Open source libraries and frameworks for mass spectrometry based proteomics: A developer's perspective (English)
- New search for: Perez-Riverol, Yasset
- New search for: Wang, Rui
- New search for: Hermjakob, Henning
- New search for: Müller, Markus
- New search for: Vesada, Vladimir
- New search for: Vizcaíno, Juan Antonio
- New search for: Perez-Riverol, Yasset
- New search for: Wang, Rui
- New search for: Hermjakob, Henning
- New search for: Müller, Markus
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- New search for: Vizcaíno, Juan Antonio
In:
Biochimica et Biophysica Acta - Proteins and Proteomics
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1844
, 1
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63-76
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2013
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ISSN:
- Article (Journal) / Electronic Resource
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Title:Open source libraries and frameworks for mass spectrometry based proteomics: A developer's perspective
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Contributors:Perez-Riverol, Yasset ( author ) / Wang, Rui ( author ) / Hermjakob, Henning ( author ) / Müller, Markus ( author ) / Vesada, Vladimir ( author ) / Vizcaíno, Juan Antonio ( author )
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Published in:Biochimica et Biophysica Acta - Proteins and Proteomics ; 1844, 1 ; 63-76
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Publisher:
- New search for: Elsevier B.V.
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Publication date:2013-02-22
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Size:14 pages
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ISSN:
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DOI:
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Type of media:Article (Journal)
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Type of material:Electronic Resource
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Language:English
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Keywords:AMT , Accurate Mass Tag , ATAQS , Automated and Targeted Analysis with Quantitative SRM , CV , Controlled Vocabulary , DAO , Data Access Object , EBI , European Bioinformatics Institute , emPAI , exponentially modified Protein Abundance Index , FDR , False Discovery Rate , (HUPO)-PSI , (Human Proteome Organization) — Proteomics Standards Initiative , GUI , Graphical User Interface , ICAT , Isotope-Coded Affinity Tags , ICPL , Isotope-Coded Protein Label , IPTL , Isobaric Peptide Termini Labeling , ISB , Institute for Systems Biology , iTRAQ , Isobaric Tag for Relative and Absolute Quantitation , JPL , Java Proteomic Library , LC-MS , Liquid Chromatography–Mass Spectrometry , LIMS , Laboratory Information Management System , MGF , Mascot Generic Format , MIAPE , Minimum Information About a Proteomics Experiment , MS , Mass Spectrometry , SILAC , Stable Isotope Labeling by Amino acids in Cell culture , PASSEL , PeptideAtlas SRM Experiment Library , PRIDE , PRoteomics IDEntifications (database) , PSM , Peptide Spectrum Match , PTM , Post-Translational Modifications , RT , Retention Time , SRM , Selected Reaction Monitoring , TMT , Tandem Mass Tag , TOPP , The OpenMS Proteomics Pipeline , TPP , Trans-Proteomic Pipeline , Proteomics , Databases , Bioinformatics , Software libraries , Application programming interface , Open source software
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Source:
Table of contents – Volume 1844, Issue 1
The tables of contents are generated automatically and are based on the data records of the individual contributions available in the index of the TIB portal. The display of the Tables of Contents may therefore be incomplete.
- 1
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Computational proteomics in the post-identification eraEisenacher, Martin / Stephan, Christian et al. | 2013
- 2
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The amino acid's backup bone — Storage solutions for proteomics facilitiesMeckel, Hagen / Stephan, Christian / Bunse, Christian / Krafzik, Michael / Reher, Christopher / Kohl, Michael / Meyer, Helmut Erich / Eisenacher, Martin et al. | 2013
- 12
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Introduction to opportunities and pitfalls in functional mass spectrometry based proteomicsVaudel, Marc / Sickmann, Albert / Martens, Lennart et al. | 2013
- 21
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A practical guide to the ICPL_ESIQuant software for ICPL-based quantitative proteomicsBrunner, Achim / Kellermann, Josef / Lottspeich, Friedrich et al. | 2013
- 29
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Data processing methods and quality control strategies for label-free LC–MS protein quantificationSandin, Marianne / Teleman, Johan / Malmström, Johan / Levander, Fredrik et al. | 2013
- 42
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Using R and Bioconductor for proteomics data analysisGatto, Laurent / Christoforou, Andy et al. | 2013
- 52
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A practical data processing workflow for multi-OMICS projectsKohl, Michael / Megger, Dominik A. / Trippler, Martin / Meckel, Hagen / Ahrens, Maike / Bracht, Thilo / Weber, Frank / Hoffmann, Andreas-Claudius / Baba, Hideo A. / Sitek, Barbara et al. | 2013
- 63
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Open source libraries and frameworks for mass spectrometry based proteomics: A developer's perspectivePerez-Riverol, Yasset / Wang, Rui / Hermjakob, Henning / Müller, Markus / Vesada, Vladimir / Vizcaíno, Juan Antonio et al. | 2013
- 77
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Gene-centric content management systemPoverennaya, Ekaterina V. / Bogolubova, Nadezhda A. / Bylko, Nikolay N. / Ponomarenko, Elena A. / Lisitsa, Andrey V. / Archakov, Alexander I. et al. | 2013
- 82
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Data Standardization and Sharing—The work of the HUPO-PSIOrchard, Sandra et al. | 2013
- 88
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A tutorial for software development in quantitative proteomics using PSI standard formatsGonzalez-Galarza, Faviel F. / Qi, Da / Fan, Jun / Bessant, Conrad / Jones, Andrew R. et al. | 2013
- 98
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Controlled vocabularies and ontologies in proteomics: Overview, principles and practiceMayer, Gerhard / Jones, Andrew R. / Binz, Pierre-Alain / Deutsch, Eric W. / Orchard, Sandra / Montecchi-Palazzi, Luisa / Vizcaíno, Juan Antonio / Hermjakob, Henning / Oveillero, David / Julian, Randall et al. | 2013
- 108
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Validation of the curation pipeline of UniCarb-DB: Building a global glycan reference MS/MS repositoryCampbell, Matthew P. / Nguyen-Khuong, Terry / Hayes, Catherine A. / Flowers, Sarah A. / Alagesan, Kathirvel / Kolarich, Daniel / Packer, Nicolle H. / Karlsson, Niclas G. et al. | 2013
- 117
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2D and 3D MALDI-imaging: Conceptual strategies for visualization and data miningThiele, Herbert / Heldmann, Stefan / Trede, Dennis / Strehlow, Jan / Wirtz, Stefan / Dreher, Wolfgang / Berger, Judith / Oetjen, Janina / Kobarg, Jan Hendrik / Fischer, Bernd et al. | 2013
- 138
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A Bayesian changepoint analysis of ChIP-Seq data of Lamin BHerrmann, S. / Schwender, H. / Ickstadt, K. / Müller, P. et al. | 2013
- 145
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A practical guide to epidemiological practice and standards in the identification and validation of diagnostic markers using a bladder cancer exampleBehrens, T. / Bonberg, N. / Casjens, S. / Pesch, B. / Brüning, T. et al. | 2013
- 156
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Cheminformatics at the interface of medicinal chemistry and proteomicsKoch, Uwe / Hamacher, Michael / Nussbaumer, Peter et al. | 2013
- 163
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Computational proteomics, systems biology and clinical implicationsCai, Yudong et al. | 2013
- 165
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A sequence-based computational approach to predicting PDZ domain-peptide interactionsNakariyakul, Songyot / Liu, Zhi-Ping / Chen, Luonan et al. | 2013
- 171
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Computationally characterizing and comprehensive analysis of zinc-binding sites in proteinsLiu, Zexian / Wang, Yongbo / Zhou, Changhai / Xue, Yu / Zhao, Wei / Liu, Haiyan et al. | 2013
- 181
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Prediction and characterization of cyclic proteins from sequences in three domains of lifeKedarisetti, Pradyumna / Mizianty, Marcin J. / Kaas, Quentin / Craik, David J. / Kurgan, Lukasz et al. | 2013
- 191
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Briefing in family characteristics of microRNAs and their applications in cancer researchWang, Qicong / Wei, Leyi / Guan, Xinjun / Wu, Yunfeng / Zou, Quan / Ji, ZhiLiang et al. | 2013
- 198
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Dipeptide analysis of p53 mutations and evolution of p53 family proteinsHuang, Qiang / Yu, Long / Levine, Arnold J. / Nussinov, Ruth / Ma, Buyong et al. | 2013
- 207
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Prediction of drug target groups based on chemical–chemical similarities and chemical–chemical/protein connectionsChen, Lei / Lu, Jing / Luo, Xiaomin / Feng, Kai-Yan et al. | 2013
- 214
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Predicting network of drug–enzyme interaction based on machine learning methodNiu, Bing / Zhang, Yuchao / Ding, Juan / Lu, Yin / Wang, Miao / Lu, Wencong / Yuan, Xiaochen / Yin, Jinyuan et al. | 2013
- 224
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Global analysis of phosphorylation networks in humansHu, Jianfei / Rho, Hee-Sool / Newman, Robert H. / Hwang, Woochang / Neiswinger, John / Zhu, Heng / Zhang, Jin / Qian, Jiang et al. | 2013
- 232
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The p53 protein and its molecular network: Modelling a missing link between DNA damage and cell fateEliaš, Ján / Dimitrio, Luna / Clairambault, Jean / Natalini, Roberto et al. | 2013
- 248
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Dynamic analysis of the combinatorial regulation involving transcription factors and microRNAs in cell fate decisionsYan, Fang / Liu, Haihong / Liu, Zengrong et al. | 2013
- 258
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Mesoscopic modeling as a starting point for computational analyses of cystic fibrosis as a systemic diseaseVoit, Eberhard O. et al. | 2013
- 271
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Comparative analysis of viral protein interaction networks in Hepatitis B Virus and Hepatitis C Virus infected HCCYuan, Weilan / Huang, Tao / Yu, Jian / Zeng, Lingyao / Lian, Baofeng / He, Qinwen / Li, Yixue / Zhang, Xiaoyan / Zhou, Fengli / Xie, Lu et al. | 2013
- 280
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Application of metabolomics on diagnosis and treatment of patients with psoriasis in traditional Chinese medicineLu, Chuanjian / Deng, Jingwen / Li, Li / Wang, Dongmei / Li, Guozheng et al. | 2013
- 289
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Hybrid modeling of the crosstalk between signaling and transcriptional networks using ordinary differential equations and multi-valued logicKhan, Faiz M. / Schmitz, Ulf / Nikolov, Svetoslav / Engelmann, David / Pützer, Brigitte M. / Wolkenhauer, Olaf / Vera, Julio et al. | 2013
- i
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Editorial Board| 2013
- iii
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Reviewer Acknowledgment| 2013