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Visualize: A free and open source multifunction tool for proteomics data analysis

Brian D. Halligan, Andrew S. Greene
2011 Proteomics  
Beyond that, a proteomics experiment generally requires that investigators combine and compare the results from multiple runs or groups of runs.  ...  These results then need to be further annotated and analyzed to determine quantitative differences and changes in biological pathways.  ...  Acknowledgments The authors thank Bassam Wakim and the members of the Biotechnology and Bioengineering Center for program testing, bug reports and feature requests.  ... 
doi:10.1002/pmic.201000556 pmid:21365761 pmcid:PMC3816356 fatcat:pjpw5c2gbrc47hzzvpn4vndaoa

Proteomic Feature Maps: A new visualization approach in proteomics analysis

Eugenia G. Giannopoulou, Spiros D. Garbis, Antonia Vlahou, Sofia Kossida, George Lepouras, Elias S. Manolakos
2009 Journal of Biomedical Informatics  
Acknowledgments This work is part of the 03ED306 research project, implemented within the framework of the ''Reinforcement Programme of Human Research Manpower" (PENED) and co-financed by National and  ...  -European Social Fund and 25% from the Greek Ministry of Development-General Secretariat of Research and Technology). The authors would also like to thank Dr.  ...  (A 1 ) Zoomed area of the peptides map, showing the existence of vertical streaks and peptides with different expression levels and identification confidence.  ... 
doi:10.1016/j.jbi.2009.01.007 pmid:19535004 fatcat:bkn4zgftevckvm7ae33veirvy4

MMS2plot: an R package for visualizing multiple MS/MS spectra for groups of modified and non-modified peptides [article]

Lei Li, Shawn Li, Liya Ming, Yang Zou, Yiming Zhao, Luna Zhang, Ningning He, Zhen Chen
2020 bioRxiv   pre-print
Herein, we describe MMS2plot, an R package for visualizing peptide-spectrum matches (PSMs) for multiple peptides.  ...  Such tools would preferably have the ability to allow comparison of fragment ion spectra and retention time between the modified and unmodified peptide pairs or group.  ...  Acknowledgments This work was supported, in part, by grants (to SSCL) from the Canadian Institute of  ... 
doi:10.1101/2020.03.13.989152 fatcat:6ysd5iixereapa6v2sdmfta4fm

Performing Comparative Peptidomics Analyses of Salmonella from Different Growth Conditions [chapter]

Joshua N. Adkins, Heather Mottaz, Thomas O. Metz, Charles Ansong, Nathan P. Manes, Richard D. Smith, Fred Heffron
2009 Msphere  
Comparison of peptides present in lysates prepared from Salmonella grown under different conditions provided a unique insight into cellular degradation processes as well as identification of novel peptides  ...  Pre-fractionation of peptides allowed identification of small proteins and protein degradation products that would normally be overlooked.  ...  The comparative analyses of the peptide and protein abundances are enabled with the use of data mining tools that offer clustering and heatmap visualization of the matrix form of the experimental results  ... 
doi:10.1007/978-1-60761-535-4_2 pmid:20013197 fatcat:5khw4j4d6nbirblb3axlshj3xa

SpliceVista, a Tool for Splice Variant Identification and Visualization in Shotgun Proteomics Data

Yafeng Zhu, Lina Hultin-Rosenberg, Jenny Forshed, Rui M. M. Branca, Lukas M. Orre, Janne Lehtiö
2014 Molecular & Cellular Proteomics  
The visualization module plots the exon composition of each splice variant and aligns identified peptides to its transcript positions.  ...  Here, we present SpliceVista, a tool for splice variant identification and visualization based on mass spectrometry (MS) proteomics data.  ...  Second, the given genomic coordinates of each peptide make it possible to compare with the results from RNA level experiments such as RT-PCR and RNA-seq.  ... 
doi:10.1074/mcp.m113.031203 pmid:24692640 pmcid:PMC4047474 fatcat:stdj2kivlvdwvn72yspmsvujyu

Viewing the proteome: How to visualize proteomics data?

Eystein Oveland, Thilo Muth, Erdmann Rapp, Lennart Martens, Frode S. Berven, Harald Barsnes
2015 Proteomics  
The unique challenges and current solutions for visualizing the different aspects of proteomics data, from acquired spectra via protein identification and quantification to pathway analysis, are discussed  ...  In this review we therefore present an overview of the different ways in which proteomics software supports the visualization and interpretation of proteomics data.  ...  To compare peak detection methods one can visualize raw data together with peak picking and identification results.  ... 
doi:10.1002/pmic.201400412 pmid:25504833 fatcat:6wor2knbe5cbxfrwl2bv47nrmm

Platelet Proteomics: Essentials for Understanding and Application

Jan Moebius, René-Peiman Zahedi, Albert Sickmann
2006 Transfusion Medicine and Hemotherapy  
The development of the last 10 years has provided a complex set of different separation tools and analytical techniques for proteins and their modifications.  ...  We will focus on methodical aspects of the different techniques as well as their potential and limitations in order to provide an orientation guide for further projects.  ...  Compared to MALDI-MS, this method has better identification rates due to the concentration of peptides during HPLC separation, rendering the analysis more sensitive and less susceptible to impurities.  ... 
doi:10.1159/000091372 fatcat:6wvwzn5ejbeb3minszbkf7bqn4

Broad characterization of endogenous peptides in the tree shrew visual system

Vaclav Ranc, Filomena Petruzziello, Robert Kretz, Enrike G. Argandoña, Xiaozhe Zhang, Gregor Rainer
2012 Journal of Proteomics  
We observed generally lower abundance of peptides in the LGN compared to V1 and SC.  ...  A total of 26 peptides, for example GAV and neuropeptide K were identified in the visual system for the first time.  ...  Acknowledgements This work is supported by the Research Project of the Ministry of Education of the Czech Republic No. MSM6198959216 and by the SNF R'Equip 316000-121308 and a EURYI award to GR.  ... 
doi:10.1016/j.jprot.2012.01.028 pmid:22326962 fatcat:3zkjh5cb3rafdhooaqwj6evx3m

PRIDE Inspector Toolsuite: Moving Toward a Universal Visualization Tool for Proteomics Data Standard Formats and Quality Assessment of ProteomeXchange Datasets

Yasset Perez-Riverol, Qing-Wei Xu, Rui Wang, Julian Uszkoreit, Johannes Griss, Aniel Sanchez, Florian Reisinger, Attila Csordas, Tobias Ternent, Noemi del-Toro, Jose A. Dianes, Martin Eisenacher (+2 others)
2015 Molecular & Cellular Proteomics  
The PRIDE Inspector Toolsuite supports the handling and visualization of differ-From the ‡European Molecular  ...  to design and implement a new suite of algorithms and libraries that would build upon the success of the original PRIDE Inspector and would enable users to visualize and validate PX "complete" submissions  ...  The increasing adoption of standard data formats (11) facilitates the validation, reproducibility, and comparability of results produced by different instruments and software platforms.  ... 
doi:10.1074/mcp.o115.050229 pmid:26545397 pmcid:PMC4762524 fatcat:qsbmsluw5rextnjuytbcwkixuq

Simple Sodium Dodecyl Sulfate-Assisted Sample Preparation Method for LC-MS-Based Proteomics Applications

Jian-Ying Zhou, Geoffrey P. Dann, Tujin Shi, Lu Wang, Xiaoli Gao, Dian Su, Carrie D. Nicora, Anil K. Shukla, Ronald J. Moore, Tao Liu, David G. Camp II, Richard D. Smith (+1 others)
2012 Analytical Chemistry  
(>95%) was observed for <20 μg of peptides.  ...  methods and analyzed using LC-MS/MS.  ...  Application of the SDS-assisted sample preparation methods for proteome profiling To evaluate the applicability of SDS-assisted proteomic sample preparation, we compared proteome profiling results of different  ... 
doi:10.1021/ac203394r pmid:22339560 pmcid:PMC3310275 fatcat:qz3lqgyeefe37eayyuti2bta54

Proteomic Parsimony through Bipartite Graph Analysis Improves Accuracy and Transparency

Bing Zhang, Matthew C. Chambers, David L. Tabb
2007 Journal of Proteome Research  
Supporting Information Available: Figures of the greedy set cover algorithm and the database size effect on the sensitivity of peptide identification.  ...  We use bipartite graphs for the visualization of the protein assembly results to render the parsimony analysis process transparent to users.  ...  , and provides a natural way for visualizing the results.  ... 
doi:10.1021/pr070230d pmid:17676885 pmcid:PMC2810678 fatcat:kqdjuboqpbby7ejgloqkdthcfi

DO-MS: Data-Driven Optimization of Mass Spectrometry Methods

R Gray Huffman, Albert Tian Chen, Harrison Specht, Nikolai Slavov
2019 Journal of Proteome Research  
For example, by using DO-MS to optimize the sampling of the elution peak apexes, we increased ion accumulation times and apex sampling, which resulted in a 370% more efficient delivery of ions for MS2  ...  This interdependence makes it challenging to specifically pinpoint the sources of problems in the LC-MS/MS methods and approaches for resolving them.  ...  This project was supported by a New Innovator Award from the NIGMS from the National Institutes of Health to N.S. under award number DP2GM123497.  ... 
doi:10.1021/acs.jproteome.9b00039 pmid:31081635 pmcid:PMC6737531 fatcat:ylpqzeao5facnfxsbmbo372w5y

Proline: an efficient and user-friendly software suite for large-scale proteomics

2020 Bioinformatics  
The proteomics field requires the production and publication of reliable mass spectrometry-based identification and quantification results.  ...  Here, we present Proline, a robust software suite for analysis of MS-based proteomics data which collects, processes, allows visualization and publication of proteomics datasets.  ...  Acknowledgements The authors thank Virginie Brun and Myriam Ferro for constructive criticism of the article and Maighread Gallagher-Gambarelli for advice on English usage and editing suggestions.  ... 
doi:10.1093/bioinformatics/btaa118 pmid:32096818 pmcid:PMC7214047 fatcat:xan7jh6ehbhufm6aag2p7zicea

A Fully Automatic and Efficient Methodology for Peptide Activity Identification Using their 3D Conformations

Azzam Alwan, Remi Cogranne, Pierre Beauseroy, Edith Grall-Maes, Nicolas Belloy, Stephanie Baud, Manuel Dauchez, Sebastien Almagro
2021 IEEE Access  
Another manner to visualize the results of main conformation identification is via the so-called dendogram presented in the Figure 7 .  ...  Section VI addresses the problem of comparing main conformations extracted from several different peptides.  ... 
doi:10.1109/access.2021.3091939 fatcat:esa3t7p3ifanngvacvtcph6i3u

CLMSVault: A Software Suite for Protein Cross-Linking Mass-Spectrometry Data Analysis and Visualization

Mathieu Courcelles, Jasmin Coulombe-Huntington, Émilie Cossette, Anne-Claude Gingras, Pierre Thibault, Mike Tyers
2017 Journal of Proteome Research  
CLMSVault provides filtering, comparison, and visualization tools to support CL-MS analyses, and includes a workflow for label-free quantification of cross-linked peptides.  ...  Although a number of algorithms now exist for the identification of cross-linked peptides from mass spectral data, a dearth of user-friendly analysis tools represent a practical bottleneck to the broad  ...  Acknowledgments Funding Sources We thank members of the Rappsilber lab for providing access and assistance to Xi and xiNET software tools, Éric Bonneil for his assistance with LC-MS instrumentation and  ... 
doi:10.1021/acs.jproteome.7b00205 pmid:28537071 pmcid:PMC5994346 fatcat:2kbpq45bjjfyve66khvzcmvvai
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