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

Qi, Da; Lawless, Craig; Teleman, Johan LU ; Levander, Fredrik LU ; Holman, Stephen W.; Hubbard, Simon and Jones, Andrew R. (2015) In Proteomics 15(15). p.2592-2596
Abstract
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 N-15), (iii) MS2 tag-based (iTRAQ or tandem mass tags), and (iv) spectral counting. We present an update to mzQuantML for supporting SRM techniques.... (More)
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 N-15), (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. (Less)
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author
organization
publishing date
type
Contribution to journal
publication status
published
subject
keywords
Bioinformatics, mzQuantML, Proteomics standards initiative, SRM
in
Proteomics
volume
15
issue
15
pages
2592 - 2596
publisher
John Wiley & Sons
external identifiers
  • wos:000359061800006
  • scopus:84938744390
ISSN
1615-9861
DOI
10.1002/pmic.201400281
language
English
LU publication?
yes
id
c883f5da-70c6-49aa-839a-fc38056c2e5c (old id 7979233)
date added to LUP
2015-09-25 12:49:25
date last changed
2017-07-23 03:08:36
@article{c883f5da-70c6-49aa-839a-fc38056c2e5c,
  abstract     = {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 N-15), (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.},
  author       = {Qi, Da and Lawless, Craig and Teleman, Johan and Levander, Fredrik and Holman, Stephen W. and Hubbard, Simon and Jones, Andrew R.},
  issn         = {1615-9861},
  keyword      = {Bioinformatics,mzQuantML,Proteomics standards initiative,SRM},
  language     = {eng},
  number       = {15},
  pages        = {2592--2596},
  publisher    = {John Wiley & Sons},
  series       = {Proteomics},
  title        = {Representation of selected-reaction monitoring data in the mzQuantML data standard},
  url          = {http://dx.doi.org/10.1002/pmic.201400281},
  volume       = {15},
  year         = {2015},
}