PXD032108

PXD032108 is an original dataset announced via ProteomeXchange.

Title	Comparison of matched formalin-fixed paraffin embedded and fresh frozen tissue reveals bias in proteomic profiles
Description	Tissue biopsies are most commonly archived in a paraffin block following tissue fixation with formaldehyde (FFPE) or as fresh frozen tissue (FFT). While both methods preserve biological samples, little is known about how they affect the quantifiable proteome. We performed a ‘bottom-up’ proteomic analysis (N=20) of short and long-term archived FFPE surgical samples of human meningiomas and compared them to matched FFT specimens. FFT facilitated identification of a slightly higher number of proteins compared with matched FFPE specimens (5735 vs 5670 proteins, respectively (p < 0.05), regardless of archival time. However, marked differences in the proteome composition were apparent between FFPE and FFT specimens. Twenty-three percent of FFPE-derived peptides and 8% of FFT-derived peptides contained at least one chemical modification. Methylation and formylation were most prominent in FFPE-derives peptides (36% and 17% of modified FFPE peptides, respectively) while, most of phosphorylation and iron modifications appeared in FFT-derived peptides (p<0.001). A mean 14% (2.9) of peptides identified in FFPE contained at least one modified Lysine residue. Importantly, larger proteins were significantly overrepresented in FFT specimens, while FFPE specimens were enriched with smaller proteins. This work cautions against comparing results of proteomic studies derived from different archival methods.
HostingRepository	PRIDE
AnnounceDate	2024-02-12
AnnouncementXML	Submission_2024-02-11_23:54:49.534.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD032108
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Yishai Levin
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive HF

Revision	Datetime	Status	ChangeLog Entry
0	2022-03-07 03:53:58	ID requested
⏵ 1	2024-02-11 23:54:49	announced

10.6019/PXD032108;

10.1002/PMIC.202200085;

submitter keyword: fresh frozen, cancer, tissue,FFPE

Tal Shahar
contact affiliation	Neurosurgical Oncology Unit Neurosurgery Department Shaare Zedek Medical Center
contact email	tals@szmc.org.il
lab head
Yishai Levin
contact affiliation	Weizmann Institute of Science, Israel
contact email	yishai.levin@gmail.com
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/2024/02/PXD032108

PRIDE project URI

• PRIDE
  1. PXD032108
     1. Label: PRIDE project
     2. Name: Comparison of matched formalin-fixed paraffin embedded and fresh frozen tissue reveals bias in proteomic profiles