Evaluation of Protein Purification Techniques and Effects of Storage Duration on LC-MS/MS Analysis of Archived FFPE Human CRC Tissues.
Adenocarcinoma
/ metabolism
Adult
Aged
Aged, 80 and over
Biomarkers, Tumor
/ analysis
Chromatography, Liquid
/ methods
Colorectal Neoplasms
/ metabolism
Female
Formaldehyde
/ chemistry
Humans
Male
Middle Aged
Paraffin Embedding
Peptide Fragments
/ analysis
Prognosis
Proteome
/ analysis
Retrospective Studies
Tandem Mass Spectrometry
/ methods
LC-MS/MS
SP3/HILIC-on-bead-digestion
acetone precipitation and formic acid resolubilization
detergent removal plates
formalin-fixed paraffin-embedded proteomics
mass spectrometry
Journal
Pathology oncology research : POR
ISSN: 1532-2807
Titre abrégé: Pathol Oncol Res
Pays: Switzerland
ID NLM: 9706087
Informations de publication
Date de publication:
2021
2021
Historique:
received:
29
10
2020
accepted:
01
03
2021
entrez:
14
7
2021
pubmed:
15
7
2021
medline:
4
1
2022
Statut:
epublish
Résumé
To elucidate cancer pathogenesis and its mechanisms at the molecular level, the collecting and characterization of large individual patient tissue cohorts are required. Since most pathology institutes routinely preserve biopsy tissues by standardized methods of formalin fixation and paraffin embedment, these archived FFPE tissues are important collections of pathology material that include patient metadata, such as medical history and treatments. FFPE blocks can be stored under ambient conditions for decades, while retaining cellular morphology, due to modifications induced by formalin. However, the effect of long-term storage, at resource-limited institutions in developing countries, on extractable protein quantity/quality has not yet been investigated. In addition, the optimal sample preparation techniques required for accurate and reproducible results from label-free LC-MS/MS analysis across block ages remains unclear. This study investigated protein extraction efficiency of 1, 5, and 10-year old human colorectal carcinoma resection tissue and assessed three different gel-free protein purification methods for label-free LC-MS/MS analysis. A sample size of n = 17 patients per experimental group (with experiment power = 0.7 and
Identifiants
pubmed: 34257588
doi: 10.3389/pore.2021.622855
pii: 622855
pmc: PMC8262168
doi:
Substances chimiques
Biomarkers, Tumor
0
Peptide Fragments
0
Proteome
0
Formaldehyde
1HG84L3525
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
622855Informations de copyright
Copyright © 2021 Rossouw, Bendou, Blignaut, Bell, Rigby and Christoffels.
Déclaration de conflit d'intérêts
The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.
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