Evidence map›Paper›PMID 39910438›Full record

ArticleClinical proteomics2025

The effect of storage time and temperature on the proteomic analysis of FFPE tissue sections.

Jennifer M S Koh, Erin K Sykes, Jyoti Rukhaya, Asim Anees, Qing Zhong, Christopher Jackson, Benedict J Panizza, Roger R Reddel, Rosemary L Balleine, Peter G Hains and 1 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Clinical proteomics, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.

0numbers the graph read from it
0cells of the map it votes in
8citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

8 citing papers in PubMed.

  1. Article
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  3. Review
  4. Review
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4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

11 authors.

Jennifer M S KohFaculty of Medicine and Health, ProCan®, Children's Medical Research Institute, The University of Sydney, Westmead, NSW, Australia.ORCID http://orcid.org/0000-0003-2140-3151
Erin K SykesFaculty of Medicine and Health, ProCan®, Children's Medical Research Institute, The University of Sydney, Westmead, NSW, Australia.ORCID http://orcid.org/0000-0002-1582-5238
Jyoti RukhayaFaculty of Medicine and Health, ProCan®, Children's Medical Research Institute, The University of Sydney, Westmead, NSW, Australia.
Asim AneesFaculty of Medicine and Health, ProCan®, Children's Medical Research Institute, The University of Sydney, Westmead, NSW, Australia.ORCID http://orcid.org/0000-0003-2220-0874
Qing ZhongFaculty of Medicine and Health, ProCan®, Children's Medical Research Institute, The University of Sydney, Westmead, NSW, Australia.ORCID http://orcid.org/0000-0002-5340-301X
Christopher JacksonDepartment of Otolaryngology, Head and Neck Surgery, Princess Alexandra Hospital, Brisbane, QLD, Australia.ORCID http://orcid.org/0000-0002-4930-1184
Benedict J PanizzaDepartment of Otolaryngology, Head and Neck Surgery, Princess Alexandra Hospital, Brisbane, QLD, Australia.ORCID http://orcid.org/0000-0002-3724-3773
Roger R ReddelFaculty of Medicine and Health, ProCan®, Children's Medical Research Institute, The University of Sydney, Westmead, NSW, Australia.ORCID http://orcid.org/0000-0002-6302-6107
Rosemary L BalleineFaculty of Medicine and Health, ProCan®, Children's Medical Research Institute, The University of Sydney, Westmead, NSW, Australia.ORCID http://orcid.org/0000-0003-2864-4345
Peter G HainsFaculty of Medicine and Health, ProCan®, Children's Medical Research Institute, The University of Sydney, Westmead, NSW, Australia.ORCID http://orcid.org/0000-0002-7276-1760
Phillip J RobinsonFaculty of Medicine and Health, ProCan®, Children's Medical Research Institute, The University of Sydney, Westmead, NSW, Australia. probinson@cmri.org.au.ORCID http://orcid.org/0000-0002-7878-0313

Funding

Australian Cancer Research Foundation 2017/TPG001, REG171150Medical Research Futures Fund MRFF-PDNational Health and Medical Research Council GNT1137064
6 · The paper itself

Abstract

Formalin-fixed paraffin-embedded (FFPE) tissues present an important resource for cancer proteomics. They are more readily available than fresh frozen (FF) tissues and can be stored at ambient temperature for decades. FFPE blocks are largely stable for long-term preservation of tumour histology, but the antigenicity of some proteins in FFPE sections degrades over time resulting in deteriorating performance of immunohistochemistry (IHC). It is not known whether FFPE sections that have previously been cut from blocks and used for liquid chromatography-mass spectrometry (LC-MS) analysis at a later time are affected by storage time or temperature. We determined the stability of FFPE sections stored at room temperature (RT) versus - 80 °C over 48 weeks. The stored sections were processed at different timepoints (n = 11) and compared to sections that were freshly cut from FFPE blocks at each timepoint (controls). A total of 297 sections (rat brain, kidney and liver stored at RT, - 80 °C or freshly cut) were tryptically digested and analysed on TripleTOF 6600 mass spectrometers in data-dependent acquisition (DDA) mode. Kidney and liver digests were also analysed in data-independent acquisition (DIA) mode. The number of proteins and peptides identified by DDA with ProteinPilot and some common post-translational modifications (PTMs) were unaffected by the storage time or temperature. Nine of the most common FFPE-associated modifications were quantified using DIA data and all were unaffected by storage time or temperature. Therefore, FFPE tissue sections are suitable for proteomic studies for at least 48 weeks from the time of sectioning.

Identifiers

PMID39910438
PMCPMC11796064

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Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.