The mzqLibrary – An open source Java library supporting the HUPO‐PSI quantitative proteomics standard

Qi, Da; Zhang, Huaizhong; Fan, Jun; Perkins, Simon; Pisconti, Addolorata; Simpson, Deborah M.; Bessant, Conrad; Hubbard, Simon J.; Jones, Andrew R.

doi:10.1002/pmic.201400535

Cited by 5 publications

(4 citation statements)

References 33 publications

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“…Proteins were quantified using unique peptides and protein abundance was calculated from the sum of all the unique peptide ion abundances corresponding to that protein. Protein quantification was further validated by using a separate software package, the mzqLibrary 28 , which yielded results comparable to the results obtained with ProgenesisQI.…”

Section: Methodsmentioning

confidence: 82%

“…In order to identify global changes occurring in the extracellular proteome of dystrophic muscle, we developed a method to obtain protein fractions enriched in extracellular proteins. A brief outline of the method for muscle sample preparation was previously presented 28 , however the efficiency of the method in enriching the sample preparation with extracellular proteins was not investigated. Here we provide a full description of the method and investigate its efficiency in enriching the sample preparation with extracellular proteins.…”

Section: Resultsmentioning

confidence: 99%

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Elastase levels and activity are increased in dystrophic muscle and impair myoblast cell survival, proliferation and differentiation

Arecco

Clarke

Jones

et al. 2016

Sci Rep

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In Duchenne muscular dystrophy, progressive loss of muscle tissue is accompanied by fibrosis, chronic inflammation and reduced muscle regenerative capacity. Although much is known about the development of fibrosis and chronic inflammation in muscular dystrophy, less is known about how they are mechanistically linked to loss of muscle regenerative capacity. We have developed a proteomics method to discover dystrophy-associated changes in the muscle progenitor cell niche, which identified serine proteases, and especially neutrophil elastase, as candidates. We show that elastase activity is increased in dystrophic (mdx4cv) muscle and impairs myoblast survival in culture. While the effect of elastase on C2C12 cell survival correlates with the kinetics of elastase-mediated degradation of the substrate to which the cells adhere, the effect of elastase on satellite cell-derived primary myoblast growth and differentiation is substrate-independent and even more dramatic than the effect on C2C12 cells, suggesting a detrimental role for elastase on myogenesis in vivo. Additionally, elastase impairs differentiation of both primary and C2C12 myoblasts into myotubes. Our findings evidence the importance of neutrophil-mediated inflammation in muscular dystrophy and indicate elastase-mediated regulation of myoblast behaviour as a potential mechanism underlying loss of regenerative capacity in dystrophic muscle.

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Section: Methodsmentioning

confidence: 82%

Section: Resultsmentioning

confidence: 99%

Elastase levels and activity are increased in dystrophic muscle and impair myoblast cell survival, proliferation and differentiation

Arecco

Clarke

Jones

et al. 2016

Sci Rep

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“…The goal of the Vancouver workshop was to focus on the implementation of the current set of proteomics standards and to review the steps that have been taken over the year. The program started with an overview and recent advances of the Proteomics Standards Initiative (PSI) and highlighted recent publications − on the current set of standards and the progress made at the 2015 PSI workshop in Seattle, USA which included the PSI Extended FASTA File (PEFF) format.…”

Section: B/d-hpp Workhops At 2015 Hupo World Congress In Vancouvermentioning

confidence: 99%

Highlights of the Biology and Disease-driven Human Proteome Project, 2015–2016

et al. 2016

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The Biology and Disease-driven Human Proteome Project (B/D-HPP) is aimed at supporting and enhancing the broad use of state-of-the-art proteomic methods to characterize and quantify proteins for in-depth understanding of the molecular mechanisms of biological processes and human disease. Based on a foundation of the pre-existing HUPO initiatives begun in 2002, the B/D-HPP is designed to provide standardized methods and resources for mass spectrometry and specific protein affinity reagents and facilitate accessibility of these resources to the broader life sciences research and clinical communities. Currently there are 22 B/D-HPP initiatives and 3 closely related HPP resource pillars. The B/D-HPP groups are working to define sets of protein targets that are highly relevant to each particular field to deliver relevant assays for the measurement of these selected targets and to disseminate and make publicly accessible the information and tools generated. Major developments are the 2016 publications of the Human SRM Atlas and of “popular protein sets” for six organ systems. Here we present the current activities and plans of the BD-HPP initiatives as highlighted in numerous B/D-HPP workshops at the 14th annual HUPO 2015 World Congress of Proteomics in Vancouver, Canada.

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“…As well as the tools reported here for exporting mzQuantML-SRM files, a number of other developments are on-going for importing mzQuantML. Our group and colleagues have developed the mzQuantML viewer and library ( http://code.google.com/p/mzq-lib/ ) [ 14 ]. In the viewer, users can open mzQuantML files (including those files containing SRM data) and view different QuantLayers in the file.…”

mentioning

confidence: 99%

Representation of selected‐reaction monitoring data in the mzQuantML data standard

Lawless

Teleman

et al. 2015

Proteomics

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The mzQuantML data standard was designed to capture the output of quantitative software in proteomics, to support submissions to public repositories, development of visualization software and pipeline/modular approaches. The standard is designed around a common core that can be extended to support particular types of technique through the release of semantic rules that are checked by validation software. The first release of mzQuantML supported four quantitative proteomics techniques via four sets of semantic rules: (i) intensity-based (MS1) label free, (ii) MS1 label-based (such as SILAC or N15), (iii) MS2 tag-based (iTRAQ or tandem mass tags), and (iv) spectral counting. We present an update to mzQuantML for supporting SRM techniques. The update includes representing the quantitative measurements, and associated meta-data, for SRM transitions, the mechanism for inferring peptide-level or protein-level quantitative values, and support for both label-based or label-free SRM protocols, through the creation of semantic rules and controlled vocabulary terms. We have updated the specification document for mzQuantML (version 1.0.1) and the mzQuantML validator to ensure that consistent files are produced by different exporters. We also report the capabilities for production of mzQuantML files from popular SRM software packages, such as Skyline and Anubis.

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The mzqLibrary – An open source Java library supporting the HUPO‐PSI quantitative proteomics standard

Cited by 5 publications

References 33 publications

Elastase levels and activity are increased in dystrophic muscle and impair myoblast cell survival, proliferation and differentiation

Elastase levels and activity are increased in dystrophic muscle and impair myoblast cell survival, proliferation and differentiation

Highlights of the Biology and Disease-driven Human Proteome Project, 2015–2016

Representation of selected‐reaction monitoring data in the mzQuantML data standard

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