Method for and characterization of proteins isolated by laser capture microdissection from formalin-fixed, paraffin-embedded tumors

2001 ◽  
Vol 120 (5) ◽  
pp. A170-A170
Author(s):  
S GLOVER ◽  
K MATKOWSKYJ ◽  
R BENYA
Keyword(s):  
Laser Capture Microdissection ◽  
Formalin Fixed Paraffin ◽  
Formalin Fixed Paraffin Embedded ◽  
Laser Capture ◽  
Formalin Fixed

Improved Detection ofHelicobacter pyloriDNA in Formalin-fixed Paraffin-embedded (FFPE) Tissue of Patients with Hepatocellular Carcinoma Using Laser Capture Microdissection (LCM)

Helicobacter ◽  
2013 ◽  
Vol 18 (3) ◽  
pp. 244-245 ◽  
Author(s):  
Elizabeth Maria Afonso Rabelo-Gonçalves ◽  
Ilária C. Sgardioli ◽  
Iscia Lopes-Cendes ◽  
Cecília Amélia Fazzio Escanhoela ◽  
Jazon Romilson de Souza Almeida ◽  
...  
Keyword(s):  
Hepatocellular Carcinoma ◽  
Laser Capture Microdissection ◽  
Ffpe Tissue ◽  
Formalin Fixed Paraffin ◽  
Formalin Fixed Paraffin Embedded ◽  
Laser Capture ◽  
Formalin Fixed

scholarly journals Characterization of epididymal and testicular histologic lesions and use of immunohistochemistry and PCR on formalin-fixed tissues to detect Brucella canis in male dogs

2021 ◽  
pp. 104063872098688
Author(s):  
Andrea M. Camargo-Castañeda ◽  
Lauren W. Stranahan ◽  
John F. Edwards ◽  
Daniel G. Garcia-Gonzalez ◽  
Leonardo Roa ◽  
...  
Keyword(s):  
Accurate Diagnosis ◽  
Testicular Atrophy ◽  
Detection Techniques ◽  
Formalin Fixed Paraffin ◽  
Brucella Canis ◽  
Formalin Fixed Paraffin Embedded ◽  
Variable Sensitivity ◽  
Ffpe Tissues ◽  
Formalin Fixed

In male dogs, Brucella canis frequently causes epididymitis, ultimately resulting in testicular atrophy and infertility. Although B. canis predominantly affects the epididymis, the misleading term “orchitis” is still commonly used by clinicians. Of additional concern, diagnosis in dogs remains challenging because of variable sensitivity and specificity of serologic assays and fluctuations in bacteremia levels in infected dogs, reducing the sensitivity of blood culture. We describe here the histologic lesions in the scrotal contents of 8 dogs suspected of being infected with B. canis and clinically diagnosed with orchitis. We explored the possibility of using immunohistochemistry (IHC) and real-time PCR (rtPCR) in formalin-fixed, paraffin-embedded (FFPE) tissues to detect the presence of B. canis. Epididymitis of variable chronicity was identified in all 8 dogs, with only 3 also exhibiting orchitis. Using rtPCR, the presence of B. canis was identified in 4 of 8 dogs, with 3 of these 4 dogs also positive by IHC. These results suggest that rtPCR and IHC are promising techniques that can be used in FFPE tissues to detect B. canis when other detection techniques are unavailable. Additionally, accurate recognition of epididymitis rather than orchitis in suspect cases could aid in accurate diagnosis.

scholarly journals PTM-Shepherd: analysis and summarization of post-translational and chemical modifications from open search results

2020 ◽  
pp. mcp.TIR120.002216
Author(s):  
Daniel J. Geiszler ◽  
Andy T. Kong ◽  
Dmitry M Avtonomov ◽  
Fengchao Yu ◽  
Felipe da Veiga Leprevost ◽  
...  
Keyword(s):  
Shotgun Proteomics ◽  
Chemical Modifications ◽  
Bioinformatics Tool ◽  
Site Specific ◽  
Search Results ◽  
Formalin Fixed Paraffin ◽  
Formalin Fixed Paraffin Embedded ◽  
Small Set ◽  
Formalin Fixed

Open searching has proven to be an effective strategy for identifying both known and unknown modifications in shotgun proteomics experiments. Rather than being limited to a small set of user-specified modifications, open searches identify peptides with any mass shift that may correspond to a single modification or a combination of several modifications. Here we present PTM-Shepherd, a bioinformatics tool that automates characterization of PTM profiles detected in open searches based on attributes such as amino acid localization, fragmentation spectra similarity, retention time shifts, and relative modification rates. PTM-Shepherd can also perform multi-experiment comparisons for studying changes in modification profiles, e.g. in data generated in different laboratories or under different conditions. We demonstrate how PTM-Shepherd improves the analysis of data from formalin-fixed paraffin-embedded samples, detects extreme underalkylation of cysteine in some datasets, discovers an artefactual modification introduced during peptide synthesis, and uncovers site-specific biases in sample preparation artifacts in a multi-center proteomics profiling study.

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