EuPA’s tribute to Juan Pablo Albar
Publication date: Available online 29 July 2015 Source:EuPA Open Proteomics Author(s): Concha Gil, Fernando Corrales, Garry Corthals, Gyorgy Marko-varga, Peter Verhaert (Source: EuPA Open Proteomics)
Source: EuPA Open Proteomics - July 29, 2015 Category: Bioinformatics Source Type: research
Ten years of public proteomics data: how things have evolved, and where the next ten years should lead us
Publication date: Available online 29 July 2015 Source:EuPA Open Proteomics Author(s): Kenneth Verheggen, Lennart Martens Ten years ago, the first public proteomics repositories became available online. This anniversary is therefore an excellent occasion to look back on the past decade and evaluate what has changed in this time period. At the same time however, one should also dare to look forward, and therefore prepare for the next ten years of proteomics data sharing. Graphical abstract (Source: EuPA Open Proteomics)
Source: EuPA Open Proteomics - July 29, 2015 Category: Bioinformatics Source Type: research
Bottom–up protein identifications from microliter quantities of individual human tear samples. Important steps towards clinical relevance.
Publication date: December 2015 Source:EuPA Open Proteomics, Volume 9 Author(s): Peter Raus, Bharath Raghuraman Kumar, Martijn Pinkse, Peter Verhaert A relatively simple combination of Schirmer strip sampling with straightforward sensitive nanoLC quadrupole-Orbitrap tandem mass spectrometry after a minimum of sample processing steps allows for replicate proteomic analysis of single human tears, i.e., without the requirement for sample pooling. This opens the way to clinical applications of the analytical workflow, e.g., to monitor disease progression or treatment efficacy within individual patients. Proof of co...
Source: EuPA Open Proteomics - July 25, 2015 Category: Bioinformatics Source Type: research
Optimization of calmodulin-affinity chromatography for brain and organelles
Publication date: Available online 23 July 2015 Source:EuPA Open Proteomics Author(s): Katarzyna Kulej, Simone Sidoli, Giuseppe Palmisano, Alistair V.G. Edwards, Phillip J. Robinson, Martin R. Larsen Calmodulin (CaM) is a Ca2+-binding signaling protein that binds to and activates many target proteins, known as calmodulin-binding proteins (CaM-BPs). They are involved in multiple cellular processes. Despite the diversity and importance of CaM-BPs, many remain to be identified and characterized. We performed extensive optimization of a CaM-affinity capture method, using commercial CaM-chromatographic material....
Source: EuPA Open Proteomics - July 23, 2015 Category: Bioinformatics Source Type: research
Long time storage (archiving) of peptide, protein and tryptic digest samples on disposable nano-coated polymer targets for MALDI-MS
Publication date: Available online 15 July 2015 Source:EuPA Open Proteomics Author(s): Stefan Bugovsky, Wolfgang Winkler, Werner Balika, Günter Allmaier Archiving of biological specimens is important due to the importance of reanalysis of already prepared MALDI-MS samples or simultaneuous analysis of a sample series. Proteins/peptides and digests were prepared for measurement on a polymer-based metal nano-coated MALDI target and subjected to various storage conditions (-80°C to RT) in a vacuum-sealed pouch and at atmosphere for 6 months. The MS data gathered from these preparations illustrate trends in the ag...
Source: EuPA Open Proteomics - July 17, 2015 Category: Bioinformatics Source Type: research
The proteomic landscape of glioma stem-like cells
Publication date: Available online 17 July 2015 Source:EuPA Open Proteomics Author(s): Cheryl F. Lichti, Norelle C. Wildburger, Alexander S. Shavkunov, Ekaterina Mostovenko, Huiling Liu, Erik P. Sulman, Carol L. Nilsson Glioma stem-like cells (GSCs) are hypothesized to provide a repository of cells in tumors that can self-replicate and are radio- and chemo-resistant. GSC lines, representing several glioma subtypes, have been isolated and characterized at the transcript level. We sought to characterize 35 GSC lines at the protein level using label-free quantitative proteomics. Resulting relative fold chang...
Source: EuPA Open Proteomics - July 17, 2015 Category: Bioinformatics Source Type: research
A Quality Control of Proteomic Experiments Based on Multiple Isotopologous Internal Standards
Publication date: Available online 13 July 2015 Source:EuPA Open Proteomics Author(s): Adele Bourmaud , Sebastien Gallien , Bruno Domon The harmonization of proteomics experiments facilitates the exchange and comparison of results. The definition of standards and metrics ensures reliable and consistent data quality. An internal quality control procedure was developed to assess the different steps of a proteomic analysis workflow and perform a system suitability test. The method relies on a straightforward protocol using a simple mixture of exogenous proteins, and the sequential addition of two sets of isotopically l...
Source: EuPA Open Proteomics - July 13, 2015 Category: Bioinformatics Source Type: research
Comparison of serum fractionation methods by data independent label-free proteomics
Publication date: Available online 9 July 2015 Source:EuPA Open Proteomics Author(s): D. Baiwir , G. Mazzucchelli , N. Smargiasso , F. Quesada-Calvo , E.De Pauw , M. Malaise , E. Louis , M.-A. Meuwis Off-line sample prefractionations applied prior to biomarker discovery proteomics are options to enable more protein identifications and detect low-abundance proteins. This work compared five commercial methods efficiency to raw serum analysis using label-free proteomics. The variability of the protein quantities determined for each process was similar to the unprefractionated serum. A 49% increase in protein ident...
Source: EuPA Open Proteomics - July 10, 2015 Category: Bioinformatics Source Type: research
Workflow for large-scale analysis of melanoma tissue samples
Publication date: Available online 10 July 2015 Source:EuPA Open Proteomics Author(s): Maria E. Yakovleva , Charlotte Welinder , Yutaka Sugihara , Krzysztof Pawłowski , Melinda Rezeli , Elisabet Wieslander , Johan Malm , György Marko-Varga The aim of the present study was to create an optimal workflow for analysing a large cohort of malignant melanoma tissue samples. Samples were lysed with urea and enzymatically digested with trypsin or trypsin/Lys C. Buffer exchange or dilution was used to reduce urea concentration prior to digestion. The tissue digests were analysed directly or following strong cation exch...
Source: EuPA Open Proteomics - July 10, 2015 Category: Bioinformatics Source Type: research
Quantitative Proteomics and Transcriptomics Reveals Metabolic Differences in Attracting and Non-Attracting Human-in-Mouse Glioma Stem Cell Xenografts and Stromal Cells
Publication date: Available online 7 July 2015 Source:EuPA Open Proteomics Author(s): Norelle C. Wildburger , Cheryl F. Lichti , Richard D. LeDuc , Mary Schmidt , Roger A. Kroes , Joseph R. Moskal , Carol L. Nilsson Bone marrow-derived human mesenchymal stem cells (BM-hMSCs) show promise as cell-based delivery vehicles for anti-glioma therapeutics, due to innate tropism for gliomas. However, in clinically relevant human-in-mouse glioma stem cell xenograft models, BM-hMSCs tropism is variable. We compared the proteomic profile of cancer and stromal cells in GSCXs that attract BM-hMSCs (“attractors”) with thos...
Source: EuPA Open Proteomics - July 7, 2015 Category: Bioinformatics Source Type: research
De novo sequencing of two novel peptides homologous to calcitonin-like peptides, from skin secretion of the Chinese Frog, Odorrana schmackeri
Publication date: Available online 6 July 2015 Source:EuPA Open Proteomics Author(s): Geisa P.C. Evaristo , Martijn W.H. Pinkse , Tianbao Chen , Lei Wang , Shabaz Mohammed , Albert J.R. Heck , Isabella Mathes , Friedrich Lottspeich , Chris Shaw , Juan Pablo Albar , Peter D.E.M. Verhaert An MS/MS based analytical strategy was followed to solve the complete sequence of two new peptides from frog (O. schmackeri) skin secretion. This involved reduction and alkylation with two different alkylating agents followed by high resolution tandem mass spectrometry. De novo sequencing was achieved by complementary CID and...
Source: EuPA Open Proteomics - July 6, 2015 Category: Bioinformatics Source Type: research
Transforming Growth Factor-β, MAPK and Wnt Signaling Interactions in Colorectal Cancer
Publication date: Available online 2 July 2015 Source:EuPA Open Proteomics Author(s): Harish R Cheruku , Abidali Mohamedali , David I Cantor , Sock Hwee Tan , Edouard C Nice , Mark S Baker In non-cancerous cells, transforming growth factor-β (TGFβ) regulates cellular responses primarily through Smad signaling. However, during cancer progression (including colorectal) TGFβ promotes tumoral growth via Smad-independent mechanisms and is involved in crosstalk with various pathways like the mitogen-activated protein kinases (MAPK) and Wnt. Crosstalk between these pathways following activation by TGFβ and subsequen...
Source: EuPA Open Proteomics - July 2, 2015 Category: Bioinformatics Source Type: research
The EuPA Company Club: Emphasis on the synergy with EuPA's Initiatives beyond education – Towards further integration with EuPA's goals and objectives
Publication date: Available online 2 July 2015 Source:EuPA Open Proteomics Author(s): Andrea Urbani , Andrey Lisitsa , Peter Verhaert (Source: EuPA Open Proteomics)
Source: EuPA Open Proteomics - July 2, 2015 Category: Bioinformatics Source Type: research
Bottom-up protein identifications from microliter quantities of individual human tear samples. Important steps towards clinical relevance.
Publication date: Available online 29 June 2015 Source:EuPA Open Proteomics Author(s): Peter Raus , Bharath Kumar Raguraman , Martijn Pinkse , Peter Verhaert A relatively simple combination of Schirmer strip sampling with straightforward sensitive nanoLC quadrupole-orbitrap tandem mass spectrometry after a minimum of sample processing steps allows for replicate proteomic analysis of single human tears, i.e. without the requirement for sample pooling. This opens the way to clinical applications of the analytical workflow, e.g. to monitor disease progression or treatment efficacy within individual patients. Proof of ...
Source: EuPA Open Proteomics - June 29, 2015 Category: Bioinformatics Source Type: research
A Breast Cell Atlas: Organelle analysis of the MDA-MB-231 cell line by density-gradient fractionation using isotopic marking and label-free analysis
We present an analysis of the distribution of proteins amongst organelles in the human breast cell line, MDA-MB-231 using two approaches: an isotopic labelling and a label-free approach. Graphical abstract (Source: EuPA Open Proteomics)
Source: EuPA Open Proteomics - June 26, 2015 Category: Bioinformatics Source Type: research
