PXD001978

PXD001978 is an original dataset announced via ProteomeXchange.

Title	Proteomic and Clinical Analysis of a Fine-needle Aspirate Biopsy from a Single Cold Thyroid Nodule: A Case Study
Description	Purpose: To clinically and proteomically profile a fine-needle aspirate biopsy (FNAB) from a single in situ cold thyroid nodule (CTN). Experimental Design: The FNAB lysate was digested with trypsin, and analysed by LC-MSMS on an LTQ Orbitrap Velos. Remaining peptides were separated by reversed-phase chromatography and fractions analysed as technical duplicates. Identified proteins were analysed by Gene Ontology and protein abundance were calculated using the Top3 label-free method. The proteomic data was complemented with ultrasonography and scintigraphy of the thyroid gland; and cytology of the CTN FNAB. Results: Sixty seven and 2,595 non-redundant protein groups (2 unique peptides) were identified from unfractionated and fractionated CTN FNAB, respectively. Label-free protein abundance ranged over 6 orders of magnitude from the most abundant proteins, haemoglobin and thyroglobulin; to the low-abundance protein SON. Many previously-reported markers of thyroid cancer were in the top 23% of the identified proteins. GO analysis revealed high-enrichment for extracellular vesicular exosome and vesicle (cellular component); regulation of biological quality (biological processes); and structural molecule activity (molecular function). Conclusions and Clinical Significance: The CTN was clinically-classified as benign. Proteomic data from FNAB can provide additional diagnostic candidates indicative of benign or cancerous CTN without the need for invasive surgical intervention.
HostingRepository	PRIDE
AnnounceDate	2017-10-26
AnnouncementXML	Submission_2018-05-23_06:05:45.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Fernando Sialana
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	3': 3''; monohydroxylated residue; L-thyroxine; iodoacetamide derivatized residue
Instrument	LTQ Orbitrap Velos

Revision	Datetime	Status	ChangeLog Entry
0	2015-03-26 02:41:37	ID requested
1	2017-10-26 05:16:30	announced
⏵ 2	2018-05-23 06:05:45	announced	Updated publication reference for DOI(s): 10.4172/2165-7920.1000766.

10.4172/2165-7920.1000766;

curator keyword: Biomedical

submitter keyword: thyroid nodule, FNAB, cytology, ultrasonography, scintigraphy, proteome, orbitrap velos

Keiryn L. Bennett
contact affiliation	Mass Spectrometry & Proteomics CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences Vienna, Austria
contact email	kbennett@cemm.oeaw.ac.at
lab head
Fernando Sialana
contact affiliation	CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences
contact email	FSialana@cemm.oeaw.ac.at
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD001978
     1. Label: PRIDE project
     2. Name: Proteomic and Clinical Analysis of a Fine-needle Aspirate Biopsy from a Single Cold Thyroid Nodule: A Case Study