Dataset Information

Evaluation of two methods for LS-MS/MS proteomic analysis of formalin fixed and paraffin embedded tissues

ABSTRACT: 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.

INSTRUMENT(S): Synapt MS

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Prostate Gland

SUBMITTER: Katarina Davalieva

LAB HEAD: Katarina Davalieva

PROVIDER: PXD021074 | Pride | 2021-01-15

REPOSITORIES: Pride

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Dataset's files

Source:

			Action	DRS
	FASP_FFPE_UDMSe_250ng_pool_1_1.mgf	Mgf
	FASP_FFPE_UDMSe_250ng_pool_1_1.mzid.gz	Mzid
	FASP_FFPE_UDMSe_250ng_pool_1_1.raw.zip	Raw
	FASP_FFPE_UDMSe_250ng_pool_1_1_IA_Log.txt	Txt
	FASP_FFPE_UDMSe_250ng_pool_1_1_IA_final_fragment.csv	Csv

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Publications

Comparative evaluation of two methods for LC-MS/MS proteomic analysis of formalin fixed and paraffin embedded tissues.

Davalieva Katarina K Kiprijanovska Sanja S Dimovski Aleksandar A Rosoklija Gorazd G Dwork Andrew J AJ

Journal of proteomics 20210114

The proteomics of formalin-fixed, paraffin-embedded (FFPE) samples has advanced significantly during the last two decades, but there are many protocols and few studies comparing them directly. There is no consensus on the most effective protocol for shotgun proteomic analysis. We compared the in-solution digestion with RapiGest and Filter Aided Sample Preparation (FASP) of FFPE prostate tissues stored 7 years and mirroring fresh frozen samples, using two label-free data-independent LC-MS/MS acqu ...[more]

PMID: 33453434

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