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The field of clinical proteomics has rapidly evolved during the past few years and is continuously growing as new methodologies and technologies emerge.
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Either by signing into your account or linking your membership details before your order is placed. Your points will be added to your account once your order is shipped. Click on the cover image above to read some pages of this book! The field of clinical proteomics has rapidly evolved during the past few years and is continuously growing as new methodologies and technologies emerge. In Clinical Proteomics , a select group of leading researchers has contributed their state-of-the-art methodologies on protein profiling and identification of disease biomarkers in tissues, microdissected cells and body fluids.

With its multi-disciplinary approach, Clinical Proteomics provides integrated, cutting-edge techniques sure to be invaluable to a wide range of researchers including clinicians, molecular biologists, chemists, bioinformaticians and computational biologists. This multiauthored book provides state-of-the-art information and practical protocols on these topics and many other related areas.

Overall, this is an excellent book whose natural readership includes both newcomers to the field and seasoned biomarker hunters who wish to update their knowledge or explore new techniques. Country of Publication: US Dimensions cm : Help Centre. My Wishlist Sign In Join. Be the first to write a review. Add to Wishlist. Read the full text. Tools Request permission Export citation Add to favorites Track citation. Share Give access Share full text access. Share full text access. Please review our Terms and Conditions of Use and check box below to share full-text version of article. Volume 4 , Issue 1 January Related Information.

Close Figure Viewer. Numbers of missed cleavages for all replicates. For each replicate, the percentages of missed cleavages are plotted. We furthermore assessed different physicochemical properties and Gene Ontology GO term distributions to exclude enrichment of proteins with extreme properties by the DTR protocol. The molecular weight distribution does not show major differences between the protocols Fig. The protocols do not differ substantially in high molecular weight proteins in contrast to a study from Tanca et al.

Physicochemical properties of the proteins identified with each protocol. This means that the proteins show no major differences in terms of their charge or their hydrophobic properties, validating the physicochemical similarity of the two detergents RapiGest and SDS. The physicochemical similarity between detected proteins with the direct trypsinization protocol compared to the FASP approach can be lost when omitting the RapiGest in the extraction buffer as reported by Tanca et al.

On the other hand, Drummond et al. The basis of these conflicting results remains unclear. The distribution of the percentage of proteins belonging to each GO term is plotted in Fig. The distribution of cellular compartment and molecular function GO terms is highly similar for the three different protocols Fig. Distribution of gene ontology GO terms of identified proteins. Distribution of the identified proteins according to the cellular compartment a and to the molecular function b gene ontology terms.

In our study, each slice consisted of 0. We did not titrate down the tissue amount to keep the conditions suitable for both protocols. Although FASP is reported to be usable for small sample amounts as little as laser micro dissected cells [ 9 , 40 , 43 ] several studies consider it non-ideal for small tissue samples [ 20 , 22 , 44 ].

Three recent publications highlighted the need for robust protocols that can be applied to smaller FFPE tissue specimens and two of them used the direct trypsinization approach, one with and the other without Rapigest [ 20 , 22 , 45 ]. We stained four single FFPE tonsil tissue slices, derived from two patients, with different standard histological stainings and analyzed them with the DTR protocol.

More than proteins were on average identified from the tissues in each analysis, comprising unstained slices or slices stained with hematoxylin and hemalaun. The LFQ intensities were distributed equally for all replicates Additional file 5. As expected, Pearson correlation coefficients are slightly higher in the comparison of tissue slices from the same patient than from the two different patients. Additional file 6 depicts the proteome overlaps and Pearson correlation coefficients between all replicates.

For each staining, the mean and standard deviation SD of the ID as well as the proteome overlap were calculated. The plots and Pearson correlation coefficient of the first two replicates for technical and biological replicates are shown while for the other correlations the range of the obtained r-values is given for each staining method. The comparison of the three different staining methods and the unstained control illustrates that staining does not severely impair proteome coverage and quantitation, as suggested by similar proteome overlap of identified proteins in all four replicates and correlations of mean protein quantitation values Fig.

Our study aimed to investigate compatibility of commonly used histopathological staining procedures with the DTR method and it remained beyond the scope of the present study to probe whether shortened incubation times yield further improved proteome coverage. In other studies, hematoxylin has been found to be compatible with mass-spectrometry proteomics [ 39 , 46 ].

In summary, there is no consensus perspective on the impact of histopathological staining on proteome coverage. However, in many situations there is the need to source archived specimens for retrospective proteome studies, irrespective of any procedural details of their staining.

Our results encourage considering such specimens for proteome studies. When possible, it might be beneficial to perform a small pretest to find the optimal staining method. Comparison of identified and quantified proteins between the four different staining methods.

Josip Blonder - Mass spectrometry based clinical proteomics in biomarker research

The heat map depicts the percentage of proteins, which were shared between two staining methods. The compatibility of stained FFPE tissue with the DTR protocol might be astonishing as no dedicated cleanup step is performed during sample preparation. Our findings go along with a study by Drummond et al. Recently, Azimi et al. We conclude that DTR is compatible with commonly used tissue staining procedures, thus opening the possibility to use previously stained tissues for proteomic analysis.


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The protocols showed no major difference for the physicochemical properties and GO terms annotations of the detected proteins. Cell-based proteome analysis: the first stage in the pipeline for biomarker discovery. Biochim Biophys Acta Proteins Proteomics. Impact of pre-analytical factors on the proteomic analysis of formalin-fixed paraffin-embedded tissue.

Clinical Proteomics

Proteomics Clin Appl. Formaldehyde fixation. J Histochem Cytochem. Identification of formaldehyde-induced modifications in proteins: reactions with model peptides. J Biol Chem. Generation of high-quality protein extracts from formalin-fixed, paraffin-embedded tissues. Proteome analysis of microdissected formalin-fixed and paraffin-embedded tissue specimens. Antigen retrieval for proteomic characterization of formalin-fixed and paraffin-embedded tissues.

J Proteome Res. Proteome, phosphoproteome, and N-glycoproteome are quantitatively preserved in formalin-fixed paraffin-embedded tissue and analyzable by high-resolution mass spectrometry.

High recovery FASP applied to the proteomic analysis of microdissected formalin fixed paraffin embedded cancer tissues retrieves known colon cancer markers. Initial development and validation of a novel extraction method for quantitative mining of the formalin-fixed, paraffin-embedded tissue proteome for biomarker investigations. Standardization of a sample preparation and analytical workflow for proteomics of archival endometrial cancer tissue standardization of a sample preparation and analytical workflow for proteomics of archival endometrial cancer tissue gynecologic oncology.

Quantitative proteomic analysis of formalin-fixed, paraffin-embedded clear cell renal cell carcinoma tissue using stable isotopic dimethylation of primary amines. BMC Genomics. Proteomic analysis of formalin-fixed prostate cancer tissue. Mol Cell Proteomics.

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Gastric Cancer. Antigen retrieval in formalin-fixed, paraffin-embedded tissues: an enhancement method for immunohistochemical staining based on microwave oven heating of tissue sections. Universal sample preparation method for proteome analysis. Nat Methods.

Clinical Proteomics

Equivalence of protein inventories obtained from formalin-fixed paraffin-embedded and frozen tissue in multidimensional liquid chromatography-tandem mass spectrometry shotgun proteomic analysis. N-linked glycoproteomic analysis of formalin-fixed and paraffin-embedded tissues. Protein profiling of formalin fixed paraffin embedded tissue: identification of potential biomarkers for pediatric brainstem glioma.

A laser microdissection-based workflow for FFPE tissue microproteomics: important considerations for small sample processing. In silico analysis validates proteomic findings of formalin-fixed paraffin embedded cutaneous squamous cell carcinoma tissue. Cancer Genomics Proteomics.


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Sci Rep. Enzyme-friendly, mass spectrometry-compatible surfactant for in-solution enzymatic digestion of proteins.

Anal Chem. Formalin-fixed, paraffin-embedded tissues as a robust source for the profiling of native and protease-generated protein amino termini. Impact of routinely employed procedures for tissue processing on the proteomic analysis of formalin-fixed paraffin-embedded tissue. Proteomic workflow for analysis of archival formalin-fixed and paraffin-embedded clinical samples to a depth of proteins.