB, Sackett SD, Odorico JS, Li L, In Depth Quantification of Extracellular Matrix Proteins from Human Pancreas. J Proteome Res, 18(8):3156-3165(2019) [pubmed]

curator keyword: Biomedical

submitter keyword: ECM, quantitative proteomics, sample preparation,tissue engineering

Lingjun Li
contact affiliation	School of Pharmacy and Department of Chemistry University of Wisconsin-Madison
contact email	lingjun.li@wisc.edu
lab head
Fengfei Ma
contact affiliation	UW Madison
contact email	fma9@wisc.edu
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD012460
     1. Label: PRIDE project
     2. Name: In depth quantification of extracellular matrix proteins from human pancreas