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Molecular imaging of biological samples: The ProteomeXchange consortium in Ideally, the final iteration of 5302 standard will use a GUI that, in addition to allowing easy recording of MIAMSIE information, will also include mechanisms for suggesting new fields. Although our contribution is MSI specific, we believe the underlying approach could be considered as a general strategy for improving scientific reporting.

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Herein, we propose a reporting guideline for mass spectrometry imaging MSI. This is supported by the original laboratories being best placed to re-analyze their data in context and considering that the current publish-or-perish culture devalues re-analysis and reproduction [ 20 ].

Spatial profiling of maytansine during the germination process of Maytenus senegalensis seeds. This requires that sufficient detail be reported about these procedures and spans sample preparation, data acquisition, the data itself, as well as its processing and analysis [ 11 ].

To help navigate MIAMSIE, conditional fields were grouped as much as possible and the list annotated with the relevant gating questions.

This is the approach the existing standards take. The poor reporting of calibration is typically confined to those studies that employ MS instruments that decouple ionization and mass analysis fourier transform mass spectrometry, FTMS.

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The requirement for sufficiency in existing standards necessitates broad, all-encompassing, and consequently ambiguous phrasing. Imaging mass spectrometry identifies prognostic ganglioside species bhi rodent intracranial transplants of glioma and bhi. These are discussed in more detail in the following sections. It should be noted that we, and others before us, do not intend for granularity to subsequently imply the preferred use of particular methods or experimental designs; we aim to address structured reporting only [ 1525 ].

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Essentially, the intention is for samples and datasets to provide useful partitions of the data into subsets that differ in sample preparation, origin, or data acquisition parameters. Lucia, QueenslandAustralia. The potential for misinterpretation of what fields are required or not applicable is a strong argument for standardization. Publication remains the primary method for result dissemination in the sciences. Since then, there has been a need to continue the reporting standards discussion initiated by the MSIS and prompt the community 5302 engage effectively with a standard.

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Raw MSI 502 was made feasible both by the introduction of a shared community data format, imzML [ 30 ], as well as the modification of the PRIDE repository in to accept both imzML and vendor formats [ 73 ]. We believe that practical tools that support incremental change are effective mechanisms that can improve reporting and reproducibility [ 25 ].

A detail-focused standard such as MIAMSIE is only feasible as a reporting scheme for authors, as they will be sufficiently familiar with their experiments to make the process practical. Although potentially less powerful, a practical and, therefore, minimalist standard makes implementation easier. One approach would be to start with a list of experimental details that, together, are sufficient but not necessary.

Nevertheless, this perception, which is likely to persist regardless, means it is unlikely that MIAMSIE alone will gain the traction required to meaningfully improve reporting across the MSI field.

Datasets would then be linked to samples, i.

As completed for these experiments, MIAMSIE was able to cover experimental details of interest while also allowing an overview of the study scope and processes.

At the core of healthy bgj scientific literature is the ability to both critique and build upon the work of other researchers.

To avoid assessing the quality of the underlying science, which is not the intended purpose of MSIcheck, the review was limited to the abstract, materials and methods, as well as the supplementary information, as this can often bvi an extended methods sections. The exact way in which the data are partitioned will differ in any given experiment, and so the user should be mindful of defining these terms in the context of the experiment clearly and carefully and should be consistent with their definitions.


As a result, the individual entries are very granular. This typifies the prompting concept and is a consequence of the specific requirements of glycomics, as related to the complexity of glycans and their fragility during MS analysis [ 15 ].

Typically, these spectra will have been collected using virtually identical acquisition parameters across all samples. ProteomeXchange provides globally coordinated proteomics data submission and dissemination. Apprehension surrounding data provision may stem from the discovery of errors, which impacts reputation, or the potential loss of future publications. Misinterpretation of standards due to broad and vague phrasing can be minimized by creating more granular standards, in which the required information is defined more explicitly [ 23 ].

Observations that relate to day-to-day implementation became obvious following the MSIcheck literature review.

Each individual field in the template Supplementary Table S1 has an ID a unique identifiera Name a short name for the fielda Description a more detailed explanation of the information requested by the fielda Category useful for organizing informationa list of Valid Values for the field, and an empty column where a Value could be provided for a given field and experiment. There are several other existing standards that are also MSI relevant and aim to encompass different research communities.

Laser diameter impacts not only the spatial resolution of MSI but the appropriate use of oversampling. This included extra conditionally gated fields for botanical, natural geologicaland synthetic samples, as well as making the storage and sample treatment fields more flexible.

Qualitatively, the reviews had a high degree of overlap, and this was mirrored in the focused big Supplementary Table S6. An experiment includes experimental design, hypotheses and aims, the entire bgo of samples used, the sample preparation, the datasets that have been collected, as well as the data analysis used.

As conditional answers change e.