Blar i Faculty of Medicine på forfatter "Barsnes, Harald"

Viser treff 21-30 av 30

    • PathwayMatcher: proteoform-centric network construction enables fine-granularity multi-omics pathway mapping 

      Hernández Sánchez, Luis Francisco; Burger, Bram; Horro Marcos, Carlos; Fabregat, Antonio; Johansson, Stefan; Njølstad, Pål Rasmus; Barsnes, Harald; Hermjakob, Henning; Vaudel, Marc (Peer reviewed; Journal article, 2019-07-30)
      Background Mapping biomedical data to functional knowledge is an essential task in bioinformatics and can be achieved by querying identifiers (e.g., gene sets) in pathway knowledge bases. However, the isoform and ...

    • PeptideShaker Online: A User-Friendly Web-Based Framework for the Identification of Mass Spectrometry-Based Proteomics Data 

      Farag, Yehia Mokhtar; Horro Marcos, Carlos; Vaudel, Marc; Barsnes, Harald (Journal article; Peer reviewed, 2021)
      Mass spectrometry-based proteomics is a high-throughput technology generating ever-larger amounts of data per project. However, storing, processing, and interpreting these data can be a challenge. A key element in simplifying ...

    • Practical considerations for omics experiments in biomedical sciences 

      Vaudel, Marc; Barsnes, Harald; Bjerkvig, Rolf; Bikfalvi, Andreas; Selheim, Frode; Berven, Frode; Daubon, Thomas (Peer reviewed; Journal article, 2016)
      Modern analytical techniques provide an unprecedented insight to biomedical samples, allowing an in depth characterization of cells or body fluids, to the level of genes, transcripts, peptides, proteins, metabolites, or ...

    • The PRoteomics IDEntification (PRIDE) Converter 2 Framework: An Improved Suite of Tools to Facilitate Data Submission to the PRIDE Database and the ProteomeXchange Consortium 

      Côté, Richard G.; Griss, Johannes; Dianes, José A.; Wang, Rui; Wright, James C.; van den Toorn, Henk W.P.; van Breukelen, Bas; Heck, Albert J. R.; Hulstaert, Niels; Martens, Lennart; Reisinger, Florian; Csordas, Attila; Ovelleiro, David; Perez-Rivevol, Yasset; Barsnes, Harald; Hermjakob, Henning; Vizcaíno, Juan Antonio (Peer reviewed; Journal article, 2012-12)
      The original PRIDE Converter tool greatly simplified the process of submitting mass spectrometry (MS)-based proteomics data to the PRIDE database. However, after much user feedback, it was noted that the tool had some ...

    • Proteomics Standards Initiative Extended FASTA Format 

      Binz, Pierre-Alain; Shofstahl, Jim; Vizcaino, Juan Antonio; Barsnes, Harald; Chalkley, Robert J.; Menschaert, Gerben; Alpi, Emanuele; Clauser, Karl; Eng, Jimmy K.; Lane, Lydie; Seymour, Sean L.; Hernández Sánchez, Luis Francisco; Mayer, Gerhard; Eisenacher, Martin; Perez-Riverol, Yasset; Kapp, Eugene A.; Mendoza, Luis; Baker, Peter R.; Collins, Andrew; Van Den Bossche, Tim; Deutsch, Eric W. (Peer reviewed; Journal article, 2019)
      Mass-spectrometry-based proteomics enables the high-throughput identification and quantification of proteins, including sequence variants and post-translational modifications (PTMs) in biological samples. However, most ...

    • SearchGUI: a highly adaptable common interface for proteomics search and de novo engines 

      Barsnes, Harald; Vaudel, Marc (Peer reviewed; Journal article, 2018)
      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 the underlying peptide ...

    • Shedding light on black boxes in protein identification 

      Vaudel, Marc; Venne, A. Saskia; Berven, Frode; Zahedi, René P.; Martens, Lennart; Barsnes, Harald (Peer reviewed; Journal article, 2014-05)
      Performing a well thought-out proteomics data analysis can be a daunting task, especially for newcomers to the field. Even researchers experienced in the proteomics field can find it challenging to follow existing publication ...

    • thermo-msf-parser: An Open Source Java Library to Parse and Visualize Thermo Proteome Discoverer msf Files 

      Colaert, Niklaas; Barsnes, Harald; Vaudel, Marc; Helsens, Kenny; Timmerman, Evy; Sickmann, Albert; Gevaert, Kris; Martens, Lennart (Peer reviewed; Journal article, 2011)
      The Thermo Proteome Discoverer program integrates both peptide identification and quantification into a single workflow for peptide-centric proteomics. Furthermore, its close integration with Thermo mass spectrometers has ...

    • Use of stable isotope dimethyl labeling coupled to selected reaction monitoring to enhance throughput by multiplexing relative quantitation of targeted proteins 

      Aye, Thin Thin; Low, Teck Yew; Bjørlykke, Yngvild; Barsnes, Harald; Heck, Albert J.R.; Berven, Frode (Peer reviewed; Journal article, 2012)
      In this manuscript, we present a proof-of-concept study for targeted relative protein quantitation workflow using chemical labeling in the form of dimethylation, coupled with selected reaction monitoring (dimethyl-SRM). ...

    • Viewing the proteome: How to visualize proteomics data? 

      Oveland, Eystein; Muth, Thilo; Rapp, Erdmann; Martens, Lennart; Berven, Frode; Barsnes, Harald (Peer reviewed; Journal article, 2015-04)
      Proteomics has become one of the main approaches for analyzing and understanding biological systems. Yet similar to other high-throughput analysis methods, the presentation of the large amounts of obtained data in easily ...