Proteome analysis of tissues by mass spectrometry
| Autor: | Irena Dapic, Naomi Uwugiaren, Jesper Kers, David R. Goodlett, Garry L. Corthals, Lucia Baljeu‐Neuman |
|---|---|
| Přispěvatelé: | Supramolecular Separations (HIMS, FNWI) |
| Jazyk: | angličtina |
| Rok vydání: | 2019 |
| Předmět: |
0301 basic medicine
Proteomics Lysis Sample (material) Biopsy proteome protocols Computational biology FF FFPE 01 natural sciences General Biochemistry Genetics and Molecular Biology Mass Spectrometry Analytical Chemistry 03 medical and health sciences Lysis buffer Animals Humans Spectroscopy Laser capture microdissection Protocol (science) sample preparation Chemistry 010401 analytical chemistry Tissue Processing Proteins tissue Radioimmunoprecipitation Assay Condensed Matter Physics 0104 chemical sciences LC-MS 030104 developmental biology Proteome Proteolysis Tissue Preservation Chromatography Liquid |
| Zdroj: | Mass Spectrometry Reviews, 38(4-5), 403-441. WILEY Mass Spectrometry Reviews, 38(4-5), 403-441. John Wiley and Sons Inc. |
| ISSN: | 0277-7037 |
| Popis: | 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. |
| Databáze: | OpenAIRE |
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