Faegis Ultimately, standards such as MIAMSIE are useful despite the lack of data provision in the field, particularly as diagnostics and for in-house record keeping. However, the intent is for community engagement to drive expansion to encompass the entirety of the field. In this context, we propose a template of reporting fields, MIAMSIE, that directly prompts the collection of very specific granular information, reminiscent of a methods section ggi lists materials and processes, rather than providing this as prose. Assuming the review is correct, its results contrast with the trend of increased data sharing in other MS-specific fields such as proteomics [ 62 ]. Lucia, QueenslandAustralia. European Molecular Biology Laboratory.
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R package version 1. An overview of the retrospective MSIcheck results are presented in Fig. As such, the fields were placed into one of four categories summarizing the degree to which the information was included in the paper.
The characterization of laser ablation patterns and a new definition of resolution in matrix assisted laser desorption ionization imaging mass spectrometry Vgi. These three parts are methods, results, and inferential reproducibility. 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.
Conversely, confirming methods reproducibility is not easy in practice but ultimately should at least be possible, if not also straightforward. The 19 articles selected were reviewed using MSIcheck [ ]. Registered reports describing an experiment [ 10 ], e. Fortunately, there are solutions in place or under development that standardize and incentivize MSI data sharing. Naturally, applying it to the entire MSI literature is unrealistic and beyond the scope of this work, and so here we applied MSIcheck to a one-month snapshot from Rather than stoking fears, raw data provision supports the contention that discovery of conflicting findings is welcomed, that any mistakes are honest, and ultimately that authors value their legacy in the literature [ 66 ].
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.
We believe true change will be underpinned by our capacity to measure, report on, and promote the provision of data across the entire MSI field, in line with efforts across the sciences to create an open data culture.
MALDI imaging mass spectrometry of N-linked glycans on formalin-fixed paraffin-embedded murine kidney. Oversampling can be inferred if both spatial resolution and laser diameter are reported; this is not the norm. Laser diameter impacts not only the spatial resolution of MSI but the appropriate use of oversampling.
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 ]. Although it contains more than fields, one co-author estimated their completion at less than 20 minutes. 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 ].
This is a reasonable time frame for completion of MIAMSIE by the principal researcher sparticularly when balanced against the amount of information being recorded. Fields that were important to a study but not strictly necessary for complete reporting of an experiment itself were removed e.
In practice they end up being sufficient, but not necessary, conditions for reporting quality. This is an unfortunate status quo. One approach would be to start with a list of experimental details that, together, are sufficient but not necessary. In contrast, results reproducibility is the ability of other groups to follow the reported procedures as closely as practicalgenerate new data, and arrive at similar results.
Spatial profiling of maytansine during the germination process of Maytenus senegalensis seeds. This is beyond the scope of the discussion presented here but is the ultimate driver of this work. Using MSIcheck as is, there are two caveats that may indicate that data availability was overlooked. A good example is that not many of the publications modified their surfaces Surface Mods. 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 ].
Collating this information is a Herculean task for published studies that follow a sufficient guideline but provide this information as unstructured prose. Secondary, but still important, was the inclusion of MSIcheck for journal article reviewers. Reproducibility, or a lack thereof, is an increasingly important topic across many research fields.
Similar to journal checklists, MSIcheck allows for rapid nonexhaustive publication assessment. Depending on sample preservation, preparation, and MS settings, MSI can investigate bgj spatial distributions for a wide variety of analytes, including small molecules drugs, lipids [ 2 ], N -glycans [ 3 ] or peptides, and proteins [ 4 ]. To use the example of FTMS, the latest versions of ftmsControl solarix instruments enable filtering for significant data reduction and also remove gbi introduced by the signal processing i.
However, during development, it bbi clear that a large number of fields are only required conditionally. 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 ].
This included extra conditionally gated fields for botanical, natural geologicaland synthetic samples, as well as making the storage sample treatment fields more flexible. As a side effect, an increase in specificity may also lead to greater ease of use and therefore greater reporting compliance [ 24 ]. Related Posts.
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