mzIdentML 1.3.0 – Essential progress on the support of crosslinking and other identifications based on multiple spectra Article Swipe
Colin Combe
,
Lars Kolbowski
,
Lutz Fischer
,
Ville Koskinen
,
Joshua Klein
,
Alexander Leitner
,
Andrew R. Jones
,
Juan Antonio Vizcaíno
,
Juri Rappsilber
·
YOU?
·
· 2024
· Open Access
·
· DOI: https://doi.org/10.1002/pmic.202300385
YOU?
·
· 2024
· Open Access
·
· DOI: https://doi.org/10.1002/pmic.202300385
The mzIdentML data format, originally developed by the Proteomics Standards Initiative in 2011, is the open XML data standard for peptide and protein identification results coming from mass spectrometry. We present mzIdentML version 1.3.0, which introduces new functionality and support for additional use cases. First of all, a new mechanism for encoding identifications based on multiple spectra has been introduced. Furthermore, the main mzIdentML specification document can now be supplemented by extension documents which provide further guidance for encoding specific use cases for different proteomics subfields. One extension document has been added, covering additional use cases for the encoding of crosslinked peptide identifications. The ability to add extension documents facilitates keeping the mzIdentML standard up to date with advances in the proteomics field, without having to change the main specification document. The crosslinking extension document provides further explanation of the crosslinking use cases already supported in mzIdentML version 1.2.0, and provides support for encoding additional scenarios that are critical to reflect developments in the crosslinking field and facilitate its integration in structural biology. These are: (i) support for cleavable crosslinkers, (ii) support for internally linked peptides, (iii) support for noncovalently associated peptides, and (iv) improved support for encoding scores and the corresponding thresholds.
Related Topics
Concepts
Computer science
Proteomics
XML
Encoding (memory)
Extension (predicate logic)
Identification (biology)
Computational biology
Field (mathematics)
Peptide
Mass spectrometry
Database
Combinatorial chemistry
Data mining
Chemistry
Programming language
Biology
Artificial intelligence
World Wide Web
Biochemistry
Mathematics
Chromatography
Pure mathematics
Botany
Gene
Metadata
- Type
- article
- Language
- en
- Landing Page
- https://doi.org/10.1002/pmic.202300385
- https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/pmic.202300385
- OA Status
- hybrid
- Cited By
- 5
- References
- 21
- Related Works
- 10
- OpenAlex ID
- https://openalex.org/W4400609120
All OpenAlex metadata
Raw OpenAlex JSON
- OpenAlex ID
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https://openalex.org/W4400609120Canonical identifier for this work in OpenAlex
- DOI
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https://doi.org/10.1002/pmic.202300385Digital Object Identifier
- Title
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mzIdentML 1.3.0 – Essential progress on the support of crosslinking and other identifications based on multiple spectraWork title
- Type
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articleOpenAlex work type
- Language
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enPrimary language
- Publication year
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2024Year of publication
- Publication date
-
2024-07-12Full publication date if available
- Authors
-
Colin Combe, Lars Kolbowski, Lutz Fischer, Ville Koskinen, Joshua Klein, Alexander Leitner, Andrew R. Jones, Juan Antonio Vizcaíno, Juri RappsilberList of authors in order
- Landing page
-
https://doi.org/10.1002/pmic.202300385Publisher landing page
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https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/pmic.202300385Direct link to full text PDF
- Open access
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YesWhether a free full text is available
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hybridOpen access status per OpenAlex
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https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/pmic.202300385Direct OA link when available
- Concepts
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Computer science, Proteomics, XML, Encoding (memory), Extension (predicate logic), Identification (biology), Computational biology, Field (mathematics), Peptide, Mass spectrometry, Database, Combinatorial chemistry, Data mining, Chemistry, Programming language, Biology, Artificial intelligence, World Wide Web, Biochemistry, Mathematics, Chromatography, Pure mathematics, Botany, GeneTop concepts (fields/topics) attached by OpenAlex
- Cited by
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5Total citation count in OpenAlex
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2025: 4, 2024: 1Per-year citation counts (last 5 years)
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21Number of works referenced by this work
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10Other works algorithmically related by OpenAlex
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| abstract_inverted_index.introduced. | 60 |
| abstract_inverted_index.thresholds. | 203 |
| abstract_inverted_index.Furthermore, | 61 |
| abstract_inverted_index.crosslinking | 133, 141, 165 |
| abstract_inverted_index.developments | 162 |
| abstract_inverted_index.supplemented | 70 |
| abstract_inverted_index.corresponding | 202 |
| abstract_inverted_index.crosslinkers, | 180 |
| abstract_inverted_index.functionality | 38 |
| abstract_inverted_index.noncovalently | 190 |
| abstract_inverted_index.specification | 65, 130 |
| abstract_inverted_index.spectrometry. | 29 |
| abstract_inverted_index.identification | 24 |
| abstract_inverted_index.identifications | 53 |
| abstract_inverted_index.identifications. | 103 |
| cited_by_percentile_year.max | 98 |
| cited_by_percentile_year.min | 90 |
| corresponding_author_ids | https://openalex.org/A5076844877 |
| countries_distinct_count | 4 |
| institutions_distinct_count | 9 |
| corresponding_institution_ids | https://openalex.org/I4210134627, https://openalex.org/I4577782, https://openalex.org/I98677209 |
| sustainable_development_goals[0].id | https://metadata.un.org/sdg/17 |
| sustainable_development_goals[0].score | 0.5099999904632568 |
| sustainable_development_goals[0].display_name | Partnerships for the goals |
| citation_normalized_percentile.value | 0.82306271 |
| citation_normalized_percentile.is_in_top_1_percent | False |
| citation_normalized_percentile.is_in_top_10_percent | False |