Editorial
Publication date: Available online 25 July 2019Source: EuPA Open ProteomicsAuthor(s): Maarten Dhaenens (Source: EuPA Open Proteomics)
Source: EuPA Open Proteomics - July 27, 2019 Category: Bioinformatics Source Type: research
Proteomics—An unexpected journey into the complexity of protein structures and functions
Publication date: Available online 17 November 2018Source: EuPA Open ProteomicsAuthor(s): Friedrich Lottspeich (Source: EuPA Open Proteomics)
Source: EuPA Open Proteomics - November 23, 2018 Category: Bioinformatics Source Type: research
Proteomics – An unexpected journey into the complexity of protein structures and functions
Publication date: Available online 17 November 2018Source: EuPA Open ProteomicsAuthor(s): Friedrich Lottspeich (Source: EuPA Open Proteomics)
Source: EuPA Open Proteomics - November 18, 2018 Category: Bioinformatics Source Type: research
The author identified by his method: EuPA YPIC challenge solved
Publication date: Available online 13 October 2018Source: EuPA Open ProteomicsAuthor(s): M.I. Indeykina, D.A. Podgrudkov, A.S. KononikhinAbstractHere we present the results of our attempt on the EuPA YPIC challenge. The task was to sequence the provided synthetic peptides, build the sentence encrypted in them and determine from which book the sentence originated.The task itself, while holding no direct scientific value, offers an insight in less formal terms (for participants at least) on how the overall process of a scientific study of a “new protein” looks like. Hence, we decided to look at the challenge as if it was...
Source: EuPA Open Proteomics - October 14, 2018 Category: Bioinformatics Source Type: research
Expression, Characterization and One step Purification of Heterologous Glucose oxidase Gene from Aspergillus niger ATCC 9029 in Pichia pastoris
In this study, GOD gene was cloned into the expression vector, pPIC9 and screened by the alcohol oxidase promoter. The enzyme production increased at 28 °C. GOD activity induced by 1.0% methanol and the highest level of GOD production was the result of shaking rate at 225 rpm. The highest enzyme activity obtained at a pH value ranged from 5 to 7 at 50 °C. The enzyme was stable at a broad pH range and temperature. (Source: EuPA Open Proteomics)
Source: EuPA Open Proteomics - September 4, 2018 Category: Bioinformatics Source Type: research
Proteomic analysis reveals differential protein expression in variants of papillary thyroid carcinoma
ConclusionIn the present study, mass spectrometry based label free quantification approach was applied to investigate the protein profiles of FV-PTC, CV-PTC and benign thyroid tissues. This study pointed out that actin cytoskeleton proteins, IQGAP proteins and changes in energy metabolism play predominant roles in thyroid pathology.Graphical abstract (Source: EuPA Open Proteomics)
Source: EuPA Open Proteomics - July 10, 2018 Category: Bioinformatics Source Type: research
Proteomic analysis of a Candida albicans pga1 Null Strain
Publication date: June 2018Source: EuPA Open Proteomics, Volume 18Author(s): Andy Awad, Pamela El Khoury, Brigitte Wex, Roy A. KhalafAbstractWe previously characterized Pga1, a Candida albicans (C. albicans) cell wall protein necessary for proper virulence, adhesion, and resistance to oxidative stress. By utilizing tandem mass spectrometry coupled with bioinformatics to investigate cell wall proteome expression in a pga1 null fourteen and 36 proteins were identified in the wild type grown under filamentous and non-filamentous conditions respectively, but were not detected in the mutant, including members of the PGA GPI anc...
Source: EuPA Open Proteomics - July 10, 2018 Category: Bioinformatics Source Type: research
Proteomic analysis reveals differential protein expression in variants of papillary thyroid carcinoma
ConclusionIn the present study, mass spectrometry based label free quantification approach was applied to investigate the protein profiles of FV-PTC, CV-PTC and benign thyroid tissues. This study pointed out that actin cytoskeleton proteins, IQGAP proteins and changes in energy metabolism play predominant roles in thyroid pathology.Graphical abstract (Source: EuPA Open Proteomics)
Source: EuPA Open Proteomics - July 5, 2018 Category: Bioinformatics Source Type: research
Proteomic analysis of a Candida albicans pga1 Null Strain
Publication date: June 2018Source: EuPA Open Proteomics, Volume 18Author(s): Andy Awad, Pamela El Khoury, Brigitte Wex, Roy A. KhalafAbstractWe previously characterized Pga1, a Candida albicans (C. albicans) cell wall protein necessary for proper virulence, adhesion, and resistance to oxidative stress. By utilizing tandem mass spectrometry coupled with bioinformatics to investigate cell wall proteome expression in a pga1 null fourteen and 36 proteins were identified in the wild type grown under filamentous and non-filamentous conditions respectively, but were not detected in the mutant, including members of the PGA GPI anc...
Source: EuPA Open Proteomics - July 5, 2018 Category: Bioinformatics Source Type: research
Proteomic Analysis of a Candida albicans pga1 Null Strain
Publication date: Available online 22 February 2018 Source:EuPA Open Proteomics Author(s): Andy Awad, Pamela El Khoury, Brigitte Wex, Roy A. Khalaf We previously characterized Pga1, a Candida albicans (C. albicans) cell wall protein necessary for proper virulence, adhesion, and resistance to oxidative stress. By utilizing tandem mass spectrometry coupled with bioinformatics to investigate cell wall proteome expression in a pga1 null fourteen and 36 proteins were identified in the wild type grown under filamentous and non-filamentous conditions respectively, but were not detected in the mutant, including members of th...
Source: EuPA Open Proteomics - February 23, 2018 Category: Bioinformatics Source Type: research
Proteomic Analysis Reveals Differential Protein Expression in Variants of Papillary Thyroid Carcinoma
Conclusion In the present study, mass spectrometry based label free quantification approach was applied to investigate the protein profiles of FV-PTC, CV-PTC and benign thyroid tissues. This study pointed out that actin cytoskeleton proteins, IQGAP proteins and changes in energy metabolism play predominant roles in thyroid pathology. Graphical abstract (Source: EuPA Open Proteomics)
Source: EuPA Open Proteomics - September 13, 2017 Category: Bioinformatics Source Type: research
Quantitative proteomic analysis identifies proteins and pathways related to neuronal development in differentiated SH-SY5Y neuroblastoma cells
Publication date: Available online 23 June 2017 Source:EuPA Open Proteomics Author(s): Jimmy Rodriguez Murillo, Livia Goto-Silva, Aniel Sánchez, Fábio C.S. Nogueira, Gilberto B. Domont, Magno Junqueira 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 rel...
Source: EuPA Open Proteomics - June 23, 2017 Category: Bioinformatics Source Type: research
Novel Kazal-type proteinase inhibitors from the skin secretion of the Splendid leaf frog, Cruziohyla calcarifer
Publication date: June 2017 Source:EuPA Open Proteomics, Volume 15 Author(s): Carolina Proaño-Bolaños, Renjie Li, Mei Zhou, Lei Wang, Xinping Xi, Elicio E. Tapia, Luis A. Coloma, Tianbao Chen, Chris Shaw Peptidase inhibitors have an important role controlling a variety of biological processes. Here, we employed a peptidomic approach including molecular cloning, tandem mass spectrometry and enzymatic assays to reveal 7 Kazal-type proteinase inhibitors (CCKPs) (18 variants) in the skin secretion of the unexplored frog, Cruziohyla calcarifer. All 18 proteins shared the Kazal pattern C-X(7)-C-X(6,7)-C-X(6,7)-Y-X(3...
Source: EuPA Open Proteomics - April 6, 2017 Category: Bioinformatics Source Type: research
Novel Kazal-type Protease inhibitors from the skin secretion of the Splendid leaf frog, Cruziohyla calcarifer
Publication date: Available online 27 February 2017 Source:EuPA Open Proteomics Author(s): Carolina Proaño-Bolaños, Renjie Li, Mei Zhou, Lei Wang, Elicio E. Tapia, Luis A. Coloma, Tianbao Chen, Chris Shaw Protease inhibitors have an important role controlling a variety of biological processes. Here, we employed a peptidomic approach including molecular cloning, tandem mass spectrometry and enzymatic assays to reveal 7 Kazal-type proteinase inhibitors (CCKPs) (18 variants) in the skin secretion of the unexplored frog, Cruziohyla calcarifer. All 18 proteins shared the Kazal pattern (CX(6-7)-CX(6-7)-Y-X(2-3)-CX(2)...
Source: EuPA Open Proteomics - February 26, 2017 Category: Bioinformatics Source Type: research
Introducing the Affinity Binder Knockdown Initiative ⿿A public⿿private partnership for validation of affinity reagents
Publication date: March 2016 Source:EuPA Open Proteomics, Volume 10 Author(s): Tove Alm, Emma Lundberg, Mathias Uhlén 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 avail...
Source: EuPA Open Proteomics - February 2, 2017 Category: Bioinformatics Source Type: research
