PXD011492

PXD011492 is an original dataset announced via ProteomeXchange.

Title	In Silico Analysis Validates Proteomic Findings of Formalin-fixed Paraffin Embedded Cutaneous Squamous Cell Carcinoma Tissue
Description	Background: Cutaneous squamous cell carcinoma (cSCC) is a common type of skin cancer but there are no comprehensive proteomic studies on this entity. Materials and Methods: We employed liquid chromatography coupled with tandem mass spectrometry (MS/MS) using formalin-fixed paraffin-embedded (FFPE) cSCC material to study the tumor and normal skin tissue proteomes. Ingenuity Pathway Analysis (IPA) was used to interpret the role of altered proteins in cSCC pathophysiology. Results were validated using the Human Protein Atlas and Oncomine database in silico. Results: Of 1,310 unique proteins identified, expression of an average of 144 and 88 proteins were significantly (p<0.05) increased and decreased, respectively, in the tumor samples compared to their normal counterparts. IPA analysis revealed disruptions in proteins associated with cell proliferation, apoptosis, and migration. In silico analysis confirmed that proteins corresponding to 12 antibodies, and genes corresponding to 18 proteins were differentially expressed between the two categories, validating our proteomic measurements. Conclusion: Label-free MS-based proteomics is useful for analyzing FFPE cSCC tissues.
HostingRepository	PRIDE
AnnounceDate	2018-11-07
AnnouncementXML	Submission_2018-11-07_01:28:16.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Ali Azimi
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	LTQ Orbitrap

Revision	Datetime	Status	ChangeLog Entry
0	2018-10-29 03:00:35	ID requested
⏵ 1	2018-11-07 01:28:18	announced

Azimi A, Kaufman KL, Ali M, Kossard S, Fernandez-Penas P, In Silico Analysis Validates Proteomic Findings of Formalin-fixed Paraffin Embedded Cutaneous Squamous Cell Carcinoma Tissue. Cancer Genomics Proteomics, 13(6):453-465(2016) [pubmed]

curator keyword: Biomedical

submitter keyword: Cutaneous squamous cell carcinoma

formalin-fixed paraffin embedded

label-free mass spectrometry

laser capture microdissection

proteomics

Professor Pablo Fernandez-Penas
contact affiliation	Head | Department of Dermatology - Westmead Hospital Academic Leader (HDR PGC) | Sydney Medical School Director | Centre for Translational Skin Research
contact email	pablo.fernandezpenas@sydney.edu.au
lab head
Ali Azimi
contact affiliation	The University of Sydney
contact email	ali.azimi@sydney.edu.au
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2018/11/PXD011492

PRIDE project URI

• PRIDE
  1. PXD011492
     1. Label: PRIDE project
     2. Name: In Silico Analysis Validates Proteomic Findings of Formalin-fixed Paraffin Embedded Cutaneous Squamous Cell Carcinoma Tissue