mzTab
The aim of the format is to present the results of a proteomics experiment in a computationally accessible overview. The aim is not to provide the detailed evidence for these results, or allow recreating the process which led to the results. Both of these functions are established through links to more detailed representations in other formats, in particular mzIdentML and mzQuantML. mzTab is meant to be a light-weight, tab-delimited file format for proteomics data. The target audience for this format are primarily researchers outside of proteomics. It should be easy to parse and only contain the minimal information required to evaluate the results of a proteomics experiment. One of the goals of this file format is that it, for example, should be possible for a biologist to open such a file in Excel and still be able to "see" the data. This format should also become a way to disseminate proteomics results through protocols such as DAS.
Description
More detailed information about this field from each metasource.
The aim of the format is to present the results of a proteomics experiment in a computationally accessible overview. The aim is not to provide the detailed evidence for these results, or allow recreating the process which led to the results. Both of these functions are established through links to more detailed representations in other formats, in particular mzIdentML and mzQuantML. mzTab is meant to be a light-weight, tab-delimited file format for proteomics data. The target audience for this format are primarily researchers outside of proteomics. It should be easy to parse and only contain the minimal information required to evaluate the results of a proteomics experiment. One of the goals of this file format is that it, for example, should be possible for a biologist to open such a file in Excel and still be able to "see" the data. This format should also become a way to disseminate proteomics results through protocols such as DAS.
metasource: Fairsharing.orgversion: FAIRsharing.org: mzTab; mzTab; DOI: https://doi.org/10.25504/FAIRsharing.c12tyk; Last edited: Jan. 8, 2019, 1:39 p.m.; Last accessed: Jan 03 2022 7:11 p.m.
Webpage:
http://www.psidev.info/mztabWebpage
More detailed information about this field from each metasource.
http://www.psidev.info/mztab
metasource: Fairsharing.orgversion: FAIRsharing.org: mzTab; mzTab; DOI: https://doi.org/10.25504/FAIRsharing.c12tyk; Last edited: Jan. 8, 2019, 1:39 p.m.; Last accessed: Jan 03 2022 7:11 p.m.
Publications:
Publications
More detailed information about this field from each metasource.
The mzTab data exchange format: communicating mass-spectrometry-based proteomics and metabolomics experimental results to a wider audience
PMID: 24980485
metasource: Fairsharing.org
version: FAIRsharing.org: mzTab; mzTab; DOI: https://doi.org/10.25504/FAIRsharing.c12tyk; Last edited: Jan. 8, 2019, 1:39 p.m.; Last accessed: Jan 03 2022 7:11 p.m.
Publications
More detailed information about this field from each metasource.
The mzTab data exchange format: communicating mass-spectrometry-based proteomics and metabolomics experimental results to a wider audience
PMID: 24980485
metasource: Fairsharing.org
version: FAIRsharing.org: mzTab; mzTab; DOI: https://doi.org/10.25504/FAIRsharing.c12tyk; Last edited: Jan. 8, 2019, 1:39 p.m.; Last accessed: Jan 03 2022 7:11 p.m.
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The mzTab data exchange format: communicating mass-spectrometry-based proteomics and metabolomics experimental results to a wider audience
PubMed citations: 49.
49 articles citing: The mzTab data exchange format: communicating mass-spectrometry-based proteomics and metabolomics experimental results to a wider audience
A Current Encyclopedia of Bioinformatics Tools, Data Formats and Resources for Mass Spectrometry Lipidomics. PMID:35888710
A learned embedding for efficient joint analysis of millions of mass spectra. PMID:35637305
Proteomics Standards Initiative's ProForma 2.0: Unifying the Encoding of Proteoforms and Peptidoforms. PMID:35290070
A knowledge graph to interpret clinical proteomics data. PMID:35102292
ProMetIS, deep phenotyping of mouse models by combined proteomics and metabolomics analysis. PMID:34862403
The PRIDE database resources in 2022: a hub for mass spectrometry-based proteomics evidences. PMID:34723319
A proteomics sample metadata representation for multiomics integration and big data analysis. PMID:34615866
MaxDIA enables library-based and library-free data-independent acquisition proteomics. PMID:34239088
Implementing FAIR data management within the German Network for Bioinformatics Infrastructure (de.NBI) exemplified by selected use cases. PMID:33589928
LabPipe: an extensible bioinformatics toolkit to manage experimental data and metadata. PMID:33267792
Argonaut: A Web Platform for Collaborative Multi-omic Data Visualization and Exploration. PMID:33154995
Towards standardization guidelines for in silico approaches in personalized medicine. PMID:32827396
A computational platform for high-throughput analysis of RNA sequences and modifications by mass spectrometry. PMID:32066737
The ProteomeXchange consortium in 2020: enabling 'big data' approaches in proteomics. PMID:31686107
Towards a standardized bioinformatics infrastructure for N- and O-glycomics. PMID:31332201
Interactive Peptide Spectral Annotator: A Versatile Web-based Tool for Proteomic Applications. PMID:31088857
Proteomics Standards Initiative Extended FASTA Format. PMID:31081335
mzTab-M: A Data Standard for Sharing Quantitative Results in Mass Spectrometry Metabolomics. PMID:30688441
The European Bioinformatics Institute in 2018: tools, infrastructure and training. PMID:30445657
The PRIDE database and related tools and resources in 2019: improving support for quantification data. PMID:30395289
iProX: an integrated proteome resource. PMID:30252093
MetaboAnalystR: an R package for flexible and reproducible analysis of metabolomics data. PMID:29955821
Challenges and Opportunities for Biological Mass Spectrometry Core Facilities in the Developing World. PMID:29623005
The proBAM and proBed standard formats: enabling a seamless integration of genomics and proteomics data. PMID:29386051
Proteomics Standards Initiative: Fifteen Years of Progress and Future Work. PMID:28849660
The mzIdentML Data Standard Version 1.2, Supporting Advances in Proteome Informatics. PMID:28515314
A Golden Age for Working with Public Proteomics Data. PMID:28118949
Global open data management in metabolomics. PMID:28092796
The ProteomeXchange consortium in 2017: supporting the cultural change in proteomics public data deposition. PMID:27924013
jPOSTrepo: an international standard data repository for proteomes. PMID:27899654
CSF-PR 2.0: An Interactive Literature Guide to Quantitative Cerebrospinal Fluid Mass Spectrometry Data from Neurodegenerative Disorders. PMID:27890865
Flexible Data Analysis Pipeline for High-Confidence Proteogenomics. PMID:27786492
Greazy: Open-Source Software for Automated Phospholipid Tandem Mass Spectrometry Identification. PMID:27186799
Data standards can boost metabolomics research, and if there is a will, there is a way. PMID:26612985
PRIDE Inspector Toolsuite: Moving Toward a Universal Visualization Tool for Proteomics Data Standard Formats and Quality Assessment of ProteomeXchange Datasets. PMID:26545397
2016 update of the PRIDE database and its related tools. PMID:26527722
Exploring the potential of public proteomics data. PMID:26449181
The mzqLibrary--An open source Java library supporting the HUPO-PSI quantitative proteomics standard. PMID:26037908
ms-data-core-api: an open-source, metadata-oriented library for computational proteomics. PMID:25910694
Introducing the PRIDE Archive RESTful web services. PMID:25904633
Development of data representation standards by the human proteome organization proteomics standards initiative. PMID:25726569
Trans-Proteomic Pipeline, a standardized data processing pipeline for large-scale reproducible proteomics informatics. PMID:25631240
Workflows for automated downstream data analysis and visualization in large-scale computational mass spectrometry. PMID:25604327
Computational phosphoproteomics: from identification to localization. PMID:25475148
Identifying novel biomarkers through data mining-a realistic scenario? PMID:25347964
Making proteomics data accessible and reusable: current state of proteomics databases and repositories. PMID:25158685
A standardized framing for reporting protein identifications in mzIdentML 1.2. PMID:25092112
BiNA: a visual analytics tool for biological network data. PMID:24551056
A tutorial for software development in quantitative proteomics using PSI standard formats. PMID:23584085
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