• An accessible proteogenomics informatics resource for cancer researchers 

      Chambers, Matthew C.; Jagtap, Pratik D.; Johnson, James E.; McGowan, Thomas; Kumar, Praveen; Onsongo, Getiria; Guerrero, Candace R.; Barsnes, Harald; Vaudel, Marc; Martens, Lennart; Grüning, Björn; Cooke, Ira R.; Heydarian, Mohammad; Reddy, Karen L.; Griffin, Timothy J. (Peer reviewed; Journal article, 2017)
      Proteogenomics has emerged as a valuable approach in cancer research, which integrates genomic and transcriptomic data with mass spectrometry–based proteomics data to directly identify expressed, variant protein sequences ...
    • Analyzing the Structure of Pathways and Its Influence on the Interpretation of Biomedical Proteomics Data Sets 

      Burger, Bram; Hernández Sánchez, Luis Francisco; Lereim, Ragnhild Reehorst; Barsnes, Harald; Vaudel, Marc (Peer reviewed; Journal article, 2018)
      Biochemical pathways are commonly used as a reference to conduct functional analysis on biomedical omics data sets, where experimental results are mapped to knowledgebases comprising known molecular interactions collected ...
    • Anatomy and evolution of database search engines — a central component of mass spectrometry based proteomic workflows 

      Verheggen, Kenneth; Ræder, Helge; Berven, Frode; Martens, Lennart Martens; Barsnes, Harald; Vaudel, Marc (Peer reviewed; Journal article, 2017-09-13)
      Sequence database search engines are bioinformatics algorithms that identify peptides from tandem mass spectra using a reference protein sequence database. Two decades of development, notably driven by advances in mass ...
    • BioContainers: An open-source and community-driven framework for software standardization 

      Leprevost, Felipe da Veiga; Grüning, Björn A.; Alves Aflitos, Saulo; Röst, Hannes L.; Uszkoreit, Julian; Barsnes, Harald; Vaudel, Marc; Moreno, Pablo; Gatto, Laurent; Weber, Jonas; Bai, Mingze; Jimenez, Rafael C.; Sachsenberg, Timo; Pfeuffer, Julianus; Vera Alvarez, Roberto; Griss, Johannes; Nesvizhskii, Alexey I.; Perez-Riverol, Yasset (Peer reviewed; Journal article, 2017-03-30)
      Motivation BioContainers (biocontainers.pro) is an open-source and community-driven framework which provides platform independent executable environments for bioinformatics software. BioContainers allows labs of all sizes ...
    • Blind search for post-translational modifications and amino acid substitutions using peptide mass fingerprints from two proteases 

      Barsnes, Harald; Mikalsen, Svein-Ole; Eidhammer, Ingvar (Peer reviewed; Journal article, 2008-12-19)
      Background: Mass spectrometric analysis of peptides is an essential part of protein identification and characterization, the latter meaning the identification of modifications and amino acid substitutions. There are two ...
    • Compomics-utilities: an open-source Java library for computational proteomics 

      Barsnes, Harald; Vaudel, Marc; Colaert, Niklaas; Helsens, Kenny; Sickmann, Albert; Berven, Frode S.; Martens, Lennart (Peer reviewed; Journal article, 2011-03-08)
      Background The growing interest in the field of proteomics has increased the demand for software tools and applications that process and analyze the resulting data. And even though the purpose of these tools can vary ...
    • Crowdsourcing in proteomics: public resources lead to better experiments 

      Barsnes, Harald; Martens, Lennart (Peer reviewed; Journal article, 2013-04)
      With the growing interest in the field of proteomics, the amount of publicly available proteome resources has also increased dramatically. This means that there are many useful resources available for almost all aspects ...
    • DeNovoGUI: an open source graphical user interface for de novo sequencing of tandem mass spectra 

      Muth, Thilo; Weilnböck, Lisa; Rapp, Erdmann; Huber, Christian G.; Martens, Lennart; Vaudel, Marc; Barsnes, Harald (Peer reviewed; Journal article, 2014)
      De novo sequencing is a popular technique in proteomics for identifying peptides from tandem mass spectra without having to rely on a protein sequence database. Despite the strong potential of de novo sequencing algorithms, ...
    • Detecting single amino acids and small peptides by combining isobaric tags and peptidomics 

      Burger, Bram; Lereim, Ragnhild Reehorst; Berven, Frode; Barsnes, Harald (Peer reviewed; Journal article, 2019)
      Single amino acids and small endogenous peptides play important roles in maintaining a properly functioning organism. These molecules are however currently only routinely identified in targeted approaches. In a small ...
    • Development of Tools for Analyzing and Sharing Proteomics Data 

      Barsnes, Harald (Doctoral thesis, 2010-03-22)
    • Discovery and initial verification of differentially abundant proteins between multiple sclerosis patients and controls using iTRAQ and SID-SRM 

      Kroksveen, Ann Cathrine; Aasebø, Elise; Vethe, Heidrun; van Pesch, Vincent; Franciotta, Diego; Teunissen, Charlotte E.; Ulvik, Rune Johan; Vedeler, Christian A.; Myhr, Kjell-Morten; Barsnes, Harald; Berven, Frode (Peer reviewed; Journal article, 2013-01)
      In the present study, we aimed to discover cerebrospinal fluid (CSF) proteins with significant abundance difference between early multiple sclerosis patients and controls, and do an initial verification of these proteins ...
    • Distributed computing and data storage in proteomics: many hands make light work, and a stronger memory 

      Verheggen, Kenneth; Barsnes, Harald; Martens, Lennart (Peer reviewed; Journal article, 2014-03)
      Modern day proteomics generates ever more complex data, causing the requirements on the storage and processing of such data to outgrow the capacity of most desktop computers. To cope with the increased computational demands, ...
    • Essential Features and Use Cases of the Cerebrospinal Fluid Proteome Resource (CSF-PR) 

      Guldbrandsen, Astrid; Farag, Yehia Mohamed Mokhtar; Lereim, Ragnhild Reehorst; Berven, Frode; Barsnes, Harald (Peer reviewed; Journal article, 2019)
      Every year, a large number of published studies present biomarkers for various neurological disorders. Many of these studies are based on mass spectrometry proteomics data and describe comparison of the abundance of proteins ...
    • Exploring the potential of public proteomics data 

      Vaudel, Marc; Verheggen, Kenneth; Csordas, Attila; Ræder, Helge; Berven, Frode; Martens, Lennart; Vizcaíno, Juan Antonio; Barsnes, Harald (Peer reviewed; Journal article, 2016)
      In a global effort for scientific transparency, it has become feasible and good practice to share experimental data supporting novel findings. Consequently, the amount of publicly available MS‐based proteomics data has ...
    • In-depth cerebrospinal fluid quantitative proteome and deglycoproteome analysis: presenting a comprehensive picture of pathways and processes affected by multiple sclerosis 

      Kroksveen, Ann Cathrine; Guldbrandsen, Astrid; Vaudel, Marc; Lereim, Ragnhild Reehorst; Barsnes, Harald; Myhr, Kjell-Morten; Torkildsen, Øivind; Berven, Frode (Peer reviewed; Journal article, 2017)
      In the current study, we conducted a quantitative in-depth proteome and deglycoproteome analysis of cerebrospinal fluid (CSF) from relapsing-remitting multiple sclerosis (RRMS) and neurological controls using mass spectrometry ...
    • In-depth characterization of the cerebrospinal fluid (CSF) proteome displayed through the CSF proteome resource (CSF-PR) 

      Guldbrandsen, Astrid; Vethe, Heidrun; Farag, Yehia Mohamed Mokhtar; Oveland, Eystein; Garberg, Hilde Kristin; Berle, Magnus Foldal; Myhr, Kjell-Morten; Opsahl, Jill Anette; Barsnes, Harald; Berven, Frode (Peer reviewed; Journal article, 2014-11)
      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 the global CSF ...
    • Machine learning applications in proteomics research: How the past can boost the future 

      Kelchtermans, Pieter; Bittremieux, Wout; De Grave, Kurt; Degroeve, S; Ramon, Jan; Laukens, Kris; Valkenborg, Dirk; Barsnes, Harald; Martens, Lennart (Peer reviewed; Journal article, 2014)
      Machine learning is a subdiscipline within artificial intelligence that focuses on algorithms that allow computers to learn solving a (complex) problem from existing data. This ability can be used to generate a solution ...
    • MassSorter: a tool for administrating and analyzing data from mass spectrometry experiments on proteins with known amino acid sequences 

      Barsnes, Harald; Mikalsen, Svein-Ole; Eidhammer, Ingvar (Peer reviewed; Journal article, 2006-01-26)
      Background: Proteomics is the study of the proteome, and is critical to the understanding of cellular processes. Two central and related tasks of proteomics are protein identification and protein characterization. Many ...
    • The mzIdentML data standard version 1.2, supporting advances in proteome informatics 

      Vizcaíno, Juan Antonio; Mayer, Gerhard; Perkins, Simon; Barsnes, Harald; Vaudel, Marc; Perez-Riverol, Yasset; Ternent, Tobias; Uszkoreit, Julian; Eisenacher, Martin; Fischer, Lutz; Rappsilber, Juri; Netza, Eugen; Walzer, Mathias; Kohlbacher, Oliver; Leitner, Alexander; Chalkley, Robert J.; Ghali, Fawaz; Martínez-Bartolomé, Salvador; Deutsch, Eric W.; Jones, Andrew R. (Peer reviewed; Journal article, 2017-07-01)
      The first stable version of the Proteomics Standards Initiative mzIdentML open data standard (version 1.1) was published in 2012—capturing the outputs of peptide and protein identification software. In the intervening ...
    • OLS Client and OLS Dialog: Open source tools to annotate public omics datasets 

      Perez-Riverol, Yasset; Ternent, Tobias; Koch, Maximilian; Barsnes, Harald; Vrousgou, Olga; Jupp, Simon; Vizcaíno, Juan Antonio (Peer reviewed; Journal article, 2017)
      The availability of user‐friendly software to annotate biological datasets and experimental details is becoming essential in data management practices, both in local storage systems and in public databases. The Ontology ...