A5028703668- Advanced Proteomics Techniques and Applications
- Mass Spectrometry Techniques and Applications
- Metabolomics and Mass Spectrometry Studies
- Genomics and Phylogenetic Studies
- Bioinformatics and Genomic Networks
- Advanced Biosensing Techniques and Applications
- Biomedical Text Mining and Ontologies
- Genetics, Bioinformatics, and Biomedical Research
- Scientific Computing and Data Management
- Lung Cancer Research Studies
- Identification and Quantification in Food
- Microbial Metabolic Engineering and Bioproduction
- Machine Learning in Bioinformatics
- Gene expression and cancer classification
- Computational Drug Discovery Methods
- Statistical Methods in Clinical Trials
- Multiple Sclerosis Research Studies
- Glycosylation and Glycoproteins Research
- Clusterin in disease pathology
- Pancreatic function and diabetes
- RNA and protein synthesis mechanisms
- vaccines and immunoinformatics approaches
- Multiple Myeloma Research and Treatments
- Semantic Web and Ontologies
- Forensic and Genetic Research
University of Bergen
2015-2024
Haukeland University Hospital
2013-2016
Primary Health Care
2013
Ghent University
2013
Uni Research (Norway)
2011
University of Oslo
2010
Norwegian University of Life Sciences
2010
Oslo University Hospital
2010
Massachusetts Institute of Technology
2009
Wellcome Trust
2009
BioContainers (biocontainers.pro) is an open-source and community-driven framework which provides platform independent executable environments for bioinformatics software. allows labs of all sizes to easily install software, maintain multiple versions the same software combine tools into powerful analysis pipelines. based on popular projects Docker rkt frameworks, that allow be installed executed under isolated controlled environment. Also, it infrastructure basic guidelines create, manage...
Abstract The identification of proteins by mass spectrometry is a standard technique in the field proteomics, relying on search engines to perform identifications acquired spectra. Here, we present user‐friendly, lightweight and open‐source graphical user interface called SearchGUI ( http://searchgui.googlecode.com ), for configuring running freely available OMSSA (open algorithm) X!Tandem simultaneously. Freely under permissible Apache2 license, supported Windows, Linux OSX.
The Proteomics Identifications database (PRIDE, http://www.ebi.ac.uk/pride) at the European Bioinformatics Institute has become one of main repositories mass spectrometry-derived proteomics data. For last 2 years, PRIDE data holdings have grown substantially, comprising 60 different species, more than 2.5 million protein identifications, 11.5 peptides and over 50 spectra by September 2009. We here describe several new improved features in PRIDE, including revised submission process, which...
The field of computational proteomics is approaching the big data age, driven both by a continuous growth in number samples analyzed per experiment as well growing amount obtained each analytical run. In order to process these large amounts data, it increasingly necessary use elastic compute resources such Linux-based cluster environments and cloud infrastructures. Unfortunately, vast majority cross-platform tools are not able operate directly on proprietary formats generated diverse mass...
Mass-spectrometry-based proteomics has become the standard approach for identifying and quantifying proteins. A vital step consists of analyzing experimentally generated mass spectra to identify underlying peptide sequences later mapping originating We here present latest developments in SearchGUI, a common open-source interface most frequently used freely available search de novo engines that evolved into central component numerous bioinformatics workflows.
In this study, the human cerebrospinal fluid (CSF) proteome was mapped using three different strategies prior to Orbitrap LC-MS/MS analysis: SDS-PAGE and mixed mode reversed phase-anion exchange for mapping global CSF proteome, hydrazide-based glycopeptide capture glycopeptides. A maximal protein set of 3081 proteins (28,811 peptide sequences) identified, which 520 were identified as glycoproteins from enrichment strategy, including 1121 glycopeptides their glycosylation sites. To our...
The Ontology Lookup Service (OLS; http://www.ebi.ac.uk/ols) has been providing several means to query, browse and navigate biomedical ontologies controlled vocabularies since it first went into production 4 years ago, usage statistics indicate that become a heavily accessed service with millions of hits monthly. volume data available for querying increased 7-fold its inception. OLS functionality integrated high-usage databases entry tools. Improvements in the model loaders, as well interface...
The original PRIDE Converter tool greatly simplified the process of submitting mass spectrometry (MS)-based proteomics data to database. However, after much user feedback, it was noted that had some limitations and could not handle several requirements were now becoming commonplace. This prompted us design implement a whole new suite tools would build on successes allow users generate submission-ready, well-annotated XML files. 2 allows convert search result files into (the format needed for...
Abstract Background The growing interest in the field of proteomics has increased demand for software tools and applications that process analyze resulting data. And even though purpose these can vary significantly, they usually share a basic set features, including handling protein peptide sequences, visualization (and interaction with) spectra chromatograms, parsing results from various search engines. Developers typically spend considerable time effort implementing support structures,...
Isobaric peptide labeling plays an important role in relative quantitative comparisons of proteomes. techniques utilize MS/MS spectra for quantification, which can be either based on the intensities reporter ions low mass region (iTRAQ and TMT) or quantification signatures throughout spectrum due to isobaric termini (IPTL). Due increased information found fragment generated by recently developed IPTL approach, new software was required extract information. IsobariQ specifically this purpose;...
De novo sequencing is a popular technique in proteomics for identifying peptides from tandem mass spectra without having to rely on protein sequence database. Despite the strong potential of de algorithms, their adoption threshold remains quite high. We here present user-friendly and lightweight graphical user interface called DeNovoGUI running parallelized versions freely available software PepNovo+, greatly simplifying use proteomics. Our platform-independent under permissible Apache2 open...
The first stable version of the Proteomics Standards Initiative mzIdentML open data standard (version 1.1) was published in 2012-capturing outputs peptide and protein identification software. In intervening years, has become well-supported both commercial software, as well a submission download format for public repositories. Here we report new release 1.2) that is required to keep pace with emerging practice proteome informatics. New features have been added support: (1) scores associated...
Randomization is used in experimental design to reduce the prevalence of unanticipated confounders. Complete randomization can however create imbalanced designs, for example, grouping all samples same condition batch. Block an approach that prevent severe imbalances sample allocation with respect both known and unknown This feature provides reader introduction blocking randomization, insights into how effectively organize during design, special considerations proteomics.
MS-based proteomics produces large amounts of mass spectra that require processing, identification and possibly quantification before interpretation can be undertaken. High-throughput studies automation these various steps, management the data in association with results obtained. We here present ms_lims (http://genesis.UGent.be/ms_lims), a freely available, open-source system based on central database to automate processing MS-driven analyses.
Identification of proteins by MS plays an important role in proteomics. A crucial step concerns the identification peptides from MS/MS spectra. The X!Tandem Project (http://www.thegpm.org/tandem) supplies open-source search engine for this purpose. In study, we present Java library called XTandem Parser that parses XML result files into easily accessible and fully functional object model (http://xtandem-parser.googlecode.com). addition, a graphical user interface is provided functions as...
The rapidly growing number of biomedical studies supported by mass spectrometry based quantitative proteomics data has made it increasingly difficult to obtain an overview the current status research field. A better way organizing information from these and making available community is therefore called for. In presented work, we have investigated scientific publications describing analysis cerebrospinal fluid proteome in relation multiple sclerosis, Parkinson's disease Alzheimer's disease....
The Thermo Proteome Discoverer program integrates both peptide identification and quantification into a single workflow for peptide-centric proteomics. Furthermore, its close integration with mass spectrometers has made it increasingly popular in the field. Here, we present Java library to parse msf files that constitute output of Discoverer. parser is also implemented as graphical user interface allowing convenient access information found files, Rover, analyze validate quantitative...
Multiple sclerosis (MS) is a chronic inflammatory disease of the CNS with unknown cause. Proteins different abundance in cerebrospinal fluid (CSF) from relapsing-remitting MS (RRMS) patients and neurological controls could give novel insight to pathogenesis be used improve diagnosis, predict prognosis course, guide therapy decisions. We combined iTRAQ labeling Orbitrap mass spectrometry discover proteins CSF between six RRMS 18 controls. From 777 quantified seven were selected as biomarker...