PXD020157

PXD020157 is an original dataset announced via ProteomeXchange.

Title	Clinical proteomics workflow for high quality quantitative proteome and PTM analysis of biologically relevant FFPE tissue samples
Description	In recent years, the use of formalin-fixed paraffin-embedded (FFPE) tissues has increased within cancer research and clinical proteomics. However, the use of FFPE tissues can be demanding due to paraffin embedding and cross-links introduced by the formaldehyde. Here, we developed a workflow implementing efficient paraffin removal and protein extraction from FFPE tissues, followed by optimized digestion using suspension trapping (S-trap), with different clinical proteomics strategies. To gain proteomic depth, the optimized sample preparation protocol was combined with isobaric labeling and applied to three lung adenocarcinoma patient samples. The peptides eluted from the S-trap were labeled with TMT without any desalting step in between. In total, 8,163 proteins were commonly quantified across all channels, and specific proteins related to clinical outcome and histopathological subtype were detected. In addition, we developed a protocol in the S-trap for studying endogenous lysine acetylation stoichiometry using FFPE tonsil tissue. Our method allows identification and localization of lysine acetylation and relative quantification comparison between samples. We could identify 1,839 acetylated peptides belonging to 1,339 protein groups. The results were compared to frozen tissue samples and no notable differences in acetylation pattern were observed. In summary, we present a reproducible sample preparation workflow optimized for FFPE tissues that is easy to scale up using the S-trap 96-well plate. Our results demonstrate compatibility of the S-trap with TMT labeling. And, for the first time, we showed that it is biologically relevant to study endogenous lysine acetylation in FFPE tissues, contributing to a better use of the existing FFPE collections around the world.
HostingRepository	PRIDE
AnnounceDate	2021-03-04
AnnouncementXML	Submission_2021-03-04_14:24:02.079.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD020157
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Magdalena Kuras
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	TMT6plex-126 reporter+balance reagent acylated residue; acetylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive HF

Revision	Datetime	Status	ChangeLog Entry
0	2020-07-02 15:31:15	ID requested
⏵ 1	2021-03-04 14:24:02	announced

Kuras M, Woldmar N, Kim Y, Hefner M, Malm J, Moldvay J, D, ö, me B, Fillinger J, Pizzatti L, Gil J, Marko-Varga G, Rezeli M, Proteomic Workflows for High-Quality Quantitative Proteome and Post-Translational Modification Analysis of Clinically Relevant Samples from Formalin-Fixed Paraffin-Embedded Archives. J Proteome Res, 20(1):1027-1039(2021) [pubmed]

submitter keyword: FFPE, S-trap, suspension trapping, proteomics, mass spectrometry, cancer, tissue, sample preparation, throughput, TMT, isobaric labeling, lung adenocarcinoma, clinical proteomics, lysine acetylation stoichiomtery

Gyorgy Marko-Varga
contact affiliation	Div. Clinical Protein Science & Imaging, Dept. of Clinical Sciences (Lund) and Dept. of Biomedical Engineering, Lund University, Lund, Sweden
contact email	gyorgymarkovarga@hotmail.com
lab head
Magdalena Kuras
contact affiliation	Lund University
contact email	magdalena.kuras@med.lu.se
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD020157
     1. Label: PRIDE project
     2. Name: Clinical proteomics workflow for high quality quantitative proteome and PTM analysis of biologically relevant FFPE tissue samples