A software toolkit and interface for performing stable isotope labeling and top3 quantification using Progenesis LC-MS.
Da Qi,Philip Brownridge,Dong Xia,Katherine Mackay,Faviel F. Gonzalez-Galarza,Jenna Kenyani,Victoria M. Harman,Robert J. Beynon,Andrew R. Jones +8 more
TLDR
A Java programming interface is developed that can use the output files produced by Progenesis, allowing the basic MS features quantified across replicates to be used in a range of different experimental methods.Abstract:
Numerous software packages exist to provide support for quantifying peptides and proteins from mass spectrometry (MS) data. However, many support only a subset of experimental methods or instrument types, meaning that laboratories often have to use multiple software packages. The Progenesis LC-MS software package from Nonlinear Dynamics is a software solution for label-free quantitation. However, many laboratories using Progenesis also wish to employ stable isotope-based methods that are not natively supported in Progenesis. We have developed a Java programming interface that can use the output files produced by Progenesis, allowing the basic MS features quantified across replicates to be used in a range of different experimental methods. We have developed post-processing software (the Progenesis Post-Processor) to embed Progenesis in the analysis of stable isotope labeling data and top3 pseudo-absolute quantitation. We have also created export ability to the new data standard, mzQuantML, produced by the Proteomics Standards Initiative to facilitate the development and standardization process. The software is provided to users with a simple graphical user interface for accessing the different features. The underlying programming interface may also be used by Java developers to develop other routines for analyzing data produced by Progenesis.read more
Citations
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Journal ArticleDOI
Label-free quantification in ion mobility-enhanced data-independent acquisition proteomics.
TL;DR: A detailed protocol for a label-free quantitative proteomics workflow based on ion mobility–enhanced DIA, which synchronizes precursor ion drift times with collision energies to improve precursor fragmentation efficiency.
Journal ArticleDOI
Critical assessment of proteome-wide label-free absolute abundance estimation strategies.
TL;DR: Five popular low‐cost and easily implemented quantification methods are evaluated and it is shown that only the Top3 method is directly proportional to protein abundance over the full quantification range and is the preferred method in the absence of reference protein measurements.
Journal ArticleDOI
ANPELA: analysis and performance assessment of the label-free quantification workflow for metaproteomic studies.
Jing Tang,Jing Tang,Jianbo Fu,Yunxia Wang,Bo Li,Yinghong Li,Yinghong Li,Qingxia Yang,Qingxia Yang,Xuejiao Cui,Xuejiao Cui,Jiajun Hong,Xiaofeng Li,Xiaofeng Li,Yu Zong Chen,Weiwei Xue,Feng Zhu,Feng Zhu +17 more
TL;DR: ANPELA has a unique ability to evaluate the performance of whole LFQ workflow and enables the discovery of the optimal LFQs by the comprehensive performance ranking of all 560 workflows.
Journal ArticleDOI
The mzQuantML Data Standard for Mass Spectrometry–based Quantitative Studies in Proteomics
Mathias Walzer,Da Qi,Gerhard Mayer,Julian Uszkoreit,Martin Eisenacher,Timo Sachsenberg,Faviel F. Gonzalez-Galarza,Jun Fan,Conrad Bessant,Eric W. Deutsch,Florian Reisinger,Juan Antonio Vizcaíno,J. Alberto Medina-Aunon,Juan Pablo Albar,Oliver Kohlbacher,Andrew R. Jones +15 more
TL;DR: The mzQuantML data standard is developed, which can represent quantitative data about regions in two-dimensional retention time versus mass/charge space, peptides, and proteins and protein groups, and it offers limited support for small molecule (metabolomic) data.
Journal ArticleDOI
Quantitative proteomics in the field of microbiology.
TL;DR: This review will focus on the vast range of techniques practically applied in current research with an introduction of the workflows used for quantitative comparisons, a description of the advantages/disadvantages of the various methods, reference to hallmark publications and presentation of applications in current microbial research.
References
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MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification.
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Multiplexed Protein Quantitation in Saccharomyces cerevisiae Using Amine-reactive Isobaric Tagging Reagents
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Absolute Quantification of Proteins by LCMSE A Virtue of Parallel ms Acquisition
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