Comparison of different tissue sampling methods for protein extraction from formalin-fixed and paraffin-embedded tissue specimens

Gräntzdörffer, Ilona; Yumlu, Saniye; Gioeva, Zarina; Wasielewski, Reinhard von; Ebert, Matthias P.; Röcken, Christoph

doi:10.1016/j.yexmp.2009.09.009

Cited by 35 publications

(31 citation statements)

References 23 publications

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“…However, many questions remain in terms of quantification of the expression levels of proteins extracted from FFPE tissue samples and this approach has proven to be a daunting task with success varying according to the biomarker of interest and the tissue type [109,110]. In fact, the protein extraction efficiency is reduced by the extensive molecular crosslinking that occurs upon formalin fixation, with possible interferences in immunoreactivity or even in protein identification by mass spectrometry [111], imposing the development of efficient extraction methods [109,110,112,113].…”

Section: Electrophoresis In Formalin-fixed and Paraffin-embedded Tissmentioning

confidence: 99%

“…In fact, the protein extraction efficiency is reduced by the extensive molecular crosslinking that occurs upon formalin fixation, with possible interferences in immunoreactivity or even in protein identification by mass spectrometry [111], imposing the development of efficient extraction methods [109,110,112,113]. The achievement of protein recovery with minimal losses in immunoreactivity is particularly relevant in studies needing immunoblotting.…”

Section: Electrophoresis In Formalin-fixed and Paraffin-embedded Tissmentioning

confidence: 99%

“…Several studies report methods of collecting and processing tissues directly from selected areas of histological sections using different tissue types [see extensive review in [113]], including salivary glands [114][115][116]. Most studies revealed comparability between protein extracts from FFPE and from unfixed fresh frozen tissue samples by different validation methods including SDS-PAGE and Western blotting [105,109,114,116,117].…”

Section: Electrophoresis In Formalin-fixed and Paraffin-embedded Tissmentioning

confidence: 99%

“…Nonetheless, with optimized extraction methods, FFPE tissue samples can be a valuable source of protein, allowing reproducible and biologically relevant proteomic profiles for research on biomarkers and biological molecular mechanisms [109,110,112,136], with particular interest in systematic analysis of saliva and salivary gland feed-back regulation. However, despite the number of studies taking advantage of electrophoresis in FFPE tissue samples, currently, there is no consensus on the optimal protocol for protein extraction, neither accepted standards for…”

Section: Electrophoresis In Formalin-fixed and Paraffin-embedded Tissmentioning

confidence: 99%

See 3 more Smart Citations

The Use of Electrophoresis for the Study of Saliva Involvement in Ingestive Behavior

Lamy¹,

Morzel²,

Rodrigues³

et al. 2015

Field Effect Electroosmosis - A Novel Phenomenon in Electrokinetics and Its Applications in Capillary Electrophoresis

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Section: Electrophoresis In Formalin-fixed and Paraffin-embedded Tissmentioning

confidence: 99%

Section: Electrophoresis In Formalin-fixed and Paraffin-embedded Tissmentioning

confidence: 99%

Section: Electrophoresis In Formalin-fixed and Paraffin-embedded Tissmentioning

confidence: 99%

Section: Electrophoresis In Formalin-fixed and Paraffin-embedded Tissmentioning

confidence: 99%

See 2 more Smart Citations

The Use of Electrophoresis for the Study of Saliva Involvement in Ingestive Behavior

Lamy¹,

Morzel²,

Rodrigues³

et al. 2015

Field Effect Electroosmosis - A Novel Phenomenon in Electrokinetics and Its Applications in Capillary Electrophoresis

View full text Add to dashboard Cite

“…[24][25][26] The longevity of FFPE tissue has led to the accumulation of substantial patient sample archives, which have been collected alongside clinico-pathological data. [27] With suitable methods for accessing FFPE tissues, these archives represent a rich resource for tissue characterization using MALDI-IMS. [26] In order to circumvent the formalin-induced cross-links most groups have either adopted a proteolytic enzyme [7,28] or antigen retrieval and enzyme combination treatment.…”

Section: Introductionmentioning

confidence: 99%

Matrix‐assisted laser desorption/ionization imaging protocol for in situ characterization of tryptic peptide identity and distribution in formalin‐fixed tissue

Gustafsson

Eddes

Meding

et al. 2013

Rapid Comm Mass Spectrometry

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RATIONALE: Matrix-assisted laser desorption/ionization (MALDI) imaging mass spectrometry provides the means to map the in situ distribution of tryptic peptides in formalin-fixed clinical tissue samples. The ability to analyze clinical samples is of great importance to further developments in the imaging field. However, there is a requirement in this field of research for additional methods describing the characterization of tryptic peptides by MALDI imaging. METHODS AND RESULTS: This protocol gives highly detailed instructions, with examples, for (1) successfully performing tryptic peptide MALDI imaging on formalin-fixed cancer tissue using a MALDI-TOF/TOF MS instrument, (2) tentatively generating identifications through nLC/MS/MS, and (3) validating these identifications by in situ MS/MS of peptides of interest. CONCLUSIONS: This protocol provides a detailed and straightforward description of the methods required for groups new to MALDI imaging to begin analysis of formalin-fixed clinical samples.

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Proteome analysis of tissues by mass spectrometry

Đapić

Baljeu‐Neuman

Uwugiaren

et al. 2019

Mass Spectrometry Reviews

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Tissues and biofluids are important sources of information used for the detection of diseases and decisions on patient therapies. There are several accepted methods for preservation of tissues, among which the most popular are fresh‐frozen and formalin‐fixed paraffin embedded methods. Depending on the preservation method and the amount of sample available, various specific protocols are available for tissue processing for subsequent proteomic analysis. Protocols are tailored to answer various biological questions, and as such vary in lysis and digestion conditions, as well as duration. The existence of diverse tissue‐sample protocols has led to confusion in how to choose the best protocol for a given tissue and made it difficult to compare results across sample types. Here, we summarize procedures used for tissue processing for subsequent bottom‐up proteomic analysis. Furthermore, we compare protocols for their variations in the composition of lysis buffers, digestion procedures, and purification steps. For example, reports have shown that lysis buffer composition plays an important role in the profile of extracted proteins: the most common are tris(hydroxymethyl)aminomethane, radioimmunoprecipitation assay, and ammonium bicarbonate buffers. Although, trypsin is the most commonly used enzyme for proteolysis, in some protocols it is supplemented with Lys‐C and/or chymotrypsin, which will often lead to an increase in proteome coverage. Data show that the selection of the lysis procedure might need to be tissue‐specific to produce distinct protocols for individual tissue types. Finally, selection of the procedures is also influenced by the amount of sample available, which range from biopsies or the size of a few dozen of mm2 obtained with laser capture microdissection to much larger amounts that weight several milligrams.

show abstract

Comparison of different tissue sampling methods for protein extraction from formalin-fixed and paraffin-embedded tissue specimens

Cited by 35 publications

References 23 publications

The Use of Electrophoresis for the Study of Saliva Involvement in Ingestive Behavior

The Use of Electrophoresis for the Study of Saliva Involvement in Ingestive Behavior

Matrix‐assisted laser desorption/ionization imaging protocol for in situ characterization of tryptic peptide identity and distribution in formalin‐fixed tissue

Proteome analysis of tissues by mass spectrometry

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