• 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 ...
    • 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 ...
    • 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, ...
    • Exploring the human plasma proteome for humoral mediators of remote ischemic preconditioning - A word of caution 

      Helgeland, Erik; Breivik, Lars Ertesvåg; Vaudel, Marc; Svendsen, Øyvind Sverre; Garberg, Hilde Kristin; Nordrehaug, Jan Erik; Berven, Frode S.; Jonassen, Anne Kristin (Peer reviewed; Journal article, 2014-10-15)
      Despite major advances in early revascularization techniques, cardiovascular diseases are still the leading cause of death worldwide, and myocardial infarctions contribute heavily to this. Over the past decades, it has ...
    • 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 ...
    • Genome-wide association study of offspring birth weight in 86 577 women identifies five novel loci and highlights maternal genetic effects that are independent of fetal genetics 

      Beaumont, Robin N.; Warrington, Nicole M.; Cavadino, Alana; Tyrrell, Jessica; Nodzenski, Michael; Horikoshi, Momoko; Geller, Frank; Myhre, Ronny; Richmond, Rebecca C.; Paternoster, Lavinia; Bradfield, Jonathan P.; Kreiner-Møller, Eskil; Huikari, Ville; Metrustry, Sarah; Lunetta, Kathryn L.; Painter, Jodie N.; Hottenga, Jouke-Jan; Allard, Catherine; Barton, Sheila J.; Espinosa, Ana; Marsh, Julie A.; Potter, Catherine; Zhang, Ge; Ang, Wei; Berry, Diane J.; Bouchard, Luigi; Das, Shikta; Hakonarson, Hakon; Heikkinen, Jani; Helgeland, Øyvind; Hocher, Berthold; Hofman, Albert; Inskip, Hazel M.; Jones, Samuel E.; Kogevinas, Manolis; Lind, Penelope A.; Marullo, Letizia; Medland, Sarah E.; Murray, Anna; Murray, Jeffrey C.; Njølstad, Pål Rasmus; Nohr, Ellen A.; Reichetzeder, Christoph; Ring, Susan M.; Ruth, Katherine S.; Santa-Marina, Loreto; Scholtens, Denise M.; Sebert, Sylvain; Sengpiel, Verena; Tuke, Marcus A.; Vaudel, Marc; Weedon, Michael N.; Willemsen, Gonneke; Wood, Andrew R.; Yaghootkar, Hanieh; Muglia, Louis J.; Bartels, Meike; Relton, Caroline L.; Pennell, Craig E.; Chatzi, Leda; Estivill, Xavier; Holloway, John W.; Boomsma, Dorret I.; Montgomery, Grant W.; Murabito, Joanne M.; Spector, Tim D.; Power, Christine; Järvelin, Marjo-Riitta; Bisgaard, Hans; Grant, Struan F.A.; Sørensen, Thorkild I.A.; Jaddoe, Vincent W.; Jacobsson, Bo; Melbye, Mads; McCarthy, Mark I.; Hattersley, Andrew T.; Hayes, M. Geoffrey; Hivert, Marie-France; Frayling, Timothy M.; Felix, Janine F.; Hyppönen, Elina; Lowe, William L.; Evans, David M.; Lawlor, Debbie A.; Feenstra, Bjarke; Freathy, Rachel M. (Peer reviewed; Journal article, 2018-02)
      Genome-wide association studies of birth weight have focused on fetal genetics, whereas relatively little is known about the role of maternal genetic variation. We aimed to identify maternal genetic variants associated ...
    • Genome-wide association study reveals dynamic role of genetic variation in infant and early childhood growth 

      Helgeland, Øyvind; Vaudel, Marc; Juliusson, Petur Benedikt; Holmen, Oddgeir Lingaas; Juodakis, Julius; Bacelis, Jonas; Jacobsson, Bo; Lindekleiv, Haakon; Hveem, Kristian; Lie, Rolv T.; Knudsen, Gun Peggy Strømstad; Stoltenberg, Camilla; Magnus, Per; Sagen, Jørn V.; Molven, Anders; Johansson, Stefan; Njølstad, Pål Rasmus (Peer reviewed; Journal article, 2019-10-01)
      Infant and childhood growth are dynamic processes with large changes in BMI during development. By performing genome-wide association studies of BMI at 12 time points from birth to eight years (9286 children, 74,105 ...
    • 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 ...
    • Introduction to opportunities and pitfalls in functional mass spectrometry based proteomics 

      Vaudel, Marc; Sickmann, Albert; Martens, Lennart (Peer reviewed; Journal article, 2014-01)
      With the advent of mass spectrometry based proteomics, the identification of thousands of proteins has become commonplace in biology nowadays. Increasingly, efforts have also been invested toward the detection and localization ...
    • 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 ...
    • 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 ...
    • A Potential Golden Age to Come-Current Tools, Recent Use Cases, and Future Avenues for De Novo Sequencing in Proteomics 

      Muth, Thilo; Hartkopf, Felix; Vaudel, Marc; Renard, Bernhard Y (Peer reviewed; Journal article, 2018-07-02)
      In shotgun proteomics, peptide and protein identification is most commonly conducted using database search engines, the method of choice when reference protein sequences are available. Despite its widespread use the ...
    • 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 ...
    • Reliable FASP-based procedures for optimal quantitative proteomic and phosphoproteomic analysis on samples from acute myeloid leukemia patients 

      Hernandez-Valladares, Maria; Aasebø, Elise; Mjaavatten, Olav; Vaudel, Marc; Bruserud, Øystein; Berven, Frode; Selheim, Frode (Peer reviewed; Journal article, 2016-06-21)
      Background Satisfactory sample preparation for mass spectrometry-based analysis is a critical step in the proteomics workflow. The quality and reproducibility of sample preparation can determine the coverage and confidence ...
    • Reprogrammed Cells Display Distinct Proteomic SignaturesAssociated with Colony Morphology Variability 

      Bjørlykke, Yngvild; Søviknes, Anne Mette; Hoareau, Laurence; Vethe, Heidrun; Mathisen, Andreas; Chera, Simona; Vaudel, Marc; Ghila, Luiza; Ræder, Helge (Peer reviewed; Journal article, 2019-11-18)
      Human induced pluripotent stem cells (hiPSCs) are of high interest because they can be differentiated into a vast range of different cell types. Ideally, reprogrammed cells should sustain long-term culturing in an ...
    • 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 ...