BGI 5032 PDF

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Receive exclusive 502 and updates from Oxford Academic. One of the broadest is the minimum information for biological and biomedical investigations guidelines [ 14 ], which provide a framework of standards for the integrated reporting i.

Although our contribution is MSI specific, we believe the underlying approach could be considered as a general strategy for improving scientific reporting. An experiment includes experimental design, hypotheses and aims, the entire collection of samples used, the sample preparation, the ggi that have been collected, as well as the data analysis used.

With MSIcheck defined, we applied it to a review of two example studies from the laboratory of the last author P. Availability of supporting data.

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One way to determine if research is being reported well would be to evaluate its methods reproducibility. Second, raw data submission to a repository may have been delayed until after publication. Assuming the review is correct, its results contrast with the trend of increased data sharing in other MS-specific fields such as proteomics [ 62 ]. This identifies the conditional fields mentioned above, and the purpose of the gating questions is essentially to identify the fields that can be ignored given a value of NA.

Although potentially less powerful, a practical and, therefore, minimalist standard makes implementation easier. To illustrate the way in which we anticipate that MIAMSIE will evolve with peer contribution, we briefly describe its iterative development pre-publication.

To use an additional example, if the laser power or some other data acquisition parameter was optimized for each section, then the sections could be defined as separate datasets, each with a unique identifying dataset name, and the laser power for each one would be identified using these names.

The suggestion is a good one and necessary to evaluate sample preparation quality. This can result in the unintentional omission of experimental detail s. There is a degree of subjectivity in the choice of what results are presented in a figure. This was significant as PRIDE can support and curate large datasets, maintain privacy of the data until manuscript acceptance, and is part of the ProteomeXchange consortium, which integrates MS data from multiple repositories [ 62 ].


The focus was ultimately if the information required by each field was included, rather than on the information itself. However, granular and explicit terms make it unrealistic to be broad and all-encompassing, at least initially before such standards have had time to evolve as the research community interacts with them.

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bfi This is achieved by ensuring standardized data entry for MSIcheck fields in a readily accessible file format e. The implication is that if these are addressed, a demonstrable and relatively rapid improvement to the field would result. This approach could regularly capture the state-of-the-field with respect to the direction hgi composition of MSI in a more transparent way than anonymous surveys [ 35 ] but also highlight progress made in addressing key perceived issues in MSI.

Scan resolution determines the accuracy of optical alignment to sample stage vgi prior to MSI data acquisition and bi impacts the quality of surface region selection for MSI. However, they are either being misinterpreted—the assumption being that all scientists will interpret a reporting requirement similarly—or simply not being used. Spatial profiling of maytansine during the germination process of Maytenus senegalensis seeds. If used on a regular basis for a large enough portion of vgi literature, MSIcheck could track uptake over time and inform its own further development by presenting quantifiable metrics see Fig.

Imaging mass spectrometry identifies prognostic ganglioside species in rodent intracranial transplants of glioma and medulloblastoma. N-glycan MALDI imaging mass spectrometry on formalin-fixed paraffin-embedded tissue enables the delineation of ovarian cancer tissues. In line with these discussions between the authors, several changes were made to MIAMSIE while maintaining its core content, including The gating questions were added to create an improved template user interface.

Oxford University Press is a department of the University of Oxford. Herein, we propose a reporting guideline for mass spectrometry imaging MSI.

One goal of reporting should be to convince reviewers and the community that reproduction would be possible given time and resources, not to complicate design or data such that reproduction is deemed impractical.


One of the core concepts affecting reproducibility is insufficient quality checks and reporting at both the experimental and data processing levels [ 10 ]. In progress issue alert. This included extra conditionally gated fields for botanical, natural geologicaland synthetic samples, as well as making the storage and sample treatment fields more flexible.

As suggested above, a further review of a much larger number of articles 6 months—1 year could allow modification of MSIcheck, based on the quantitative assessment resulting from such a review see Fig.

If the concept is popular, MIAMSIE should evolve to encompass existing ontologies, the requirements of varied experimental MSI niches, and a tool that streamlines provision of these reports in a structured format that can also be examined effectively by nonexperts. In line with these findings, and assuming the case for raw data provision in MSI can be supported by monitoring MSIcheckit would be beneficial to examine the re-use rates and citation metrics for random selections of primary MSI articles that do and do not provide access to raw data; the expectation being that raw data provides a citation advantage [ 77 ].

If software can be updated or altered without the user being able to return to a prior version, methods reproducibility becomes even harder to achieve. Sign In or Create an Account.

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.

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. A sample 50322 to the surface to which MSI is applied and can be from a synthetic, natural, or biological source.

However, we anticipate that this information will provide an incentive to be a visible contributor to improving the field [ 20 ]. It is in the MSI context that we address the current lack of standardization in reported research. Finally, the initial MSIcheck review 0532 performed by two of the authors.