Analysis of the Surface, Secreted, and Intracellular Proteome of Propionibacterium acnes
Publication date: Available online 16 June 2015 Source:EuPA Open Proteomics Author(s): Yang Yu , Jackson Champer , Jenny Kim Propionibacterium acnes, plays an important role in acne vulgaris and other diseases. However, understanding of the exact mechanisms of P. acnes pathogenesis is limited. Few studies have investigated its proteome, which is essential for vaccine development. Here, we comprehensively investigate the proteome of P. acnes strain ATCC 6919, including secreted, cell wall, membrane, and cytosolic fractions in three types of growth media. A total of 531 proteins were quantified using an Orbitrap mass...
Source: EuPA Open Proteomics - June 17, 2015 Category: Bioinformatics Source Type: research
Inter-laboratory Evaluation of Instrument Platforms and Experimental Workflows for Quantitative Accuracy and Reproducibility Assessment
Publication date: Available online 11 June 2015 Source:EuPA Open Proteomics Author(s): Andrew J. Percy , Jessica Tamura-Wells , Juan Pablo Albar , Kerman Aloria , Gabriel D.T. Araujo , Jesus M. Arizmendi , Francisco J. Blanco , Francesco Canals , Jin-Young Cho , Núria Colomé-Calls , Fernando J. Corrales , Gilberto Domont , Guadalupe Espadas , Patricia Fernandez-Puente , Concha Gil , Maria Luisa Hernáez , Jin Young Kim , Arthur Kopylov , Miguel Marcilla , Mathew J. McKay , Mark P. Molloy , Leanne B. Ohlund , Young-Ki Paik , Alberto Paradela , Mark Raftery , Eduard Sabidó , Lekha Sleno , Da...
Source: EuPA Open Proteomics - June 12, 2015 Category: Bioinformatics Source Type: research
Reducing Protein Oxidation in Low-Flow Electrospray Enables Deeper Investigation of Proteoforms by Top Down Proteomics
Publication date: Available online 5 June 2015 Source:EuPA Open Proteomics Author(s): Kyunggon Kim , Philip D. Compton , Timothy K. Toby , Paul M. Thomas , John T. Wilkins , R.Kannan Mutharasan , Neil L. Kelleher Enabling the implementation of top down proteomic techniques within clinical workflows requires a dramatic increase in sensitivity. It has been previously demonstrated that electrospray ionization (ESI) becomes more efficient with decreasing volumetric flow rates at the emitter. Therefore, narrow inner diameter (I.D.) columns used in front-end chromatographic separations yield increased sensitivity. How...
Source: EuPA Open Proteomics - June 6, 2015 Category: Bioinformatics Source Type: research
Seeing beyond the tip of the iceberg: a deep analysis of the venome of the Brazilian Rattlesnake, Crotalus durissus terrificus.
Publication date: Available online 6 June 2015 Source:EuPA Open Proteomics Author(s): Rafael D. Melani , Gabriel D.T. Araujo , Paulo C. Carvalho , Livia Goto , Fábio C.S. Nogueira , Magno Junqueira , Gilberto B. Domont The complete characterization of the snake venom protein components is a requirement for a systems-wide understanding of their biological context. In this work, we provide a deep proteomic characterization of Crotalus durissus terrificus venom using different bottom-up approaches. We identified more than five times more protein families than the sum of all identifications previously reported. For...
Source: EuPA Open Proteomics - June 6, 2015 Category: Bioinformatics Source Type: research
New TripleTOF® 6600 and SWATHTM(2.0 for next generation proteomics and quantitative biology
Publication date: December 2014 Source:EuPA Open Proteomics, Volume 5 Author(s): Jörg Dojahn (Source: EuPA Open Proteomics)
Source: EuPA Open Proteomics - May 31, 2015 Category: Bioinformatics Source Type: research
Deciphering metabolic networks by blue native polyacrylamide gel electrophoresis: A functional proteomic exploration
Publication date: Available online 26 May 2015 Source:EuPA Open Proteomics Author(s): Christopher Auger , Nishma D. Appanna , Azhar Alhasawi , Vasu D. Appanna Metabolism is the consortium of reactions within a cell which directs a variety of processes including energy synthesis, signalling and the behaviour of a biological system. Metabolic networks, and more specifically the activity of enzymes within them, provide an accurate status of how cellular information is being executed. The performance of these networks and their ability to siphon metabolites in a number of directions may be the difference between a heal...
Source: EuPA Open Proteomics - May 27, 2015 Category: Bioinformatics Source Type: research
Pathway-centric analysis of the DNA damage response to chemotherapeutic agents in two breast cell lines
We present data from both a shotgun and a targeted, pathway-centric approach to highlight the different DNA repair pathway modulation in the cell lines and the correlation with viability and DNA damage assays. This type of focussed profiling may be of utility in rapidly defining non-responders undergoing systemic neoadjuvant therapy. Graphical abstract (Source: EuPA Open Proteomics)
Source: EuPA Open Proteomics - May 27, 2015 Category: Bioinformatics Source Type: research
Quantitative analysis of the erythrocyte membrane proteins in polycythemia vera patients treated with hydroxycarbamide
Publication date: Available online 5 May 2015 Source:EuPA Open Proteomics Author(s): Darshana Kottahachchi , Lallindra Gooneratne , Anil Jayasekera , Dorota Muth-Pawlak , Robert Moulder , Susumu Y. Imanishi , Ari Ariyaratne , Anne Rokka , Garry L. Corthals More than 90% of polycythemia vera (PV) patients have a mutation in the protein JAK2, which is closely associated with the erythrocyte membrane. With the comparison of 1-D gels of erythrocyte membranes obtained from PV patients treated with hydroxycarbamide and those of untreated controls we observed significant differences in the region of 40–55kDa. On th...
Source: EuPA Open Proteomics - May 16, 2015 Category: Bioinformatics Source Type: research
Proteopathogen2, a database and web tool to store and display proteomics identification results in the mzIdentML standard
Publication date: Available online 6 May 2015 Source:EuPA Open Proteomics Author(s): Vital Vialas , Concha Gil The Proteopathogen database was the first proteomics online resource focused on experiments related to Candida albicans and other fungal pathogens and their interaction with the host. Since then, the HUPO-PSI standards were implemented and settled, and the first large scale C. albicans proteomics resource appeared as a C. albicans PeptideAltas. This has enabled the remodeling of Proteopathogen to take advantage and benefit from the use of the HUPO-PSI adopted format for peptide and protein identification mzI...
Source: EuPA Open Proteomics - May 16, 2015 Category: Bioinformatics Source Type: research
Aspirin-mediated acetylation of haemoglobin increases in presence of high glucose concentration and decreases protein glycation
Publication date: Available online 8 May 2015 Source:EuPA Open Proteomics Author(s): Francesco Finamore , Feliciano Priego-Capote , Severine Nolli , Pierre Fontana , Jean-Charles Sanchez Glycation represents the first stage in the development of diabetic complications. Aspirin was shown to prevent sugars reacting with proteins, but the exact mechanism of this interaction was not well defined. We performed a quantitative analysis to calculate the levels of acetylation and glycation of haemoglobin, among others red blood cell (RBC) proteins, using a label free approach. After glucose incubation, increases in the ace...
Source: EuPA Open Proteomics - May 16, 2015 Category: Bioinformatics Source Type: research
Low molecular weight peptides derived from sarcoplasmic proteins produced by an autochthonous starter culture in a beaker sausage model
This study focuses on meat protein degradation by different starter cultures. Sausage models inoculated with Lactobacillus curvatus CRL705 and Staphylococcus vitulinus GV318 alone and as a mixture were incubated 10 days at 22°C. Low molecular weight peptides (<3kDa) derived from sarcoplasmic proteins were analyzed by a peptidomic approach. A diverse number of protein fragments were identified. The greatest peptides diversity was obtained when the mixed starter culture was present. Peptides mainly arose from myoglobin, creatine-kinase, glyceraldehyde-3-phosphate-dehydrogenase and fructose-biphosphate-aldolase (ALDOA...
Source: EuPA Open Proteomics - May 16, 2015 Category: Bioinformatics Source Type: research
pI-Control in Comparative Fluorescence Gel Electrophoresis (CoFGE) Using Amphoteric Azo Dyes
Publication date: Available online 9 April 2015 Source:EuPA Open Proteomics Author(s): Marina Hanneken , Karel Šlais , Simone König Gel-to-gel variation is a major problem in two-dimensional (2D) gel electrophoresis. Vertical and horizontal Comparative Fluorescence Gel Electrophoresis (v/hCoFGE) were recently introduced to improve the reproducibility of protein spot assignment. There, in a combination of 1D- and 2D-PAGE, protein analytes were overlaid with a reference grid which allowed correcting for variation in the y-direction. However, control of the first dimension, pI (x-direction), was missing so far. Here,...
Source: EuPA Open Proteomics - April 9, 2015 Category: Bioinformatics Source Type: research
Investigation of heart proteome of different consomic mouse strains. Testing the effect of polymorphisms on the proteome-wide trans-variation of proteins
Publication date: Available online 27 March 2015 Source:EuPA Open Proteomics Author(s): Stefanie Forler , Oliver Klein , Sebastian Köhler , Peter N. Robinson , Henning Witt , Marc Sultan , Murat Eravci , Vera Regitz-Zagrosek , Hans Lehrach , Joachim Klose We investigated to which extent polymorphisms of an individual affect the proteomic network. Consomic mouse strains (CS) were used to study the trans-effect of the cis-variant (polymorphic) proteins of the strain PWD/Ph on the proteins of the host strain C57BL/6J. The cardiac proteome of ten CSs was analyzed by 2-DE and MS. Cis-variant PWD proteins altered ...
Source: EuPA Open Proteomics - March 27, 2015 Category: Bioinformatics Source Type: research
Direct infusion-SIM as fast and robust method for absolute protein quantification in complex samples
Publication date: Available online 21 March 2015 Source:EuPA Open Proteomics Author(s): Christina Looße , Sara Galozzi , Linde Debor , Mattijs K. Julsing , Bruno Bühler , Andreas Schmid , Katalin Barkovits , Thorsten Müller , Katrin Marcus Relative and absolute quantification of proteins in biological and clinical samples are common approaches in proteomics. Until now, targeted protein quantification is mainly performed using a combination of HPLC-based peptide separation and selected reaction monitoring on triple quadrupole mass spectrometers. Here, we show for the first time the potential of absolute quan...
Source: EuPA Open Proteomics - March 21, 2015 Category: Bioinformatics Source Type: research
Detecting Significant Changes in Protein Abundance
Publication date: Available online 25 February 2015 Source:EuPA Open Proteomics Author(s): Kai Kammers , Robert N Cole , Calvin Tiengwe , Ingo Ruczinski We review and demonstrate how an empirical Bayes method, shrinking a protein's sample variance towards a pooled estimate, leads to far more powerful and stable inference to detect significant changes in protein abundance compared to ordinary t-tests. Using examples from isobaric mass labeled proteomic experiments we show how to analyze data from multiple experiments simultaneously, and discuss the effects of missing data on the inference. We also present easy to us...
Source: EuPA Open Proteomics - February 26, 2015 Category: Bioinformatics Source Type: research
