Proceedings ArticleDOI
QuantWiz: A Parallel Software Package for LC-MS-based Label-Free Protein Quantification
Jing Wang,Yunquan Zhang,Xianyi Zhang,Xiangzheng Sun,Zelin Hu,Sujun Li,Rong Zeng +6 more
- pp 683-687
TLDR
This paper described the framework design and prototype development of this new domestic parallel software package called QuantWiz for high performance Liquid Chromatography (short for LC)-MS-based label-free protein quantification, and implemented the parallelization version.Abstract:
Nowadays Proteomics becomes more and more popular in life science. Protein quantification, especially based on mass spectrometry (short for MS) method, is perceived as an essential part of research on proteomics. There have been some algorithms and software for protein quantification based on MS. But they have difficulties on portability, applicability and longtime running. To solve these problems, we developed a new domestic parallel software package called QuantWiz for high performance Liquid Chromatography (short for LC)-MS-based label-free protein quantification. In this paper, we described the framework design and prototype development of this high performance software package firstly. Also, user interface developed for the visualization of QuantWiz is introduced. Finally, we showed implementation of the parallelization version and performance of some experiments on this software package.read more
Citations
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Proceedings ArticleDOI
QuantWiz: A scalable parallel software package for label-free protein quantification
TL;DR: This paper compared the LC-MS-based label-free protein quantification accuracy of QuantWiz with the well-known Census software package, and designed and implemented a distributed memory version parallel algorithm for Quant Wiz.
References
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Book
Data Mining
TL;DR: In this paper, generalized estimating equations (GEE) with computing using PROC GENMOD in SAS and multilevel analysis of clustered binary data using generalized linear mixed-effects models with PROC LOGISTIC are discussed.
Journal ArticleDOI
Mass spectrometry-based proteomics
Ruedi Aebersold,Matthias Mann +1 more
TL;DR: The ability of mass spectrometry to identify and, increasingly, to precisely quantify thousands of proteins from complex samples can be expected to impact broadly on biology and medicine.
Journal ArticleDOI
A common open representation of mass spectrometry data and its application to proteomics research
Patrick G. A. Pedrioli,Jimmy K. Eng,Robert Hubley,Mathijs Vogelzang,Eric W. Deutsch,Brian Raught,Brian S. Pratt,Erik Nilsson,Ruth Hogue Angeletti,Rolf Apweiler,Kei Cheung,Catherine E. Costello,Henning Hermjakob,Sequin Huang,Randall K. Julian,Eugene A. Kapp,Mark E. McComb,Stephen G. Oliver,Gilbert S. Omenn,Norman W. Paton,Richard J. Simpson,Richard D. Smith,Chris F. Taylor,Weimin Zhu,Ruedi Aebersold +24 more
TL;DR: The 'mzXML' format is introduced, an open, generic XML (extensible markup language) representation of MS data that will facilitate data management, interpretation and dissemination in proteomics research.
Journal ArticleDOI
A uniform proteomics MS/MS analysis platform utilizing open XML file formats.
TL;DR: The Trans‐Proteomic Pipeline is described, which makes use of open XML file formats for storage of data at the raw spectral data, peptide, and protein levels, and enables uniform analysis and exchange of MS/MS data generated from a variety of different instruments, and assigned peptides using a range of different database search programs.
Journal ArticleDOI
Automated statistical analysis of protein abundance ratios from data generated by stable-isotope dilution and tandem mass spectrometry.
TL;DR: The utility of the ASAPRatio program was clearly demonstrated by its speed and the accuracy of the generated protein abundance ratios and by its capability to identify specific core components of the RNA polymerase II transcription complex within a high background of copurifying proteins.