Multidimensional LC–MS/MS analysis of liver proteins in rat, mouse and human microsomal and S9 fractions
Publication date: Available online 11 February 2015 Source:EuPA Open Proteomics Author(s): Makan Golizeh , Christina Schneider , Leanne Ohlund , Lekha Sleno Liver plays a key role in metabolism and detoxification, therefore analysis of its proteome is relevant for toxicology and drug discovery studies. To optimize for high proteome coverage, protein and peptide-level ion exchange fractionation were assessed using rat liver microsomes and S9 fractions. 2D-(SCX-RP)-LC–MS/MS analysis with peptide fractionation was subsequently employed for rat, mouse and human samples, yielding between 1400 and 1939 identified prote...
Source: EuPA Open Proteomics - February 23, 2015 Category: Bioinformatics Source Type: research
Distribution analysis of the putative cancer marker S100A4 across invasive squamous cell carcinoma penile tissue
Publication date: Available online 16 February 2015 Source:EuPA Open Proteomics Author(s): Brian Flatley , Chris Quaye , Elizabeth Johnson , Alex Freeman , Asif Muneer , Suks Minhas , Jennifer C. Paterson , Fawaz Musa , Peter Malone , Rainer Cramer MS-based proteomic methods were utilised for the first time in the discovery of novel penile cancer biomarkers. MALDI MS imaging was used to obtain the in situ biomolecular MS profile of squamous cell carcinoma of the penis which was then compared to benign epithelial MS profiles. Spectra from cancerous and benign tissue areas were examined to identify MS peaks tha...
Source: EuPA Open Proteomics - February 23, 2015 Category: Bioinformatics Source Type: research
Evaluation of phosphopeptide enrichment strategies for quantitative TMT analysis of complex network dynamics in cancer-associated cell signalling
Publication date: March 2015 Source:EuPA Open Proteomics, Volume 6 Author(s): Benedetta Lombardi , Nigel Rendell , Mina Edwards , Matilda Katan , Jasminka Godovac Zimmermann Defining alterations in signalling pathways in normal and malignant cells is becoming a major field in proteomics. A number of different approaches have been established to isolate, identify and quantify phosphorylated proteins and peptides. In the current report, a comparison between SCX prefractionation versus an antibody based approach, both coupled to TiO2 enrichment and applied to TMT labelled cellular lysates, is described. The antibody ...
Source: EuPA Open Proteomics - February 23, 2015 Category: Bioinformatics Source Type: research
In-depth characterisation of the lamb meat proteome from longissimus lumborum
In this study, we investigated the proteome of the 48h post-mortem lamb longissimus lumborum through separation of the samples into sarcoplasmic, myofibrillar and insoluble fractions, followed by an in-depth shotgun proteomic evaluation and bioinformatic analysis. As a result, 388 ovine-specific proteins were identified and characterised. The 207 proteins found in the sarcoplasmic fraction were dominated by glycolytic enzymes and mitochondrial proteins. This fraction also contained several sarcomeric proteins, e.g., myosin light chains and titin. Some of them might be the degradation products from the post-mortem proteolys...
Source: EuPA Open Proteomics - January 20, 2015 Category: Bioinformatics Source Type: research
The serum immunoglobulin G glycosylation signature of gastric cancer
Publication date: Available online 27 November 2014 Source:EuPA Open Proteomics Author(s): L. Renee Ruhaak , Donald A. Barkauskas , Javier Torres , Cara L. Cooke , Lauren D. Wu , Carol Stroble , Sureyya Ozcan , Cynthia C. Williams , Margarita Camorlinga , David M. Rocke , Carlito B. Lebrilla , Jay V. Solnick Biomarkers may facilitate detection of gastric cancer at an earlier stage and reduce mortality. Here we sought to determine if the glycosylation profile of serum immunoglobulin G (IgG) could distinguish patients with non-atrophic gastritis (NAG), duodenal ulcer (DU) and gastric cancer (GC). Serum IgG wa...
Source: EuPA Open Proteomics - December 18, 2014 Category: Bioinformatics Source Type: research
Using synthetic peptides to benchmark peptide identification software and search parameters for MS/MS data analysis
We present and discuss strategies to optimize parameter settings in order to significantly increase the number of correctly assigned fragment ion spectra and to make the analysis method robust. Graphical abstract (Source: EuPA Open Proteomics)
Source: EuPA Open Proteomics - December 18, 2014 Category: Bioinformatics Source Type: research
MS approaches to select peptides with post-translational modifications from amphibian defense secretions prior to full sequence elucidation
Publication date: December 2014 Source:EuPA Open Proteomics, Volume 5 Author(s): Martijn Pinkse , Geisa Evaristo , Mervin Pieterse , Yuanjie Yu , Peter Verhaert Peptide families are characterized by structural motifs, which often comprise specific post-translational modifications (PTMs) required for biological activity. In conventional bioactivity-based peptidomics studies natural peptide mixtures are chromatographically separated and the bioactive fractions purified to homogeneity, prior to structural characterization. In this paper we illustrate the reverse methodology, in which the primary structures of peptide...
Source: EuPA Open Proteomics - December 18, 2014 Category: Bioinformatics Source Type: research
Application of proteomics technologies to drug development – Current status and challenges
Publication date: December 2014 Source:EuPA Open Proteomics, Volume 5 Author(s): Fabian Milz (Source: EuPA Open Proteomics)
Source: EuPA Open Proteomics - December 18, 2014 Category: Bioinformatics Source Type: research
Comparative two dimensional fluorescent electrophoresis (CoFGE)
Publication date: December 2014 Source:EuPA Open Proteomics, Volume 5 Author(s): Marina Hanneken , Doreen Ackermann , Simone König (Source: EuPA Open Proteomics)
Source: EuPA Open Proteomics - December 18, 2014 Category: Bioinformatics Source Type: research
Measuring proteins’ activity, quantity and function by multiplexed Bead-Arrays – Applications in biomedical research
Publication date: December 2014 Source:EuPA Open Proteomics, Volume 5 Author(s): Oliver Pötz (Source: EuPA Open Proteomics)
Source: EuPA Open Proteomics - December 18, 2014 Category: Bioinformatics Source Type: research
Proteomics beyond boundaries with a new UHR-QTOF system
Publication date: December 2014 Source:EuPA Open Proteomics, Volume 5 Author(s): Carsten Baessmann (Source: EuPA Open Proteomics)
Source: EuPA Open Proteomics - December 18, 2014 Category: Bioinformatics Source Type: research
Development, implementation and application of performance/assessment kits for quantitative proteomic studies
Publication date: December 2014 Source:EuPA Open Proteomics, Volume 5 Author(s): Andrew Percy (Source: EuPA Open Proteomics)
Source: EuPA Open Proteomics - December 18, 2014 Category: Bioinformatics Source Type: research
New TripleTOF(r) 6600 and SWATH( 2.0 for next generation proteomics and quantitative biology
Publication date: December 2014 Source:EuPA Open Proteomics, Volume 5 Author(s): J"rg Dojahn (Source: EuPA Open Proteomics)
Source: EuPA Open Proteomics - December 18, 2014 Category: Bioinformatics Source Type: research
Detection and quantitation of twenty-seven cytokines, chemokines and growth factors pre- and post-high abundance protein depletion in human plasma
In this study, we have examined whether or not depletion of the HAPs enhances detection of the CCGFs by immuno-assays. Top 14 HAPs were depleted from 10 healthy volunteers’ plasma using MARS-14 immuno-depletion column and a total of 27 CCGFs were analyzed by bead-based multiplexed immuno-assay. All 27 CCGFs were detected in neat plasma (NP), 25 were detected in flow through fraction (FT) and 21 were detected in bound protein (BP) fraction. Concentrations of 22 CCGFs were significantly higher in NP compared to FT and BP. Only one CCGF had higher concentration in FT compared to NP. The remaining 2 CCGFs were not different ...
Source: EuPA Open Proteomics - October 13, 2014 Category: Bioinformatics Source Type: research
Automation of C-terminal sequence analysis of 2D-PAGE separated proteins
We present a fully automated protocol established on a robotic liquid-handling station. Graphical abstract (Source: EuPA Open Proteomics)
Source: EuPA Open Proteomics - October 13, 2014 Category: Bioinformatics Source Type: research
