PXD021074

PXD021074 is an original dataset announced via ProteomeXchange.

Title	Evaluation of two methods for LS-MS/MS proteomic analysis of formalin fixed and paraffin embedded tissues
Description	The proteomics of archival samples has advanced significantly during the last two decades, making possible the use of vast FFPE tissue archives in biomarker studies. However, due to the limited data regarding comparison of the performance of different protocols, there is currently no consensus on the most effective protocol for shotgun proteomic analysis of FFPE tissue. In-solution digestion method using Rapigest as detergent and FASP method, both reported to deliver superior results on FFPE tissues were compared using two label-free data-independent LC-MS/MS acquisition modes. Archival FFPE prostate tissues stored 7 years and mirroring fresh frozen samples were processed with both protocols in 3 technical replicates. Data were comparatively evaluated in terms of protein and peptide identifications in fresh frozen and FFPE samples, analysis of the fresh and FFPE tissues representative proteome (molecular weight distribution, distribution according to protein’s pI, cellular component analysis of proteins and quantitation accuracy) and technical reproducibility of the Rapigest and FASP protocols.
HostingRepository	PRIDE
AnnounceDate	2021-01-15
AnnouncementXML	Submission_2021-01-18_23:49:42.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD021074
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Katarina Davalieva
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue; iodoacetic acid derivatized residue
Instrument	Synapt MS

Revision	Datetime	Status	ChangeLog Entry
0	2020-08-24 02:27:52	ID requested
1	2021-01-15 01:18:47	announced
⏵ 2	2021-01-18 23:49:42	announced	2021-01-19: Updated publication reference for PubMed record(s): 33453434.

Davalieva K, Kiprijanovska S, Dimovski A, Rosoklija G, Dwork AJ, Comparative evaluation of two methods for LC-MS/MS proteomic analysis of formalin fixed and paraffin embedded tissues. J Proteomics, 235():104117(2021) [pubmed]

submitter keyword: Proteomics, FFPE, Protein extraction, Rapigest, FASP, LC-MS/MS, biomarker

Katarina Davalieva
contact affiliation	Research Centre for Genetic Engineering and Biotechnology “Georgi D Efremov”, Macedonian Academy of Sciences and Arts, Skopje, Krste Misirkov 2, 1000 Skopje, Republic of North Macedonia
contact email	katarina@manu.edu.mk
lab head
Katarina Davalieva
contact affiliation	Research Centre for Genetic Engineering and Biotechnology “Georgi D Efremov”, Macedonian Academy of Sciences and Arts, Skopje
contact email	katarina@manu.edu.mk
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD021074
     1. Label: PRIDE project
     2. Name: Evaluation of two methods for LS-MS/MS proteomic analysis of formalin fixed and paraffin embedded tissues