Current controlled vocabularies are insufficient to uniquely map molecular entities to mass spectrometry signal

Background The comparison of analyte mass spectrometry precursor (MS1) signal is central to many proteomic (and other -omic) workflows. Standard vocabularies for mass spectrometry exist and provide good coverage for most experimental applications yet are insufficient for concise and unambiguous desc...
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Autor*in:	Smith, Rob [verfasserIn] Taylor, Ryan M Prince, John T

Format:	E-Artikel
Sprache:	Englisch

Erschienen:	2015

Schlagwörter:	Controlled Vocabulary Proteomics Lipidomics Metabolomics

Anmerkung:	© Smith et al.; licensee BioMed Central Ltd. 2015

Übergeordnetes Werk:	Enthalten in: BMC bioinformatics - London : BioMed Central, 2000, 16(2015), Suppl 7 vom: 23. Apr.
Übergeordnetes Werk:	volume:16 ; year:2015 ; number:Suppl 7 ; day:23 ; month:04

Links:	Volltext

DOI / URN:	10.1186/1471-2105-16-S7-S2

Katalog-ID:	SPR026902389

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allfields	10.1186/1471-2105-16-S7-S2 doi (DE-627)SPR026902389 (SPR)1471-2105-16-S7-S2-e DE-627 ger DE-627 rakwb eng Smith, Rob verfasserin aut Current controlled vocabularies are insufficient to uniquely map molecular entities to mass spectrometry signal 2015 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © Smith et al.; licensee BioMed Central Ltd. 2015 Background The comparison of analyte mass spectrometry precursor (MS1) signal is central to many proteomic (and other -omic) workflows. Standard vocabularies for mass spectrometry exist and provide good coverage for most experimental applications yet are insufficient for concise and unambiguous description of data concepts spanning the range of signal provenance from a molecular perspective (e.g. from charged peptides down to fine isotopes). Without a standard unambiguous nomenclature, literature searches, algorithm reproducibility and algorithm evaluation for MS-omics data processing are nearly impossible. Results We show how terms from current official ontologies are too vague or ambiguous to explicitly map molecular entities to MS signals and we illustrate the inconsistency and ambiguity of current colloquially used terms. We also propose a set of terms for MS1 signal that uniquely, succinctly and intuitively describe data concepts spanning the range of signal provenance from full molecule downs to fine isotopes. We suggest that additional community discussion of these terms should precede any further standardization efforts. We propose a novel nomenclature that spans the range of the required granularity to describe MS data processing from the perspective of the molecular provenance of the MS signal. Conclusions The proposed nomenclature provides a chain of succinct and unique terms spanning the signal created by a charged molecule down through each of its constituent subsignals. We suggest that additional community discussion of these terms should precede any further standardization efforts. Controlled Vocabulary (dpeaa)DE-He213 Proteomics (dpeaa)DE-He213 Lipidomics (dpeaa)DE-He213 Metabolomics (dpeaa)DE-He213 Taylor, Ryan M aut Prince, John T aut Enthalten in BMC bioinformatics London : BioMed Central, 2000 16(2015), Suppl 7 vom: 23. Apr. (DE-627)326644814 (DE-600)2041484-5 1471-2105 nnns volume:16 year:2015 number:Suppl 7 day:23 month:04 https://dx.doi.org/10.1186/1471-2105-16-S7-S2 kostenfrei Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER SSG-OLC-PHA GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_370 GBV_ILN_602 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2031 GBV_ILN_2038 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2057 GBV_ILN_2061 GBV_ILN_2111 GBV_ILN_2113 GBV_ILN_2190 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4326 GBV_ILN_4335 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 16 2015 Suppl 7 23 04
spelling	10.1186/1471-2105-16-S7-S2 doi (DE-627)SPR026902389 (SPR)1471-2105-16-S7-S2-e DE-627 ger DE-627 rakwb eng Smith, Rob verfasserin aut Current controlled vocabularies are insufficient to uniquely map molecular entities to mass spectrometry signal 2015 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © Smith et al.; licensee BioMed Central Ltd. 2015 Background The comparison of analyte mass spectrometry precursor (MS1) signal is central to many proteomic (and other -omic) workflows. Standard vocabularies for mass spectrometry exist and provide good coverage for most experimental applications yet are insufficient for concise and unambiguous description of data concepts spanning the range of signal provenance from a molecular perspective (e.g. from charged peptides down to fine isotopes). Without a standard unambiguous nomenclature, literature searches, algorithm reproducibility and algorithm evaluation for MS-omics data processing are nearly impossible. Results We show how terms from current official ontologies are too vague or ambiguous to explicitly map molecular entities to MS signals and we illustrate the inconsistency and ambiguity of current colloquially used terms. We also propose a set of terms for MS1 signal that uniquely, succinctly and intuitively describe data concepts spanning the range of signal provenance from full molecule downs to fine isotopes. We suggest that additional community discussion of these terms should precede any further standardization efforts. We propose a novel nomenclature that spans the range of the required granularity to describe MS data processing from the perspective of the molecular provenance of the MS signal. Conclusions The proposed nomenclature provides a chain of succinct and unique terms spanning the signal created by a charged molecule down through each of its constituent subsignals. We suggest that additional community discussion of these terms should precede any further standardization efforts. Controlled Vocabulary (dpeaa)DE-He213 Proteomics (dpeaa)DE-He213 Lipidomics (dpeaa)DE-He213 Metabolomics (dpeaa)DE-He213 Taylor, Ryan M aut Prince, John T aut Enthalten in BMC bioinformatics London : BioMed Central, 2000 16(2015), Suppl 7 vom: 23. Apr. (DE-627)326644814 (DE-600)2041484-5 1471-2105 nnns volume:16 year:2015 number:Suppl 7 day:23 month:04 https://dx.doi.org/10.1186/1471-2105-16-S7-S2 kostenfrei Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER SSG-OLC-PHA GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_370 GBV_ILN_602 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2031 GBV_ILN_2038 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2057 GBV_ILN_2061 GBV_ILN_2111 GBV_ILN_2113 GBV_ILN_2190 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4326 GBV_ILN_4335 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 16 2015 Suppl 7 23 04
allfields_unstemmed	10.1186/1471-2105-16-S7-S2 doi (DE-627)SPR026902389 (SPR)1471-2105-16-S7-S2-e DE-627 ger DE-627 rakwb eng Smith, Rob verfasserin aut Current controlled vocabularies are insufficient to uniquely map molecular entities to mass spectrometry signal 2015 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © Smith et al.; licensee BioMed Central Ltd. 2015 Background The comparison of analyte mass spectrometry precursor (MS1) signal is central to many proteomic (and other -omic) workflows. Standard vocabularies for mass spectrometry exist and provide good coverage for most experimental applications yet are insufficient for concise and unambiguous description of data concepts spanning the range of signal provenance from a molecular perspective (e.g. from charged peptides down to fine isotopes). Without a standard unambiguous nomenclature, literature searches, algorithm reproducibility and algorithm evaluation for MS-omics data processing are nearly impossible. Results We show how terms from current official ontologies are too vague or ambiguous to explicitly map molecular entities to MS signals and we illustrate the inconsistency and ambiguity of current colloquially used terms. We also propose a set of terms for MS1 signal that uniquely, succinctly and intuitively describe data concepts spanning the range of signal provenance from full molecule downs to fine isotopes. We suggest that additional community discussion of these terms should precede any further standardization efforts. We propose a novel nomenclature that spans the range of the required granularity to describe MS data processing from the perspective of the molecular provenance of the MS signal. Conclusions The proposed nomenclature provides a chain of succinct and unique terms spanning the signal created by a charged molecule down through each of its constituent subsignals. We suggest that additional community discussion of these terms should precede any further standardization efforts. Controlled Vocabulary (dpeaa)DE-He213 Proteomics (dpeaa)DE-He213 Lipidomics (dpeaa)DE-He213 Metabolomics (dpeaa)DE-He213 Taylor, Ryan M aut Prince, John T aut Enthalten in BMC bioinformatics London : BioMed Central, 2000 16(2015), Suppl 7 vom: 23. Apr. (DE-627)326644814 (DE-600)2041484-5 1471-2105 nnns volume:16 year:2015 number:Suppl 7 day:23 month:04 https://dx.doi.org/10.1186/1471-2105-16-S7-S2 kostenfrei Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER SSG-OLC-PHA GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_370 GBV_ILN_602 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2031 GBV_ILN_2038 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2057 GBV_ILN_2061 GBV_ILN_2111 GBV_ILN_2113 GBV_ILN_2190 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4326 GBV_ILN_4335 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 16 2015 Suppl 7 23 04
allfieldsGer	10.1186/1471-2105-16-S7-S2 doi (DE-627)SPR026902389 (SPR)1471-2105-16-S7-S2-e DE-627 ger DE-627 rakwb eng Smith, Rob verfasserin aut Current controlled vocabularies are insufficient to uniquely map molecular entities to mass spectrometry signal 2015 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © Smith et al.; licensee BioMed Central Ltd. 2015 Background The comparison of analyte mass spectrometry precursor (MS1) signal is central to many proteomic (and other -omic) workflows. Standard vocabularies for mass spectrometry exist and provide good coverage for most experimental applications yet are insufficient for concise and unambiguous description of data concepts spanning the range of signal provenance from a molecular perspective (e.g. from charged peptides down to fine isotopes). Without a standard unambiguous nomenclature, literature searches, algorithm reproducibility and algorithm evaluation for MS-omics data processing are nearly impossible. Results We show how terms from current official ontologies are too vague or ambiguous to explicitly map molecular entities to MS signals and we illustrate the inconsistency and ambiguity of current colloquially used terms. We also propose a set of terms for MS1 signal that uniquely, succinctly and intuitively describe data concepts spanning the range of signal provenance from full molecule downs to fine isotopes. We suggest that additional community discussion of these terms should precede any further standardization efforts. We propose a novel nomenclature that spans the range of the required granularity to describe MS data processing from the perspective of the molecular provenance of the MS signal. Conclusions The proposed nomenclature provides a chain of succinct and unique terms spanning the signal created by a charged molecule down through each of its constituent subsignals. We suggest that additional community discussion of these terms should precede any further standardization efforts. Controlled Vocabulary (dpeaa)DE-He213 Proteomics (dpeaa)DE-He213 Lipidomics (dpeaa)DE-He213 Metabolomics (dpeaa)DE-He213 Taylor, Ryan M aut Prince, John T aut Enthalten in BMC bioinformatics London : BioMed Central, 2000 16(2015), Suppl 7 vom: 23. Apr. (DE-627)326644814 (DE-600)2041484-5 1471-2105 nnns volume:16 year:2015 number:Suppl 7 day:23 month:04 https://dx.doi.org/10.1186/1471-2105-16-S7-S2 kostenfrei Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER SSG-OLC-PHA GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_370 GBV_ILN_602 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2031 GBV_ILN_2038 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2057 GBV_ILN_2061 GBV_ILN_2111 GBV_ILN_2113 GBV_ILN_2190 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4326 GBV_ILN_4335 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 16 2015 Suppl 7 23 04
allfieldsSound	10.1186/1471-2105-16-S7-S2 doi (DE-627)SPR026902389 (SPR)1471-2105-16-S7-S2-e DE-627 ger DE-627 rakwb eng Smith, Rob verfasserin aut Current controlled vocabularies are insufficient to uniquely map molecular entities to mass spectrometry signal 2015 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © Smith et al.; licensee BioMed Central Ltd. 2015 Background The comparison of analyte mass spectrometry precursor (MS1) signal is central to many proteomic (and other -omic) workflows. Standard vocabularies for mass spectrometry exist and provide good coverage for most experimental applications yet are insufficient for concise and unambiguous description of data concepts spanning the range of signal provenance from a molecular perspective (e.g. from charged peptides down to fine isotopes). Without a standard unambiguous nomenclature, literature searches, algorithm reproducibility and algorithm evaluation for MS-omics data processing are nearly impossible. Results We show how terms from current official ontologies are too vague or ambiguous to explicitly map molecular entities to MS signals and we illustrate the inconsistency and ambiguity of current colloquially used terms. We also propose a set of terms for MS1 signal that uniquely, succinctly and intuitively describe data concepts spanning the range of signal provenance from full molecule downs to fine isotopes. We suggest that additional community discussion of these terms should precede any further standardization efforts. We propose a novel nomenclature that spans the range of the required granularity to describe MS data processing from the perspective of the molecular provenance of the MS signal. Conclusions The proposed nomenclature provides a chain of succinct and unique terms spanning the signal created by a charged molecule down through each of its constituent subsignals. We suggest that additional community discussion of these terms should precede any further standardization efforts. Controlled Vocabulary (dpeaa)DE-He213 Proteomics (dpeaa)DE-He213 Lipidomics (dpeaa)DE-He213 Metabolomics (dpeaa)DE-He213 Taylor, Ryan M aut Prince, John T aut Enthalten in BMC bioinformatics London : BioMed Central, 2000 16(2015), Suppl 7 vom: 23. Apr. (DE-627)326644814 (DE-600)2041484-5 1471-2105 nnns volume:16 year:2015 number:Suppl 7 day:23 month:04 https://dx.doi.org/10.1186/1471-2105-16-S7-S2 kostenfrei Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER SSG-OLC-PHA GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_370 GBV_ILN_602 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2031 GBV_ILN_2038 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2057 GBV_ILN_2061 GBV_ILN_2111 GBV_ILN_2113 GBV_ILN_2190 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4326 GBV_ILN_4335 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 16 2015 Suppl 7 23 04
language	English
source	Enthalten in BMC bioinformatics 16(2015), Suppl 7 vom: 23. Apr. volume:16 year:2015 number:Suppl 7 day:23 month:04
sourceStr	Enthalten in BMC bioinformatics 16(2015), Suppl 7 vom: 23. Apr. volume:16 year:2015 number:Suppl 7 day:23 month:04
format_phy_str_mv	Article
institution	findex.gbv.de
topic_facet	Controlled Vocabulary Proteomics Lipidomics Metabolomics
isfreeaccess_bool	true
container_title	BMC bioinformatics
authorswithroles_txt_mv	Smith, Rob @@aut@@ Taylor, Ryan M @@aut@@ Prince, John T @@aut@@
publishDateDaySort_date	2015-04-23T00:00:00Z
hierarchy_top_id	326644814
id	SPR026902389
language_de	englisch
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author	Smith, Rob
spellingShingle	Smith, Rob misc Controlled Vocabulary misc Proteomics misc Lipidomics misc Metabolomics Current controlled vocabularies are insufficient to uniquely map molecular entities to mass spectrometry signal
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topic_title	Current controlled vocabularies are insufficient to uniquely map molecular entities to mass spectrometry signal Controlled Vocabulary (dpeaa)DE-He213 Proteomics (dpeaa)DE-He213 Lipidomics (dpeaa)DE-He213 Metabolomics (dpeaa)DE-He213
topic	misc Controlled Vocabulary misc Proteomics misc Lipidomics misc Metabolomics
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title	Current controlled vocabularies are insufficient to uniquely map molecular entities to mass spectrometry signal
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title_full	Current controlled vocabularies are insufficient to uniquely map molecular entities to mass spectrometry signal
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title_sort	current controlled vocabularies are insufficient to uniquely map molecular entities to mass spectrometry signal
title_auth	Current controlled vocabularies are insufficient to uniquely map molecular entities to mass spectrometry signal
abstract	Background The comparison of analyte mass spectrometry precursor (MS1) signal is central to many proteomic (and other -omic) workflows. Standard vocabularies for mass spectrometry exist and provide good coverage for most experimental applications yet are insufficient for concise and unambiguous description of data concepts spanning the range of signal provenance from a molecular perspective (e.g. from charged peptides down to fine isotopes). Without a standard unambiguous nomenclature, literature searches, algorithm reproducibility and algorithm evaluation for MS-omics data processing are nearly impossible. Results We show how terms from current official ontologies are too vague or ambiguous to explicitly map molecular entities to MS signals and we illustrate the inconsistency and ambiguity of current colloquially used terms. We also propose a set of terms for MS1 signal that uniquely, succinctly and intuitively describe data concepts spanning the range of signal provenance from full molecule downs to fine isotopes. We suggest that additional community discussion of these terms should precede any further standardization efforts. We propose a novel nomenclature that spans the range of the required granularity to describe MS data processing from the perspective of the molecular provenance of the MS signal. Conclusions The proposed nomenclature provides a chain of succinct and unique terms spanning the signal created by a charged molecule down through each of its constituent subsignals. We suggest that additional community discussion of these terms should precede any further standardization efforts. © Smith et al.; licensee BioMed Central Ltd. 2015
abstractGer	Background The comparison of analyte mass spectrometry precursor (MS1) signal is central to many proteomic (and other -omic) workflows. Standard vocabularies for mass spectrometry exist and provide good coverage for most experimental applications yet are insufficient for concise and unambiguous description of data concepts spanning the range of signal provenance from a molecular perspective (e.g. from charged peptides down to fine isotopes). Without a standard unambiguous nomenclature, literature searches, algorithm reproducibility and algorithm evaluation for MS-omics data processing are nearly impossible. Results We show how terms from current official ontologies are too vague or ambiguous to explicitly map molecular entities to MS signals and we illustrate the inconsistency and ambiguity of current colloquially used terms. We also propose a set of terms for MS1 signal that uniquely, succinctly and intuitively describe data concepts spanning the range of signal provenance from full molecule downs to fine isotopes. We suggest that additional community discussion of these terms should precede any further standardization efforts. We propose a novel nomenclature that spans the range of the required granularity to describe MS data processing from the perspective of the molecular provenance of the MS signal. Conclusions The proposed nomenclature provides a chain of succinct and unique terms spanning the signal created by a charged molecule down through each of its constituent subsignals. We suggest that additional community discussion of these terms should precede any further standardization efforts. © Smith et al.; licensee BioMed Central Ltd. 2015
abstract_unstemmed	Background The comparison of analyte mass spectrometry precursor (MS1) signal is central to many proteomic (and other -omic) workflows. Standard vocabularies for mass spectrometry exist and provide good coverage for most experimental applications yet are insufficient for concise and unambiguous description of data concepts spanning the range of signal provenance from a molecular perspective (e.g. from charged peptides down to fine isotopes). Without a standard unambiguous nomenclature, literature searches, algorithm reproducibility and algorithm evaluation for MS-omics data processing are nearly impossible. Results We show how terms from current official ontologies are too vague or ambiguous to explicitly map molecular entities to MS signals and we illustrate the inconsistency and ambiguity of current colloquially used terms. We also propose a set of terms for MS1 signal that uniquely, succinctly and intuitively describe data concepts spanning the range of signal provenance from full molecule downs to fine isotopes. We suggest that additional community discussion of these terms should precede any further standardization efforts. We propose a novel nomenclature that spans the range of the required granularity to describe MS data processing from the perspective of the molecular provenance of the MS signal. Conclusions The proposed nomenclature provides a chain of succinct and unique terms spanning the signal created by a charged molecule down through each of its constituent subsignals. We suggest that additional community discussion of these terms should precede any further standardization efforts. © Smith et al.; licensee BioMed Central Ltd. 2015
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container_issue	Suppl 7
title_short	Current controlled vocabularies are insufficient to uniquely map molecular entities to mass spectrometry signal
url	https://dx.doi.org/10.1186/1471-2105-16-S7-S2
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doi_str	10.1186/1471-2105-16-S7-S2
up_date	2024-07-03T23:21:35.790Z
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