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Qupe—a Rich Internet Application to take a step forward in the analysis of mass spectrometry-based quantitative proteomics experiments

Stefan P. Albaum, Heiko Neuweger, Benjamin Fränzel, Sita Lange, Dominik Mertens, Christian Trötschel, Dirk Wolters, Jörn Kalinowski, Tim W. Nattkemper, Alexander Goesmann
2009 Computer applications in the biosciences : CABIOS  
To demonstrate that Qupe represents a step forward in quantitative proteomics analysis an application study on Corynebacterium glutamicum has been carried out.  ...  Results: We introduce the Rich Internet Application (RIA) Qupe providing comprehensive data management and analysis functions for LC-MS/MS experiments.  ...  Funding: BMBF in the frame of the QuantPro initiative (grant 0313812, to S.P.A. and S.L.); International Graduate School in Bioinformatics and Genome Research (to H.N.).  ... 
doi:10.1093/bioinformatics/btp568 pmid:19808875 fatcat:xjvqxrxl4feglbgadliabizzki

Omics Fusion – A Platform for Integrative Analysis of Omics Data

Benedikt G. Brink, Annica Seidel, Nils Kleinbölting, Tim W. Nattkemper, Stefan P. Albaum
2016 Journal of Integrative Bioinformatics  
We present Omics Fusion, a new web-based platform for integrative analysis of omics data.  ...  It is available for free under: https://fusion.cebitec.uni-bielefeld.de/  ...  Wenzel and Ruben Christian Hamann for their invaluable contributions.  ... 
doi:10.1515/jib-2016-296 fatcat:geiaxflfcrhdrmig2s64eyzkbm

GProX, a User-Friendly Platform for Bioinformatics Analysis and Visualization of Quantitative Proteomics Data

Kristoffer T. G. Rigbolt, Jens T. Vanselow, Blagoy Blagoev
2011 Molecular & Cellular Proteomics  
GProX represents a powerful approach to proteomics data analysis providing proteomics experimenters with a toolbox for bioinformatics analysis of quantitative proteomics data.  ...  To provide the proteomics community with a user-friendly platform for comprehensive analysis, inspection and visualization of quantitative proteomics data we developed the Graphical Proteomics Data Explorer  ...  Acknowledgments-We thank all CEBI members for comments  ... 
doi:10.1074/mcp.o110.007450 pmid:21602510 pmcid:PMC3149098 fatcat:7543uuzjj5gotgzj5g5ihargdu

A Critical Appraisal of Techniques, Software Packages, and Standards for Quantitative Proteomic Analysis

Faviel F. Gonzalez-Galarza, Craig Lawless, Simon J. Hubbard, Jun Fan, Conrad Bessant, Henning Hermjakob, Andrew R. Jones
2012 Omics  
New methods for performing quantitative proteome analyses based on differential labeling protocols or label-free techniques are reported in the literature on an almost monthly basis.  ...  In parallel, a correspondingly vast number of software tools for the analysis of quantitative proteomics data has also been described in the literature and produced by private companies.  ...  This integrated platform allows quantitative analysis of different experiments, including 14 N/ 15 N, SILAC, and iTRAQ.  ... 
doi:10.1089/omi.2012.0022 pmid:22804616 pmcid:PMC3437040 fatcat:nm2cpnicavaa3nx7peowilx5fi

Visualizing post genomics data-sets on customized pathway maps by ProMeTra – aeration-dependent gene expression and metabolism of Corynebacterium glutamicum as an example

Heiko Neuweger, Marcus Persicke, Stefan P Albaum, Thomas Bekel, Michael Dondrup, Andrea T Hüser, Jörn Winnebald, Jessica Schneider, Jörn Kalinowski, Alexander Goesmann
2009 BMC Systems Biology  
In order to be able to obtain deeper insights in the generated datasets, it is of utmost importance to present the data to the researcher in an intuitive, integrated, and knowledge-based environment.  ...  The rapid progress of post-genomic analyses, such as transcriptomics, proteomics, and metabolomics has resulted in the generation of large amounts of quantitative data covering and connecting the complete  ...  Acknowledgements HN would like to thank the International Graduate School in Bioinformatics and Genome Research for providing financial support.  ... 
doi:10.1186/1752-0509-3-82 pmid:19698148 pmcid:PMC2744654 fatcat:mmit5eaw4jcbbfs6yvqus7xdii

Understanding Cervical Cancer through Proteomics

Fátima Martínez-Rodríguez, Jared E. Limones-González, Brenda Mendoza-Almanza, Edgar L. Esparza-Ibarra, Perla I. Gallegos-Flores, Jorge L. Ayala-Luján, Susana Godina-González, Eva Salinas, Gretel Mendoza-Almanza
2021 Cells  
The present review is an update on the proteomic study of CC.  ...  The cluster of differential molecular profiles in the genome, the transcriptome, or the proteome is analyzed in the disease, and it is called the molecular signature of cancer.  ...  SILAC is an MS-based quantitative proteomics approach used for internal labeling of the cell proteome or of proteins secreted into the cell culture supernatant [83] .  ... 
doi:10.3390/cells10081854 pmid:34440623 pmcid:PMC8391734 fatcat:ju3ppokde5gyleiorun5kucrq4

Systems and synthetic biology perspective of the versatile plant-pathogenic and polysaccharide-producing bacterium Xanthomonas campestris

Sarah Schatschneider, Jessica Schneider, Jochen Blom, Fabien Létisse, Karsten Niehaus, Alexander Goesmann, Frank-Jörg Vorhölter
2017 Microbiology  
This is based on insights from omics disciplines; in particular, genomics, transcriptomics, proteomics and metabolomics.  ...  In this review, we summarize the synthetic and systems biology methods and the bioinformatics tools applied to reconstruct their metabolic network and reveal the dynamic fluxes within their complex carbohydrate  ...  Acknowledgements The authors thank Rupert Norman for proofreading the manuscript. Conflicts of interest The authors declare that there are no conflicts of interest.  ... 
doi:10.1099/mic.0.000473 pmid:28795660 fatcat:4jvegng32zac3eutbury44bvmy

The Archaeal Proteome Project advances knowledge about archaeal cell biology through comprehensive proteomics

Stefan Schulze, Zachary Adams, Micaela Cerletti, Rosana De Castro, Sébastien Ferreira-Cerca, Christian Fufezan, María Inés Giménez, Michael Hippler, Zivojin Jevtic, Robert Knüppel, Georgio Legerme, Christof Lenz (+7 others)
2020 Nature Communications  
Altogether, ArcPP serves as an invaluable blueprint for comprehensive prokaryotic proteomics.  ...  While many aspects of archaeal cell biology remain relatively unexplored, systems biology approaches like mass spectrometry (MS) based proteomics offer an opportunity for rapid advances.  ...  Jonathan Stoltzfus and Ronald Rodriguez are greatly acknowledged for assisting in strain and sample generation. We also thank Dr. Uli  ... 
doi:10.1038/s41467-020-16784-7 pmid:32561711 fatcat:m52liaiambhotelzavijxjrkjy

Proteome turnover in bacteria: current status forCorynebacterium glutamicumand related bacteria

Christian Trötschel, Stefan P. Albaum, Ansgar Poetsch
2013 Microbial Biotechnology  
In this article, we summarize the technological challenges and solutions both on the biochemistry/mass spectrometry and bioinformatics level for turnover proteomics with a focus on chromatographic techniques  ...  Finally, we will comment on the advantages of integrated software solutions for biologists and briefly discuss the remaining technical challenges and upcoming possibilities for protein turnover analysis  ...  Acknowledgements The authors are grateful to Frank ter Veld for critically reading and commenting the manuscript.  ... 
doi:10.1111/1751-7915.12035 pmid:23425033 pmcid:PMC3815937 fatcat:pmvsufjrarb4djeyu2sahtgdry

MeltDB: a software platform for the analysis and integration of metabolomics experiment data

Heiko Neuweger, Stefan P. Albaum, Michael Dondrup, Marcus Persicke, Tony Watt, Karsten Niehaus, Jens Stoye, Alexander Goesmann
2008 Computer applications in the biosciences : CABIOS  
MeltDB is a web-based software platform for the analysis and annotation of datasets from metabolomics experiments.  ...  , proteomics, and transcriptomics at Bielefeld University.  ...  ProMeTra does furthermore act as an interactive interface to the experimental datasets stored in the Omics platforms MeltDB for metabolomics, Emma2 for transcriptomics , and QuPE for proteomics ) that  ... 
doi:10.1093/bioinformatics/btn452 pmid:18765459 fatcat:6kraieexyvaq7hcx4fikyqg5gq

Codon Usage Heterogeneity in the Multipartite Prokaryote Genome: Selection-Based Coding Bias Associated with Gene Location, Expression Level, and Ancestry

J. L. López, M. J. Lozano, A. Lagares, M. L. Fabre, W. O. Draghi, M. F. Del Papa, M. Pistorio, A. Becker, D. Wibberg, A. Schlüter, A. Pühler, J. Blom (+3 others)
2019 mBio  
Prokaryotes represent an ancestral lineage in the tree of life and constitute optimal resources for investigating the evolution of genomes in unicellular organisms.  ...  Many bacterial species possess multipartite genomes offering opportunities to study functional variations among replicons, how and where new genes integrate into a genome, and how genetic information within  ...  Haggerty for editing the final version of the manuscript.  ... 
doi:10.1128/mbio.00505-19 pmid:31138741 pmcid:PMC6538778 fatcat:ffubed5wcbbnnn3oloqhthdpqa

Omics visualization and its application to presymptomatic diagnosis of oral cancer

Benedikt Brink
2018
Science as well is flooded by an ever increasing amount of data.  ...  Oral cancer has a major impact worldwide, accounting for 274 000 new cases and 145 000 deaths each year, making it sixth most com- mon cancer. Developing methods for the de [...]  ...  discussion Omics Fusion is an extendible, web-based platform for the integrative analysis of omics data.  ... 
doi:10.4119/unibi/2930495 fatcat:nz7wdhjokjdwtbkhy2zjhryd64