ArticleClinical proteomics2014
Critical comparison of sample preparation strategies for shotgun proteomic analysis of formalin-fixed, paraffin-embedded samples: insights from liver tissue.
Article in Clinical proteomics, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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Who cites it
24 citing papers in PubMed.
- Assessment of Lactococcus Cremoris preparations for the pre- and post-milking teat disinfection.BMC veterinary research · 2024Article
- Global Protein Profiling in Processed Immunohistochemistry Tissue Sections.International journal of molecular sciences · 2023Article
- Systematic evaluation and optimization of protein extraction parameters in diagnostic FFPE specimens.Clinical proteomics · 2022Article
- A Non-Hazardous Deparaffinization Protocol Enables Quantitative Proteomics of Core Needle Biopsy-Sized Formalin-Fixed and Paraffin-Embedded (FFPE) Tissue Specimens.International journal of molecular sciences · 2022Article
- MicroPOTS Analysis of Barrett's Esophageal Cell Line Models Identifies Proteomic Changes after Physiologic and Radiation Stress.Journal of proteome research · 2021Article
- Comparative evaluation of two methods for LC-MS/MS proteomic analysis of formalin fixed and paraffin embedded tissues.Journal of proteomics · 2021Review
- Effect of polyethylene glycol 20 000 on protein extraction efficiency of formalin-fixed paraffin-embedded tissues in South Africa.African journal of laboratory medicine · 2021Article
- Evaluation of Protein Purification Techniques and Effects of Storage Duration on LC-MS/MS Analysis of Archived FFPE Human CRC Tissues.Pathology oncology research : POR · 2021Article
- Assessment of Protein Profiles of RNAlater Stored and Fresh PBMC Cells Using Different Protein Extraction Buffers.The protein journal · 2020Article
- Quantitative Profiling of the Human Substantia Nigra Proteome from Laser-capture Microdissected FFPE Tissue.Molecular & cellular proteomics : MCP · 2020Article
- Benchtop-compatible sample processing workflow for proteome profiling of < 100 mammalian cells.Analytical and bioanalytical chemistry · 2019Article
- Comparison of In-Solution, FASP, and S-Trap Based Digestion Methods for Bottom-Up Proteomic Studies.Journal of proteome research · 2018Article
- Assessment of Sample Preparation Bias in Mass Spectrometry-Based Proteomics.Analytical chemistry · 2018Article
- Reproducible proteomics sample preparation for single FFPE tissue slices using acid-labile surfactant and direct trypsinization.Clinical proteomics · 2018Article
- Fast and Simple Protocols for Mass Spectrometry-Based Proteomics of Small Fresh Frozen Uterine Tissue Sections.Analytical chemistry · 2017Article
- Quantitative label-free mass spectrometry analysis of formalin-fixed, paraffin-embedded tissue representing the invasive cutaneous malignant melanoma proteome.Oncology letters · 2016Article
- Atypical carcinoid and large cell neuroendocrine carcinoma of the lung: a proteomic dataset from formalin-fixed archival samples.Data in brief · 2016Article
- Formalin-Fixed, Paraffin-Embedded Tissues (FFPE) as a Robust Source for the Profiling of Native and Protease-Generated Protein Amino Termini.Molecular & cellular proteomics : MCP · 2016Article
- Assessing the impact of long term frozen storage of faecal samples on protein concentration and protease activity.Journal of microbiological methods · 2016Article
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Corrections and comments
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6 authors.
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Abstract
backgroundThe growing field of formalin-fixed paraffin-embedded (FFPE) tissue proteomics holds promise for improving translational research. Direct tissue trypsinization (DT) and protein extraction followed by in solution digestion (ISD) or filter-aided sample preparation (FASP) are the most common workflows for shotgun analysis of FFPE samples, but a critical comparison of the different methods is currently lacking. EXPERIMENTAL
designDT, FASP and ISD workflows were compared by subjecting to the same label-free quantitative approach three independent technical replicates of each method applied to FFPE liver tissue. Data were evaluated in terms of method reproducibility and protein/peptide distribution according to localization, MW, pI and hydrophobicity.
resultsDT showed lower reproducibility, good preservation of high-MW proteins, a general bias towards hydrophilic and acidic proteins, much lower keratin contamination, as well as higher abundance of non-tryptic peptides. Conversely, FASP and ISD proteomes were depleted in high-MW proteins and enriched in hydrophobic and membrane proteins; FASP provided higher identification yields, while ISD exhibited higher reproducibility.
conclusionsThese results highlight that diverse sample preparation strategies provide significantly different proteomic information, and present typical biases that should be taken into account when dealing with FFPE samples. When a sufficient amount of tissue is available, the complementary use of different methods is suggested to increase proteome coverage and depth.
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