| 11. |
- Mischak, Harald, et al.
(author)
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Comprehensive human urine standards for comparability and standardization in clinical proteome analysis
- 2010
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In: Proteomics - Clinical Applications. - : Wiley. - 1862-8346 .- 1862-8354. ; 4:4, s. 464-478
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Journal article (peer-reviewed)abstract
- Purpose: Urine proteomics is emerging as a powerful tool for biomarker discovery. The purpose of this study is the development of a well-characterized "real life" sample that can be used as reference standard in urine clinical proteomics studies. Experimental design: We report on the generation of male and female urine samples that are extensively characterized by different platforms and methods (CE-MS, LC-MS, LC-MS/MS, 1-D gel analysis in combination with nano-LC MS/MS (using LTQ-FT ultra), and 2-DE-MS) for their proteome and peptidome. In several cases analysis involved a definition of the actual biochemical entities, i.e. proteins/peptides associated with molecular mass and detected PTMs and the relative abundance of these compounds. Results: The combination of different technologies allowed coverage of a wide mass range revealing the advantages and complementarities of the different technologies. Application of these samples in "inter-laboratory" and "inter-platform" data comparison is also demonstrated. Conclusions and clinical relevance: These well-characterized urine samples are freely available upon request to enable data comparison especially in the context of biomarker discovery and validation studies. It is also expected that they will provide the basis for the comprehensive characterization of the urinary proteome.
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| 12. |
- Sandström Gerdtsson, Anna, et al.
(author)
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Serum proteome profiling of pancreatitis using recombinant antibody microarrays reveals disease-associated biomarker signatures
- 2012
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In: Proteomics Clinical Applications. - : Wiley. - 1862-8354 .- 1862-8346. ; 6:9-10, s. 96-486
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Journal article (peer-reviewed)abstract
- PURPOSE: Pancreatitis is an inflammatory state of the pancreas, for which high-performing serological biomarkers are lacking. The aim of the present study was to evaluate the use of affinity proteomics for identifying potential markers of disease and stratifying pancreatitis subtypes. EXPERIMENTAL DESIGN: High-content, recombinant antibody microarrays were applied for serum protein expression profiling of 113 serum samples from patients with chronic, acute, and autoimmune pancreatitis, as well as healthy controls. The sample groups were compared using supervised classification based on support vector machine analysis. RESULTS: This discovery study showed that pancreatitis subtypes could be discriminated with high accuracy. Using unfiltered data, the individual subtypes, as well as the combined pancreatitis cohort, were distinguished from healthy controls with high AUC values (0.96-1.00). Moreover, characteristic protein patterns and AUC values in the range of 0.69-0.95 were observed for the individual pancreatitis entities when compared to each other, and to all other samples combined. CONCLUSIONS AND CLINICAL RELEVANCE: This study demonstrated the potential of the antibody microarray approach for stratification of pancreatitis. Distinct candidate multiplex serum biomarker signatures for chronic, acute, and autoimmune pancreatitis were defined, which could enhance our fundamental knowledge of the underlying molecular mechanisms, and potentially lead to improved diagnosis.
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| 13. |
- Fornander, Louise, et al.
(author)
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Innate immunity proteins and a new truncated form of SPLUNC1 in nasopharyngeal aspirates from infants with respiratory syncytial virus infection
- 2011
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In: PROTEOMICS CLINICAL APPLICATIONS. - : Wiley-VCH Verlag Berlin. - 1862-8346. ; 5:9-10, s. 513-522
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Journal article (peer-reviewed)abstract
- Purpose: Respiratory syncytial virus (RSV) is the most common cause of severe respiratory tract infection in infants. The aim was to identify host defence components in nasopharyngeal aspirate (NPA) from infants with RSV infection and to study the expression of the novel 25 kDa innate immunity protein SPLUNC1. less thanbrgreater than less thanbrgreater thanExperimental design: NPAs from infants were analyzed with 2-DE and MS in a pilot study. The levels of SPLUNC1 were analyzed with immunoblotting in 47 NPAs, admitted for RSV diagnosis. less thanbrgreater than less thanbrgreater thanResults: Totally, 35 proteins were identified in NPA, including several innate immunity proteins such as group X phospholipase A(2), different S100 proteins and SPLUNC1. In addition, a new truncated 15 kDa form of SPLUNC1 was identified that was detected in about 50% of the aspirates admitted for RSV diagnosis. RSV-positive boys had significantly less 25 kDa SPLUNC1 than RSV-negative boys while there were no significant differences among girls. less thanbrgreater than less thanbrgreater thanConclusions and clinical relevance: Several important innate immunity proteins were identified in NPA. Notably, a new truncated form of the newly suggested anti-bacterial protein SPLUNC1 was found. It is possible that a decrease in SPLUNC1 in the upper airways may increase the risk for severe pneumonia in boys.
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| 14. |
- Tamburro, Davide, et al.
(author)
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Mass Spectrometry-based characterization of the vitreous phosphoproteome
- 2010
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In: Proteomics Clinical Applications. - : Wiley. - 1862-8346. ; 4:10-11, s. 839-846
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Journal article (peer-reviewed)abstract
- Purpose: The vitreous gel is a highly hydrated extracellular matrix containing many proteins. These proteins are likely accumulated in the vitreous by local secretion, filtration from the blood, or diffusion from the surrounding tissues and vasculature, and may be altered in disease state. In the last several years, several reports of large-scale profiling of vitreous proteins have been published; however, there is little information on the characterization of the phosphoproteome of vitreous. Here, we sought to identify phosphopeptides and their phosphorylation sites from vitreous. Experimental design: We used titanium dioxide (TiO2) to enrich phosphopeptides from vitreous and identified them by LC-MS/MS. Results: We identified 85 unique phosphopeptides and the phosphorylation sites from 44 proteins. Conclusions and clinical relevance: We present a method for characterization of phosphoproteome from vitreous samples using current MS technologies and yielded an initial assessment of the phosphoprotein/peptide content of human vitreous, thus providing important biological information toward further understanding of the post-translational modifications of vitreous proteins and their functional significance in disease.
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