PXD054596

PXD054596 is an original dataset announced via ProteomeXchange.

Title	The effect of storage time and temperature on the proteomic analysis of FFPE tissue sections
Description	Formalin-fixed paraffin-embedded (FFPE) tissues are stable when stored at ambient temperature; they are primarily used for histopathology and immunohistochemistry (IHC). The use of FFPE tissues in molecular biological applications has increased over the years and they can be used for cancer proteomic study and biomarker discovery. Prolonged storage time and poor storage conditions would affect the antigenicity of tissue sections that are cut from FFPE blocks and used for IHC. However, it is not known if these factors would have similar impacts on proteomic analysis. To determine this, tissue sections were cut from rat brain, kidney and liver FFPE blocks on day 0 and stored at RT or -80°C for up to 48 weeks before they were processed and analysed by LC-MS on 11 experiment days (1, 2, 3, 4, 8, 12, 16, 20, 24, 37 and 48 weeks after day 0). Fresh tissue sections were cut from the same FFPE blocks on the experiment day and used as controls. All peptide digests (n = 297) were analysed on Sciex TripleTOF 6600 mass spectrometers in data-dependent acquisition (DDA) mode; kidney and liver digests (n = 165) were also analysed in data-independent acquisition (DIA) mode. From both DDA and DIA analysis, the overall proteome and post-translational modifications (PTMs) that are specific for FFPE samples were not affected by the storage time and storage temperature. This indicates that FFPE tissue sections can be stored at either RT or -80°C for at least 48 weeks without compromising proteomic analysis.
HostingRepository	PRIDE
AnnounceDate	2025-03-26
AnnouncementXML	Submission_2025-03-26_02:16:25.619.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Jennifer M. S. Koh
SpeciesList	scientific name: Rattus norvegicus (Rat); NCBI TaxID: 10116; scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	iodoacetamide derivatized residue
Instrument	TripleTOF 6600

Revision	Datetime	Status	ChangeLog Entry
0	2024-08-05 04:47:26	ID requested
⏵ 1	2025-03-26 02:16:26	announced

10.1186/S12014-025-09529-5;

submitter keyword: proteomics,formalin-fixed paraffin-embedded (FFPE), DIA-MS, post-translational modification (PTM), DDA-MS

Phillip J. Robinson
contact affiliation	ProCan®, Children’s Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, NSW, Australia
contact email	probinson@cmri.org.au
lab head
Jennifer M. S. Koh
contact affiliation	ProCan®, Children’s Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, NSW, Australia
contact email	jkoh@cmri.org.au
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD054596
     1. Label: PRIDE project
     2. Name: The effect of storage time and temperature on the proteomic analysis of FFPE tissue sections