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Gustafsson OJR, Winderbaum LJ, Condina MR, Boughton BA, Hamilton BR, Undheim EAB, Becker M, Hoffmann P. Balancing sufficiency and impact in reporting standards for mass spectrometry imaging experiments. Gigascience 2018; 7:5074354. [PMID: 30124809 PMCID: PMC6203951 DOI: 10.1093/gigascience/giy102] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Revised: 07/24/2018] [Accepted: 08/07/2018] [Indexed: 02/06/2023] Open
Abstract
Reproducibility, or a lack thereof, is an increasingly important topic across many research fields. A key aspect of reproducibility is accurate reporting of both experiments and the resulting data. Herein, we propose a reporting guideline for mass spectrometry imaging (MSI). Previous standards have laid out guidelines sufficient to guarantee a certain quality of reporting; however, they set a high bar and as a consequence can be exhaustive and broad, thus limiting uptake.To help address this lack of uptake, we propose a reporting supplement-Minimum Information About a Mass Spectrometry Imaging Experiment (MIAMSIE)-and its abbreviated reporting standard version, MSIcheck. MIAMSIE is intended to improve author-driven reporting. It is intentionally not exhaustive, but is rather designed for extensibility and could therefore eventually become analogous to existing standards that aim to guarantee reporting quality. Conversely, its abbreviated form MSIcheck is intended as a diagnostic tool focused on key aspects in MSI reporting.We discuss how existing standards influenced MIAMSIE/MSIcheck and how these new approaches could positively impact reporting quality, followed by test implementation of both standards to demonstrate their use. For MIAMSIE, we report on author reviews of four articles and a dataset. For MSIcheck, we show a snapshot review of a one-month subset of the MSI literature that indicated issues with data provision and the reporting of both data analysis steps and calibration settings for MS systems. 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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Affiliation(s)
- Ove J R Gustafsson
- ARC Centre of Excellence in Convergent Bio-Nano Science & Technology (CBNS), University of South Australia, Mawson Lakes, South Australia 5095, Australia
- Future Industries Institute, University of South Australia, Mawson Lakes, South Australia 5095, Australia
| | - Lyron J Winderbaum
- Future Industries Institute, University of South Australia, Mawson Lakes, South Australia 5095, Australia
| | - Mark R Condina
- Future Industries Institute, University of South Australia, Mawson Lakes, South Australia 5095, Australia
| | - Berin A Boughton
- Metabolomics Australia, School of BioSciences, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Brett R Hamilton
- Centre for Microscopy and Microanalysis, University of Queensland, St. Lucia, Queensland 4072, Australia
- Centre for Advanced Imaging, University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Eivind A B Undheim
- Centre for Advanced Imaging, University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Michael Becker
- Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach a.d. Riss 88397, Germany
| | - Peter Hoffmann
- Future Industries Institute, University of South Australia, Mawson Lakes, South Australia 5095, Australia
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Winderbaum LJ, Koch I, Gustafsson OJR, Meding S, Hoffmann P. Feature extraction for proteomics imaging mass spectrometry data. Ann Appl Stat 2015. [DOI: 10.1214/15-aoas870] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Gustafsson OJR, Briggs MT, Condina MR, Winderbaum LJ, Pelzing M, McColl SR, Everest-Dass AV, Packer NH, Hoffmann P. MALDI imaging mass spectrometry of N-linked glycans on formalin-fixed paraffin-embedded murine kidney. Anal Bioanal Chem 2014; 407:2127-39. [PMID: 25434632 PMCID: PMC4357650 DOI: 10.1007/s00216-014-8293-7] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2014] [Revised: 10/20/2014] [Accepted: 10/21/2014] [Indexed: 11/28/2022]
Abstract
Recent developments in spatial proteomics have paved the way for retrospective in situ mass spectrometry (MS) analyses of formalin-fixed paraffin-embedded clinical tissue samples. This type of analysis is commonly referred to as matrix-assisted laser desorption/ionization (MALDI) imaging. Recently, formalin-fixed paraffin-embedded MALDI imaging analyses were augmented to allow in situ analyses of tissue-specific N-glycosylation profiles. In the present study, we outline an improved automated sample preparation method for N-glycan MALDI imaging, which uses in situ PNGase F-mediated release and measurement of N-linked glycans from sections of formalin-fixed murine kidney. The sum of the presented data indicated that N-glycans can be cleaved from proteins within formalin-fixed tissue and characterized using three strategies: (i) extraction and composition analysis through on-target MALDI MS and liquid chromatography coupled to electrospray ionization ion trap MS; (ii) MALDI profiling, where N-glycans are released and measured from large droplet arrays in situ; and (iii) MALDI imaging, which maps the tissue specificity of N-glycans at a higher resolution. Thus, we present a complete, straightforward method that combines MALDI imaging and characterization of tissue-specific N-glycans and complements existing strategies. MALDI imaging MS of N-linked glycans released from formalin-fixed paraffin-embedded murine kidney sections. Ion intensity maps for (Hex)2(HexNAc)3(Deoxyhexose)3+(Man)3(GlcNAc)2 (m/z 2304.932, red), (Hex)6+(Man)3(GlcNAc)2 (m/z 1905.742, green) and (Hex)2(HexNAc)2+(Man)3(GlcNAc)2 (m/z 1663.756, blue) ![]()
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Affiliation(s)
- Ove J R Gustafsson
- Adelaide Proteomics Centre, School of Molecular and Biomedical Science, University of Adelaide, Adelaide, South Australia, 5005, Australia
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