| 1. |
- Alm, Tove, et al.
(författare)
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Introducing the Affinity Binder Knockdown Initiative-A public-private partnership for validation of affinity reagents
- 2016
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Ingår i: EuPA Open Proteomics. - : Elsevier. - 2212-9685. ; 10, s. 56-58
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Tidskriftsartikel (refereegranskat)abstract
- The newly launched Affinity Binder Knockdown Initiative encourages antibody suppliers and users to join this public-private partnership, which uses crowdsourcing to collect characterization data on antibodies. Researchers are asked to share validation data from experiments where gene-editing techniques (such as siRNA or CRISPR) have been used to verify antibody binding. The initiative is launched under the aegis of Antibodypedia, a database designed to allow comparisons and scoring of publicly available antibodies towards human protein targets. What is known about an antibody is the foundation of the scoring and ranking system in Antibodypedia.
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| 2. |
- Ashwood, C., et al.
(författare)
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Proceedings of the EuBIC-MS 2020 Developers’ Meeting
- 2020
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Ingår i: EuPA Open Proteomics. - : Elsevier B.V.. - 2212-9685. ; 24, s. 1-6
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Tidskriftsartikel (refereegranskat)abstract
- The 2020 European Bioinformatics Community for Mass Spectrometry (EuBIC-MS) Developers’ meeting was held from January 13th to January 17th 2020 in Nyborg, Denmark. Among the participants were scientists as well as developers working in the field of computational mass spectrometry (MS) and proteomics. The 4-day program was split between introductory keynote lectures and parallel hackathon sessions. During the latter, the participants developed bioinformatics tools and resources addressing outstanding needs in the community. The hackathons allowed less experienced participants to learn from more advanced computational MS experts, and to actively contribute to highly relevant research projects. We successfully produced several new tools that will be useful to the proteomics community by improving data analysis as well as facilitating future research. All keynote recordings are available on https://doi.org/10.5281/zenodo.3890181.
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| 3. |
- Christiansson, Lisa, et al.
(författare)
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The use of multiplex platforms for absolute and relative protein quantification of clinical material
- 2014
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Ingår i: EuPA Open Proteomics. - : Elsevier BV. - 2212-9685. ; 3, s. 37-47
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Tidskriftsartikel (refereegranskat)abstract
- When introducing multiplex platforms to measure protein content in precious clinical material there is an increased risk of cross reactivity, loss of sensitivity as well as accuracy. In this paper, four multiplex platforms and one singleplex platform were compared by running pre- and post-treatment plasma samples from CML patients. We found a variation of absolute protein concentrations between platforms. For some of the analytes and platforms, relative differences between pre- and post-treatment samples correlated. We conclude that absolute concentrations measured by different platforms should be compared with caution and comparing relative differences could be more accurate.
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| 4. |
- Fasano, M., et al.
(författare)
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Towards a functional definition of the mitochondrial human proteome
- 2016
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Ingår i: EuPA Open Proteomics. - : Elsevier. - 2212-9685. ; 10, s. 24-27
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Tidskriftsartikel (refereegranskat)abstract
- The mitochondrial human proteome project (mt-HPP) was initiated by the Italian HPP group as a part of both the chromosome-centric initiative (C-HPP) and the "biology and disease driven" initiative (B/D-HPP). In recent years several reports highlighted how mitochondrial biology and disease are regulated by specific interactions with non-mitochondrial proteins. Thus, it is of great relevance to extend our present view of the mitochondrial proteome not only to those proteins that are encoded by or transported to mitochondria, but also to their interactors that take part in mitochondria functionality. Here, we propose a graphical representation of the functional mitochondrial proteome by retrieving mitochondrial proteins from the NeXtProt database and adding to the network their interactors as annotated in the IntAct database. Notably, the network may represent a reference to map all the proteins that are currently being identified in mitochondrial proteomics studies.
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| 5. |
- Fehniger, Thomas, et al.
(författare)
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International Biobanking for Lung Cancer and COPD as the Future Resource for Clinical Protein Research
- 2013
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Ingår i: EuPA Open Proteomics. - : Elsevier BV. - 2212-9685. ; 1, s. 3-7
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Tidskriftsartikel (refereegranskat)abstract
- Characterized tissue with pathological grading and blood samples as well as other biofluids forms the basis for all biobanks as a resource in modern life science. Biobanks are accessed to measure biological components that can be used to monitor the status of health and disease in individual samples and population groups. The biomarker diagnostics area, predicting drug efficacy, stratification of patient groups, can benefit from the continuous qualitative developments, where Proteomics can make a difference in lung cancer and COPD. This in turn can provide key treasures to novel drugs for personalized medicine in the future.
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| 6. |
- Murillo, Jimmy Rodriguez, et al.
(författare)
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Quantitative proteomic analysis identifies proteins and pathways related to neuronal development in differentiated SH-SY5Y neuroblastoma cells
- 2017
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Ingår i: EuPA Open Proteomics. - : Elsevier BV. - 2212-9685. ; 16, s. 1-11
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Tidskriftsartikel (refereegranskat)abstract
- SH-SY5Y neuroblastoma cells are susceptible to differentiation using retinoic acid (RA) and brain-derived neurotrophic factor (BDNF), providing a model of neuronal differentiation. We compared SH-SY5Y cells proteome before and after RA/BDNF treatment using iTRAQ and phosphopeptide enrichment strategies. We identified 5587 proteins, 366 of them with differential abundance. Differentiated cells expressed proteins related to neuronal development, and, undifferentiated cells expressed proteins involved in cell proliferation. Interactive network covered focal adhesion, cytoskeleton dynamics and neurodegenerative diseases processes and regulation of mitogen-activated protein kinase-related signaling pathways; key proteins involved in those processes might be explored as markers for neuronal differentiation.
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| 7. |
- Rezeli, Melinda, et al.
(författare)
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Inflammatory Markers in Huntington’s Disease Plasma – A Robust NanoLC-MRM-MS Assay Development
- 2014
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Ingår i: EuPA Open Proteomics. - : Elsevier BV. - 2212-9685. ; 3, s. 68-75
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Tidskriftsartikel (refereegranskat)abstract
- The development of a quantitative multiplex reaction monitoring (MRM) assay is presented for the measurements of seven inflammatory markers in human plasma, using nanoLC-MS/MS analysis with stable isotope dilution strategy. We report a robust and sensitive, mass spectrometry based, quantitative assay with a relative standard deviation of <15% that accounts for the entire sample processing, while the analytical reproducibility of the assay was 3.6%. We used plasma from Huntington´s disease (HD) gene carriers and healthy controls to compare our MRM method with established antibody based methods. Interestingly, we found a good agreement between assays for the measurement of C-reactive protein (CRP).
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| 8. |
- Rezeli, M., et al.
(författare)
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Quantification of total apolipoprotein E and its specific isoforms in cerebrospinal fluid and blood in Alzheimer's disease and other neurodegenerative diseases
- 2015
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Ingår i: EuPA Open Proteomics. - : Elsevier. - 2212-9685. ; 8, s. 137-143
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Tidskriftsartikel (refereegranskat)abstract
- A targeted mass spectrometric assay was developed for identification and quantification of apoE isoforms (apoE2, E3 and E4), and it was utilized for screening of samples from AD patients (. n=. 39) and patients with other neurodegenerative disorders (. n=. 38). The assay showed good linearity with LOQ corresponds to total apoE concentration of 0.8 and 40. ng/mL in CSF and plasma/serum, respectively. We identified apoE phenotypes with 100% accuracy in clinical samples. We found strong association between genotypes of the individuals and their apoE levels in blood; ε4 allele carriers had significantly lower apoE levels in blood than non-carriers. © 2015.
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