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What is mzXML good for?

Publication ,  Journal Article
Lin, SM; Zhu, L; Winter, AQ; Sasinowski, M; Kibbe, WA
Published in: Expert Rev Proteomics
December 2005

mzXML (extensible markup language) is one of the pioneering data formats for mass spectrometry-based proteomics data collection. It is an open data format that has benefited and evolved as a result of the input of many groups, and it continues to evolve. Due to its dynamic history, its structure, purpose and applicability have all changed with time, meaning that groups that have looked at the standard at different points during its evolution have differing impressions of the usefulness of mzXML. In discussing mzXML, it is important to understand what mzXML is not. First, mzXML does not capture the raw data. Second, mzXML is not sufficient for regulatory submission. Third, mzXML is not optimized for computation and, finally, mzXML does not capture the experiment design. In general, it is the authors' opinion that XML is not a panacea for bioinformatics or a substitute for good data representation, and groups that want to use mzXML (or other XML-based representations) directly for data storage or computation will encounter performance and scalability problems. With these limitations in mind, the authors conclude that mzXML is, nonetheless, an indispensable data exchange format for proteomics.

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Published In

Expert Rev Proteomics

DOI

EISSN

1744-8387

Publication Date

December 2005

Volume

2

Issue

6

Start / End Page

839 / 845

Location

England

Related Subject Headings

  • Proteomics
  • Programming Languages
  • Mass Spectrometry
  • Computational Biology
  • Biochemistry & Molecular Biology
  • 3205 Medical biochemistry and metabolomics
  • 3101 Biochemistry and cell biology
  • 0601 Biochemistry and Cell Biology
 

Citation

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Lin, S. M., Zhu, L., Winter, A. Q., Sasinowski, M., & Kibbe, W. A. (2005). What is mzXML good for? Expert Rev Proteomics, 2(6), 839–845. https://doi.org/10.1586/14789450.2.6.839
Lin, Simon M., Lihua Zhu, Andrew Q. Winter, Maciek Sasinowski, and Warren A. Kibbe. “What is mzXML good for?Expert Rev Proteomics 2, no. 6 (December 2005): 839–45. https://doi.org/10.1586/14789450.2.6.839.
Lin SM, Zhu L, Winter AQ, Sasinowski M, Kibbe WA. What is mzXML good for? Expert Rev Proteomics. 2005 Dec;2(6):839–45.
Lin, Simon M., et al. “What is mzXML good for?Expert Rev Proteomics, vol. 2, no. 6, Dec. 2005, pp. 839–45. Pubmed, doi:10.1586/14789450.2.6.839.
Lin SM, Zhu L, Winter AQ, Sasinowski M, Kibbe WA. What is mzXML good for? Expert Rev Proteomics. 2005 Dec;2(6):839–845.

Published In

Expert Rev Proteomics

DOI

EISSN

1744-8387

Publication Date

December 2005

Volume

2

Issue

6

Start / End Page

839 / 845

Location

England

Related Subject Headings

  • Proteomics
  • Programming Languages
  • Mass Spectrometry
  • Computational Biology
  • Biochemistry & Molecular Biology
  • 3205 Medical biochemistry and metabolomics
  • 3101 Biochemistry and cell biology
  • 0601 Biochemistry and Cell Biology