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

Qi, Da; Lawless, Craig; Teleman, Johan; Levander, Fredrik; Holman, Stephen W.; Hubbard, Simon J.; Jones, Andrew R.

doi:10.1002/pmic.201400281

Cited by 7 publications

(3 citation statements)

References 14 publications

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“…Protein profiling requires software and algorithms for protein identification, quantitation, functional and structural characterization, location, interaction, networks, integration, visualization, and deposition in databases and repositories. These softwares are continuously created, improved, and updated . Recently, Sakata and Komatsu have surveyed and reviewed plant proteomics databases and websites as well as recent technologies related to data collection and annotation.…”

Section: Wet and Dry Methodologiesmentioning

confidence: 99%

A year (2014–2015) of plants in Proteomics journal. Progress in wet and dry methodologies, moving from protein catalogs, and the view of classic plant biochemists

et al. 2016

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The present review is an update of the previous one published in Proteomics 2015 Reviews special issue [Jorrin-Novo, J. V. et al., Proteomics 2015, 15, 1089-1112] covering the July 2014-2015 period. It has been written on the bases of the publications that appeared in Proteomics journal during that period and the most relevant ones that have been published in other high-impact journals. Methodological advances and the contribution of the field to the knowledge of plant biology processes and its translation to agroforestry and environmental sectors will be discussed. This review has been organized in four blocks, with a starting general introduction (literature survey) followed by sections focusing on the methodology (in vitro, in vivo, wet, and dry), proteomics integration with other approaches (systems biology and proteogenomics), biological information, and knowledge (cell communication, receptors, and signaling), ending with a brief mention of some other biological and translational topics to which proteomics has made some contribution.

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Section: Wet and Dry Methodologiesmentioning

confidence: 99%

A year (2014–2015) of plants in Proteomics journal. Progress in wet and dry methodologies, moving from protein catalogs, and the view of classic plant biochemists

et al. 2016

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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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“…To capture the results of identification approaches, such as the use of proteomics search engines, the mzIdentML format was released as a stable version (version 1.1) in the last quarter of 2011, and published in 2012 ( 3 ). A separate format for quantitative results was built, called mzQuantML—initially defined for large scale discovery approaches ( 4 ) and updated to also support targeted approaches, such as selected reaction monitoring ( 5 ). More recently, in 2014, a lighter tab-delimited format called mzTab was also developed by the PSI to capture identification and quantification results ( 6 ).…”

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confidence: 99%

The mzIdentML Data Standard Version 1.2, Supporting Advances in Proteome Informatics

Vizcaíno

Mayer

Perkins

et al. 2017

Molecular & Cellular Proteomics

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The first stable version of the Proteomics Standards Initiative mzIdentML open data standard (version 1.1) was published in 2012—capturing the outputs of peptide and protein identification software. In the intervening years, the standard has become well-supported in both commercial and open software, as well as a submission and download format for public repositories. Here we report a new release of mzIdentML (version 1.2) that is required to keep pace with emerging practice in proteome informatics. New features have been added to support: (1) scores associated with localization of modifications on peptides; (2) statistics performed at the level of peptides; (3) identification of cross-linked peptides; and (4) support for proteogenomics approaches. In addition, there is now improved support for the encoding of de novo sequencing of peptides, spectral library searches, and protein inference. As a key point, the underlying XML schema has only undergone very minor modifications to simplify as much as possible the transition from version 1.1 to version 1.2 for implementers, but there have been several notable updates to the format specification, implementation guidelines, controlled vocabularies and validation software. mzIdentML 1.2 can be described as backwards compatible, in that reading software designed for mzIdentML 1.1 should function in most cases without adaptation. We anticipate that these developments will provide a continued stable base for software teams working to implement the standard. All the related documentation is accessible at http://www.psidev.info/mzidentml.

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

Cited by 7 publications

References 14 publications

A year (2014–2015) of plants in Proteomics journal. Progress in wet and dry methodologies, moving from protein catalogs, and the view of classic plant biochemists

A year (2014–2015) of plants in Proteomics journal. Progress in wet and dry methodologies, moving from protein catalogs, and the view of classic plant biochemists

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

The mzIdentML Data Standard Version 1.2, Supporting Advances in Proteome Informatics

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