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MS-Analyzer: preprocessing and data mining services for proteomics applications on the Grid

Mario Cannataro, Pierangelo Veltri
2007 Concurrency and Computation  
Mass spectrometry proteomics data contain much information about cell functions and disease conditions.  ...  MS data on the Grid.  ...  Mazza for their contributions to the MS-Analyzer project, to Marco Gaspari for providing the spectra data, and to G. Tradigo for his contribution on SpecDB.  ... 
doi:10.1002/cpe.1144 fatcat:2rvc3tuwpbcglexcirkoq7leva

The FAST-AIMS Clinical Mass Spectrometry Analysis System

Nafeh Fananapazir, Alexander Statnikov, Constantin F. Aliferis
2009 Advances in Bioinformatics  
As interest in this area grows, and the number of such proteomics datasets continues to increase, the need has developed for efficient, comprehensive, reproducible methods of mass spectrometry data analysis  ...  FAST-AIMS is an efficient and user-friendly stand-alone software for predictive analysis of mass spectrometry data.  ...  Acknowledgments The work was in part supported by Grant 2R56LM007948-04A1. NF was supported by the National Library of Medicine Grant T15 LM07450-01.  ... 
doi:10.1155/2009/598241 pmid:19956420 pmcid:PMC2775698 fatcat:tmn255ajlze3vkvjhk4qnompkq

The role of parallelism, web services and ontologies in bioinformatics and omics data management and analysis

Mario Cannataro, Pietro Hiram Guzzi
2013 EMBnet journal  
The increasing availability of omics data poses new challenges to bioinformatics applications regarding the efficient storage and integration of experimental data, their efficient and high-throughput preprocessing  ...  and analysis, the building of reproducible "in silico" experiments, the integration of analysis results with pre-existing knowledge repositories stored into ontologies, like Gene Ontology, or into specialised  ...  Workflow-based preprocessing and analysis of mass spectrometry-based proteomics data The analysis of mass spectrometry proteomics data requires the combination of large storage systems, effective preprocessing  ... 
doi:10.14806/ej.19.b.731 fatcat:i3tffcagufhd5ijk5cq5enzwxe

pkDACLASS: Open source software for analyzing MALDI-TOF data

Juliet Ndukum, Mourad Atlas, Susmita Datta
2011 Bioinformation  
Software Volume 6(1) ISSN 0973-2063 (online) 0973-8894 (print) Bioinformation 6(1): 45-47 (2011) 45 Abstract: In recent years, mass spectrometry has become one of the core technologies for high throughput  ...  Complete data analysis comprises data preprocessing, monoisotopic peak detection through statistical model fitting and testing, alignment of the monoisotopic peaks for multiple samples and classification  ...  Susmita Datta) and the center grant 1P30ES014443.  ... 
doi:10.6026/97320630006045 pmid:21464846 pmcid:PMC3064853 fatcat:5lc7ax6hjvhz5f32hynzfn6yim

Deep Autoencoder for Mass Spectrometry Feature Learning and Cancer Detection

Qingguo Zhou, Binbin Yong, Qingquan Lv, Jun Shen, Xin Wang
2020 IEEE Access  
In this paper, we propose to utilize deep autoencoder to learn latent representation of high-dimensional mass spectrometry data.  ...  Meanwhile, as a contrast, traditional particle swarm optimization (PSO) optimization algorithm are also used to select optimized features from mass spectrometry data.  ...  high-dimensional mass spectrometry data, so as to reduce the dimension of mass spectrometry data for cancer detection.  ... 
doi:10.1109/access.2020.2977680 fatcat:g4ymj5e4lvfspg7zc65647gu5a

Statistical Methods for Proteomic Biomarker Discovery based on Feature Extraction or Functional Modeling Approaches

Jeffrey S Morris
2012 Statistics and its Interface  
All methods are illustrated by application to two example proteomic data sets, one from mass spectrometry and one from 2D gel electrophoresis.  ...  After an overview of the feature extraction approach, specific methods for mass spectrometry (Cromwell) and 2D gel electrophoresis (Pinnacle) are described.  ...  Mass Spectrometry Mass spectrometry (MS) includes a series of methods that are used to survey the proteomic content of a biological sample by measuring the mass-to-unit charge (m/z) ratio of charged particles  ... 
pmid:23814640 pmcid:PMC3693398 fatcat:rwvve7qsvbdidi4zdoxltpubkq

Statistical methods for proteomic biomarker discovery based on feature extraction or functional modeling approaches

Jeffrey S. Morris
2012 Statistics and its Interface  
All methods are illustrated by application to two example proteomic data sets, one from mass spectrometry and one from 2D gel electrophoresis.  ...  Mass Spectrometry Mass spectrometry (MS) includes a series of methods that are used to survey the proteomic content of a biological sample by measuring the mass-to-unit charge (m/z) ratio of charged particles  ... 
doi:10.4310/sii.2012.v5.n1.a11 fatcat:o2efaendzna4fmlugj7k3h5lpe

Methodologies and experimental platforms for generating and analysing microarray and mass spectrometry-based omics data to support P4 medicine

Pietro H. Guzzi, Giuseppe Agapito, Marianna Milano, Mario Cannataro
2015 Briefings in Bioinformatics  
After introducing basic concepts of P4 medicine and omics sciences, we review some computational tools and approaches for analysing selected omics data, with a special focus on microarray and mass spectrometry  ...  Some applications of biomarker discovery and pharmacogenomics and some experiences on the study of drug reactions are also described.  ...  on the Grid [31] .  ... 
doi:10.1093/bib/bbv076 pmid:26351205 fatcat:lehrewonvfepnd33cbefzl5mci

Function-on-Scalar Quantile Regression with Application to Mass Spectrometry Proteomics Data [article]

Yusha Liu, Meng Li, Jeffrey S. Morris
2019 arXiv   pre-print
Mass spectrometry proteomics, characterized by spiky, spatially heterogeneous functional data, can be used to identify potential cancer biomarkers.  ...  We apply our model to identify proteomic biomarkers of pancreatic cancer that are differentially expressed for a subset of cancer patients compared to the normal controls, which were missed by previous  ...  an LC column over a series of elution times based on hydrophobicity or other physical properties before the mass spectrometry procedure, resulting in 2D mass spectrometry data (LC-MS) with one dimension  ... 
arXiv:1809.00266v2 fatcat:kznawli4yjha3mtahp264ky4oe

Mass spectrometry proteomic diagnosis: enacting the validation paradigm [article]

Bart J. A. Mertens, M. E. de Noo, R. A. E. M. Tollenaar, A. M. Deelder
2005 arXiv   pre-print
ability of mass spectrometry data for diagnosis in this setting.  ...  This paper presents an approach to the evaluation and validation of mass spectrometry data for construction of an 'early warning' diagnostic procedure.  ...  Acknowledgements The authors would like to give thanks to Eline Slagboom and Hans van Houwelingen for considerable support and encouragement in carrying out this study and to Aliye Ozalp for providing  ... 
arXiv:math/0510188v1 fatcat:wjapty5dpnbc3jllkyhanzip7q

MS-Helios: a Circos wrapper to visualize multi-omic datasets

Harald Marx, Joshua J. Coon
2019 BMC Bioinformatics  
Advances in high-resolution mass spectrometry facilitate the identification of hundreds of metabolites, thousands of proteins and their post-translational modifications.  ...  However, the CPM construction requires prior data transformation and extensive knowledge of the Perl-based tool, Circos.  ...  The plot construction with Circos may take more time depending on the number of data points.  ... 
doi:10.1186/s12859-018-2564-9 fatcat:hfyw7y2vgrfl3ppl2rd4yvvopm

Study on Preprocessing and Classifying Mass Spectral Raw Data Concerning Human Normal and Disease Cases [chapter]

Xenofon E. Floros, George M. Spyrou, Konstantinos N. Vougas, George T. Tsangaris, Konstantina S. Nikita
2006 Lecture Notes in Computer Science  
Here we address a feature exraction method for mass spectra which consists of two main steps : In the first step an algorithm for low level preprocessing of mass spectra is applied, including denoising  ...  The method described here for low-level preprocessing of mass spectra results in 98.3% sensitivity, 98.3% specificity and an AUC (Area Under Curve) of 0.981 in spectra classification.  ...  One of the most important tools in proteomics is mass spectrometry, as it can supply the researchers with quantitive data on the proteome itself.  ... 
doi:10.1007/11946465_35 fatcat:alwpu6icivalpedv3evqx3mf6q

Tools and strategies for visualization of large image data sets in high-resolution imaging mass spectrometry

Ivo Klinkert, Liam A. McDonnell, Stefan L. Luxembourg, A. F. Maarten Altelaar, Erika R. Amstalden, Sander R. Piersma, Ron M. A. Heeren
2007 Review of Scientific Instruments  
Mass spectrometry based proteomics is one of the scientific domains in which experiments produce a large amount of data that need special environments to interpret the results.  ...  Therefore, in the context of the virtual laboratory of enhanced science, software tools are developed to handle mass spectrometry data sets.  ...  Science ͑OC&W͒ and is part of the ICT innovation program of the Ministry of Economic Affairs ͑EZ͒.  ... 
doi:10.1063/1.2737770 pmid:17552834 fatcat:omdl2pyuyzbelfj3mmftulcou4

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  
One of the main building blocks in this field of study is proteomics where tandem mass spectrometry (LC-MS/MS) in combination with isotopic labelling techniques provides a common way to obtain a direct  ...  Starting with the import of mass spectra data the system guides the experimenter through the process of protein identification by database search, the calculation of protein abundance ratios, and in particular  ...  ACKNOWLEDGMENTS The authors wish to thank the BRF system administrators for expert technical support. We would especially like to thank the workgroups of D. Becher (Greifswald University) and A.  ... 
doi:10.1093/bioinformatics/btp568 pmid:19808875 fatcat:xjvqxrxl4feglbgadliabizzki

Tandem mass spectrometry protein identification on a PC grid

D Zosso, M Podvinec, M Müller, R Aebersold, M C Peitsch, T Schwede
2007 Studies in Health Technology and Informatics  
This allows rapid analysis of large-scale mass spectrometry experiments on existing heterogeneous hardware.  ...  We present a method to grid-enable tandem mass spectrometry protein identification. The implemented parallelization strategy embeds the open-source x!tandem tool in a grid-enabled workflow.  ...  Author contributions: MP, MM, RA, MCP and TS initiated the project, MP and TS designed the study. DZ and MP developed the application service. DZ designed the experiments and analyzed the data.  ... 
pmid:17476042 fatcat:ph4p7gxkpfhfjebbv3lz5uy42i
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