jmzML, an open-source Java API for mzML, the PSI standard for MS data
We here present jmzML, a Java API for the Proteomics Standards Initiative mzML data standard. Based on the Java Architecture for XML Binding and XPath-based XML indexer random-access XML parser, jmzML can handle arbitrarily large files in minimal memory, allowing easy and efficient processing of mzM...
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| Published in: | Proteomics (Weinheim) Vol. 10; no. 7; pp. 1332 - 1335 |
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| Main Authors: | , , |
| Format: | Journal Article |
| Language: | English |
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Weinheim
Wiley-VCH Verlag
01.04.2010
WILEY-VCH Verlag WILEY‐VCH Verlag Wiley-VCH |
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| ISSN: | 1615-9853, 1615-9861, 1615-9861 |
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| Abstract | We here present jmzML, a Java API for the Proteomics Standards Initiative mzML data standard. Based on the Java Architecture for XML Binding and XPath-based XML indexer random-access XML parser, jmzML can handle arbitrarily large files in minimal memory, allowing easy and efficient processing of mzML files using the Java programming language. jmzML also automatically resolves internal XML references on-the-fly. The library (which includes a viewer) can be downloaded from http://jmzml.googlecode.com. |
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| AbstractList | We here present jmzML, a Java API for the Proteomics Standards Initiative mzML data standard. Based on the Java Architecture for XML Binding and XPath-based XML indexer random-access XML parser, jmzML can handle arbitrarily large files in minimal memory, allowing easy and efficient processing of mzML files using the Java programming language. jmzML also automatically resolves internal XML references on-the-fly. The library (which includes a viewer) can be downloaded from http://jmzml.googlecode.com.We here present jmzML, a Java API for the Proteomics Standards Initiative mzML data standard. Based on the Java Architecture for XML Binding and XPath-based XML indexer random-access XML parser, jmzML can handle arbitrarily large files in minimal memory, allowing easy and efficient processing of mzML files using the Java programming language. jmzML also automatically resolves internal XML references on-the-fly. The library (which includes a viewer) can be downloaded from http://jmzml.googlecode.com. We here present jmzML, a Java API for the Proteomics Standards Initiative mzML data standard. Based on the Java Architecture for XML Binding and XPath‐based XML indexer random‐access XML parser, jmzML can handle arbitrarily large files in minimal memory, allowing easy and efficient processing of mzML files using the Java programming language. jmzML also automatically resolves internal XML references on‐the‐fly. The library (which includes a viewer) can be downloaded from http://jmzml.googlecode.com. |
| Author | Martens, Lennart Reisinger, Florian Côté, Richard G. |
| Author_xml | – sequence: 1 fullname: Côté, Richard G – sequence: 2 fullname: Reisinger, Florian – sequence: 3 fullname: Martens, Lennart |
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| CitedBy_id | crossref_primary_10_1002_pmic_201200268 crossref_primary_10_1016_j_chroma_2014_11_030 crossref_primary_10_1002_pmic_201100578 crossref_primary_10_1038_ncomms6277 crossref_primary_10_1089_omi_2012_0022 crossref_primary_10_1002_pmic_201400036 crossref_primary_10_1016_j_jprot_2010_06_008 crossref_primary_10_1016_j_talanta_2010_10_029 crossref_primary_10_1093_nar_gks1262 crossref_primary_10_1093_nar_gkv1145 crossref_primary_10_1016_j_chroma_2015_07_108 crossref_primary_10_1021_jasms_4c00174 crossref_primary_10_1186_1471_2105_12_70 crossref_primary_10_1002_pmic_201200532 crossref_primary_10_1586_epr_12_51 crossref_primary_10_1186_s12859_017_1883_6 crossref_primary_10_1002_pmic_201300281 crossref_primary_10_1016_j_bbapap_2013_04_004 crossref_primary_10_1002_pmic_201300560 crossref_primary_10_1016_j_bbapap_2013_02_017 crossref_primary_10_1016_j_jprot_2015_06_015 crossref_primary_10_1002_pmic_201290016 crossref_primary_10_1371_journal_pone_0125108 crossref_primary_10_1016_j_chroma_2014_09_084 crossref_primary_10_1016_j_jprot_2015_06_013 crossref_primary_10_1093_jamia_ocv001 crossref_primary_10_1186_s12859_015_0752_4 crossref_primary_10_1089_omi_2010_0111 crossref_primary_10_1038_s43586_024_00318_2 crossref_primary_10_1016_j_bbapap_2013_02_032 crossref_primary_10_1016_j_chroma_2014_11_018 |
| Cites_doi | 10.1002/pmic.200401303 10.1093/bioinformatics/btn323 10.1186/1471-2105-9-163 10.1038/nbt1031 10.1002/pmic.200900189 10.1002/pmic.200300694 10.1002/pmic.200890049 |
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| References | Kessner, D., Chambers, M., Burke, R., Agus, D., Mallick, P., ProteoWizard: open source software for rapid proteomics tools development. Bioinformatics 2008, 24, 2534-2536. Orchard, S., Hermjakob, H., Julian, R. K., Runte, K. et al., Common interchange standards for proteomics data: public availability of tools and schema. Proteomics 2004, 4, 490-491. Sturm, M., Bertsch, A., Gröpl, C., Hildebrandt, A. et al., OpenMS - an open-source software framework for mass spectrometry. BMC Bioinformatics 2008, 9, 163. Martens, L., Hermjakob, H., Jones, P., Adamski, M. et al., PRIDE: the proteomics identifications database. Proteomics 2005, 5, 3537-3545. Deutsch, E., mzML: A single, unifying data format for mass spectrometer output. Proteomics 2008, 8, 2776-2777. Montecchi-Palazzi, L., Kerrien, S., Reisinger, F., Aranda, B. et al., The PSI semantic validator: a framework to check MIAPE compliance of proteomics data. Proteomics 2009, 9, 5112-5119. Pedrioli, P. G. A., Eng, J. K., Hubley, R., Vogelzang, M. et al., A common open representation of mass spectrometry data and its application to proteomics research. Nat. Biotechnol. 2004, 22, 1459-1466. 2004; 4 2008; 9 2005; 5 2004; 22 2009; 9 2008; 8 2008; 24 e_1_2_3_5_2 e_1_2_3_4_2 e_1_2_3_3_2 e_1_2_3_2_2 e_1_2_3_8_2 e_1_2_3_7_2 e_1_2_3_6_2 |
| References_xml | – reference: Kessner, D., Chambers, M., Burke, R., Agus, D., Mallick, P., ProteoWizard: open source software for rapid proteomics tools development. Bioinformatics 2008, 24, 2534-2536. – reference: Montecchi-Palazzi, L., Kerrien, S., Reisinger, F., Aranda, B. et al., The PSI semantic validator: a framework to check MIAPE compliance of proteomics data. Proteomics 2009, 9, 5112-5119. – reference: Deutsch, E., mzML: A single, unifying data format for mass spectrometer output. Proteomics 2008, 8, 2776-2777. – reference: Pedrioli, P. G. A., Eng, J. K., Hubley, R., Vogelzang, M. et al., A common open representation of mass spectrometry data and its application to proteomics research. Nat. Biotechnol. 2004, 22, 1459-1466. – reference: Sturm, M., Bertsch, A., Gröpl, C., Hildebrandt, A. et al., OpenMS - an open-source software framework for mass spectrometry. BMC Bioinformatics 2008, 9, 163. – reference: Martens, L., Hermjakob, H., Jones, P., Adamski, M. et al., PRIDE: the proteomics identifications database. Proteomics 2005, 5, 3537-3545. – reference: Orchard, S., Hermjakob, H., Julian, R. K., Runte, K. et al., Common interchange standards for proteomics data: public availability of tools and schema. Proteomics 2004, 4, 490-491. – volume: 4 start-page: 490 year: 2004 end-page: 491 article-title: Common interchange standards for proteomics data: public availability of tools and schema publication-title: Proteomics – volume: 9 start-page: 5112 year: 2009 end-page: 5119 article-title: The PSI semantic validator: a framework to check MIAPE compliance of proteomics data publication-title: Proteomics – volume: 9 start-page: 163 year: 2008 article-title: OpenMS – an open‐source software framework for mass spectrometry publication-title: BMC Bioinformatics – volume: 5 start-page: 3537 year: 2005 end-page: 3545 article-title: PRIDE: the proteomics identifications database publication-title: Proteomics – volume: 8 start-page: 2776 year: 2008 end-page: 2777 article-title: mzML: A single, unifying data format for mass spectrometer output publication-title: Proteomics – volume: 22 start-page: 1459 year: 2004 end-page: 1466 article-title: A common open representation of mass spectrometry data and its application to proteomics research publication-title: Nat. Biotechnol. – volume: 24 start-page: 2534 year: 2008 end-page: 2536 article-title: ProteoWizard: open source software for rapid proteomics tools development publication-title: Bioinformatics – ident: e_1_2_3_8_2 doi: 10.1002/pmic.200401303 – ident: e_1_2_3_6_2 doi: 10.1093/bioinformatics/btn323 – ident: e_1_2_3_5_2 doi: 10.1186/1471-2105-9-163 – ident: e_1_2_3_4_2 doi: 10.1038/nbt1031 – ident: e_1_2_3_7_2 doi: 10.1002/pmic.200900189 – ident: e_1_2_3_3_2 doi: 10.1002/pmic.200300694 – ident: e_1_2_3_2_2 doi: 10.1002/pmic.200890049 |
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| SubjectTerms | Analytical, structural and metabolic biochemistry Bioinformatics Biological and medical sciences Databases, Protein Fundamental and applied biological sciences. Psychology Java API Mass Spectrometry Miscellaneous Programming Languages Proteins Proteomics - methods Proteomics Standards Initiative MS standard Software XML processing |
| Title | jmzML, an open-source Java API for mzML, the PSI standard for MS data |
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