PXD002847

PXD002847 is an original dataset announced via ProteomeXchange.

Title	Profiling of Native and Protease_Generated Protein Amino Termini from Formalin-Fixed, Paraffin-Embedded Tissues
Description	Dysregulated proteolysis represents a hallmark of numerous diseases. In recent years, increasing number of studies has begun looking at the protein termini in hope to unveil the physiological and pathological functions of proteases in clinical research. However, the availability of cryopreserved tissue specimens is often limited. Alternatively, formalin-fixed, paraffin-embedded (FFPE) tissues offer an invaluable resource for clinical research. Pathologically relevant tissues are often stored as FFPE, which represent the most abundant resource of archived human specimens. In this study, we established a robust workflow to investigate native and protease-generated protein N-termini from FFPE specimens. We demonstrate a comparable N-terminomes of cryopreserved and formalin fixed tissue, thereby showing that formalin fixation / paraffin embedment does not proteolytically damage proteins. Accordingly, FFPE specimens are fully amenable to N-terminal analysis. Moreover, we demonstrate feasibility of FFPE-degradomics in a quantitative N-terminomic study of FFPE liver specimens from cathepsin L deficient or wild-type mice. Using a machine learning approach in combination with the previously determined cathepsin L specificity, we successfully identified a number of potential cathepsin L cleavage sites. Our study establishes FFPE specimens as a valuable alternative to cryopreserved tissues for degradomic studies.
HostingRepository	PRIDE
AnnounceDate	2016-04-25
AnnouncementXML	Submission_2016-04-25_03:03:45.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Zon Lai
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090;
ModificationList	monomethylated residue; dimethylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2015-09-03 07:46:19	ID requested
⏵ 1	2016-04-25 03:03:46	announced

Lai ZW, Weisser J, Nilse L, Costa F, Keller E, Tholen M, Kizhakkedathu JN, Biniossek M, Bronsert P, Schilling O, Formalin-Fixed, Paraffin-Embedded Tissues (FFPE) as a Robust Source for the Profiling of Native and Protease-Generated Protein Amino Termini. Mol Cell Proteomics, 15(6):2203-13(2016) [pubmed]

curator keyword: Technical

submitter keyword: FFPE, degradome, TAILS, proteolysis, protease, N-terminomics

Oliver Schilling
contact affiliation	Institute of Molecular Medicine and Cell Research, University of Freiburg, Germany
contact email	oliver.schilling@mol-med.uni-freiburg.de
lab head
Zon Lai
contact affiliation	University of Freiburg
contact email	zon.lai@mol-med.uni-freiburg.de
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD002847
     1. Label: PRIDE project
     2. Name: Profiling of Native and Protease_Generated Protein Amino Termini from Formalin-Fixed, Paraffin-Embedded Tissues