The minimum information about a proteomics experiment (MIAPE)

Taylor, Chris; Paton, Norman W.; Lilley, Kathryn S.; Binz, Pierre‐Alain; Julian, Randall K.; Jones, Andrew R.; Zhu, Weimin; Apweiler, Rolf; Aebersold, Ruedi; Deutsch, Eric W.; Dünn, Michael J.; Heck, Albert J. R.; Leitner, Alexander; Macht, Marcus; Mann, Matthias; Martens, Lennart; Neubert, Thomas A.; Patterson, Scott D.; Ping, Peipei; Seymour, Sean L.; Souda, Puneet; Tsugita, Akira; Vandekerckhove, Joël; Vondriska, Thomas M.; Whitelegge, Julian P.; Wilkins, Marc R.; Xenarios, Ioannnis; Yates, John R.; Hermjakob, Henning

doi:10.1038/nbt1329

Cited by 675 publications

(447 citation statements)

References 43 publications

(27 reference statements)

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“…This community effort wishes to facilitate transparent experimental reporting, data sharing, and distribution and reuse of datasets and by that to advance best practice in this emerging field. The broadness of the required MIAIPE description matches to similar guidelines from other disciplines where such guidelines are more mature and therefore well implemented and acknowledged 13, 36. We anticipate that these guidelines will evolve in parallel with the field.…”

Section: Resultsmentioning

confidence: 67%

“…Furthermore, as the immunopeptidomics MS approach and the supportive bioinformatics tools are those commonly used in general proteomics techniques, several parts of the guidelines below overlap with the existing general MIAPE guidelines,10, 11, 12, 13 developed under the umbrella of the HUPO Proteomics Standards Initiative, and the Paris Guidelines on reporting and deposition of proteomics datasets (http://www.mcponline.org/site/misc/ParisReport_Final.xhtml). For the sake of completeness and clarity, we have included overlapping content and elaborate further on the immunopeptidomics specific aspects.…”

Section: Introductionmentioning

confidence: 99%

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Minimal Information About an Immuno‐Peptidomics Experiment (MIAIPE)

Lill¹,

Veelen

Admon

et al. 2018

Proteomics

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Minimal information about an immuno‐peptidomics experiment (MIAIPE) is an initiative of the members of the Human Immuno‐Peptidome Project (HIPP), an international program organized by the Human Proteome Organization (HUPO). The aim of the MIAIPE guidelines is to deliver technical guidelines representing the minimal information required to sufficiently support the evaluation and interpretation of immunopeptidomics experiments. The MIAIPE document has been designed to report essential information about sample preparation, mass spectrometric measurement, and associated mass spectrometry (MS)‐related bioinformatics aspects that are unique to immunopeptidomics and may not be covered by the general proteomics MIAPE (minimal information about a proteomics experiment) guidelines.

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Section: Resultsmentioning

confidence: 67%

Section: Introductionmentioning

confidence: 99%

Minimal Information About an Immuno‐Peptidomics Experiment (MIAIPE)

Lill¹,

Veelen

Admon

et al. 2018

Proteomics

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“…The first of these is the need for proper annotation, especially regarding experimental design. Indeed, even though minimal reporting standards have been developed for proteomics data (the so‐called MIAPE (Minimum Information About a Proteomics Experiment) guidelines 119), there remains a gap between what is reported and what ought to be reported. While it is possible to attempt to infer the missing information as, for example, done by the pride‐asap pipeline 120, this is often far from straightforward and may result in incorrect assumptions.…”

Section: Discussionmentioning

confidence: 99%

Exploring the potential of public proteomics data

et al. 2015

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In a global effort for scientific transparency, it has become feasible and good practice to share experimental data supporting novel findings. Consequently, the amount of publicly available MS‐based proteomics data has grown substantially in recent years. With some notable exceptions, this extensive material has however largely been left untouched. The time has now come for the proteomics community to utilize this potential gold mine for new discoveries, and uncover its untapped potential. In this review, we provide a brief history of the sharing of proteomics data, showing ways in which publicly available proteomics data are already being (re‐)used, and outline potential future opportunities based on four different usage types: use, reuse, reprocess, and repurpose. We thus aim to assist the proteomics community in stepping up to the challenge, and to make the most of the rapidly increasing amount of public proteomics data.

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“…Thus as we move up in scale and complexity, the databases are necessarily more sophisticated in terms of their scope and flexibility. The RNA and proteomic database/repository efforts rely on minimal information standards MIAME (Brazma et al 2001) and MIAPE (Taylor et al 2007), which help to define the scope of what information is required to unambiguously describe a given dataset.…”

Section: Initiative 3: Establishment Of a Repository Of Experimental mentioning

confidence: 99%

Cardiac cell modelling: Observations from the heart of the cardiac physiome project

Fink

Niederer

Cherry

et al. 2011

Progress in Biophysics and Molecular Biology

145

136

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In this manuscript we review the state of cardiac cell modelling in the context of international initiatives such as the IUPS Physiome and Virtual Physiological Human Projects, which aim to integrate computational models across scales and physics. In particular we focus on the relationship between experimental data and model parameterisation across a range of model types and cellular physiological systems. Finally, in the context of parameter identification and model reuse within the Cardiac Physiome, we suggest some future priority areas for this field.

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The minimum information about a proteomics experiment (MIAPE)

Cited by 675 publications

References 43 publications

Minimal Information About an Immuno‐Peptidomics Experiment (MIAIPE)

Minimal Information About an Immuno‐Peptidomics Experiment (MIAIPE)

Exploring the potential of public proteomics data

Cardiac cell modelling: Observations from the heart of the cardiac physiome project

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