Literature DB >> 30124809

Balancing sufficiency and impact in reporting standards for mass spectrometry imaging experiments.

Ove J R Gustafsson1,2, Lyron J Winderbaum2, Mark R Condina2, Berin A Boughton3, Brett R Hamilton4,5, Eivind A B Undheim5, Michael Becker6, Peter Hoffmann2.   

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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Year:  2018        PMID: 30124809      PMCID: PMC6203951          DOI: 10.1093/gigascience/giy102

Source DB:  PubMed          Journal:  Gigascience        ISSN: 2047-217X            Impact factor:   6.524


  57 in total

Review 1.  Going forward: Increasing the accessibility of imaging mass spectrometry.

Authors:  Liam A McDonnell; Ron M A Heeren; Per E Andrén; Markus Stoeckli; Garry L Corthals
Journal:  J Proteomics       Date:  2012-05-23       Impact factor: 4.044

Review 2.  MALDI imaging mass spectrometry: spatial molecular analysis to enable a new age of discovery.

Authors:  Megan M Gessel; Jeremy L Norris; Richard M Caprioli
Journal:  J Proteomics       Date:  2014-03-29       Impact factor: 4.044

Review 3.  The minimum information about a proteomics experiment (MIAPE).

Authors:  Chris F Taylor; Norman W Paton; Kathryn S Lilley; Pierre-Alain Binz; Randall K Julian; Andrew R Jones; Weimin Zhu; Rolf Apweiler; Ruedi Aebersold; Eric W Deutsch; Michael J Dunn; Albert J R Heck; Alexander Leitner; Marcus Macht; Matthias Mann; Lennart Martens; Thomas A Neubert; Scott D Patterson; Peipei Ping; Sean L Seymour; Puneet Souda; Akira Tsugita; Joel Vandekerckhove; Thomas M Vondriska; Julian P Whitelegge; Marc R Wilkins; Ioannnis Xenarios; John R Yates; Henning Hermjakob
Journal:  Nat Biotechnol       Date:  2007-08       Impact factor: 54.908

4.  Potential of Burkholderia seminalis TC3.4.2R3 as Biocontrol Agent Against Fusarium oxysporum Evaluated by Mass Spectrometry Imaging.

Authors:  Francisca Diana da Silva Araújo; Welington Luiz Araújo; Marcos Nogueira Eberlin
Journal:  J Am Soc Mass Spectrom       Date:  2017-02-13       Impact factor: 3.109

5.  Overlapping MALDI-Mass Spectrometry Imaging for In-Parallel MS and MS/MS Data Acquisition without Sacrificing Spatial Resolution.

Authors:  Rebecca L Hansen; Young Jin Lee
Journal:  J Am Soc Mass Spectrom       Date:  2017-05-10       Impact factor: 3.109

6.  Fine Needle Aspiration Combined With Matrix-assisted Laser Desorption Ionization Time-of-Flight/Mass Spectrometry to Characterize Lipid Biomarkers for Diagnosing Accuracy of Breast Cancer.

Authors:  Yi-Tzu Cho; Hung Su; Yi-Yan Chiang; Jentaie Shiea; Shyng-Shiou F Yuan; Wen-Chun Hung; Yao-Tsung Yeh; Ming-Feng Hou
Journal:  Clin Breast Cancer       Date:  2017-05-25       Impact factor: 3.225

7.  Lymph node metastasis of primary endometrial cancers: Associated proteins revealed by MALDI imaging.

Authors:  Parul Mittal; Manuela Klingler-Hoffmann; Georgia Arentz; Lyron Winderbaum; Noor A Lokman; Chao Zhang; Lyndal Anderson; James Scurry; Yee Leung; Colin Jr Stewart; Jonathan Carter; Gurjeet Kaur; Martin K Oehler; Peter Hoffmann
Journal:  Proteomics       Date:  2016-05-10       Impact factor: 3.984

8.  MALDI imaging mass spectrometry of N-linked glycans on formalin-fixed paraffin-embedded murine kidney.

Authors:  Ove J R Gustafsson; Matthew T Briggs; Mark R Condina; Lyron J Winderbaum; Matthias Pelzing; Shaun R McColl; Arun V Everest-Dass; Nicolle H Packer; Peter Hoffmann
Journal:  Anal Bioanal Chem       Date:  2014-12-02       Impact factor: 4.142

9.  mzML2ISA & nmrML2ISA: generating enriched ISA-Tab metadata files from metabolomics XML data.

Authors:  Martin Larralde; Thomas N Lawson; Ralf J M Weber; Pablo Moreno; Kenneth Haug; Philippe Rocca-Serra; Mark R Viant; Christoph Steinbeck; Reza M Salek
Journal:  Bioinformatics       Date:  2017-08-15       Impact factor: 6.937

10.  2016 update of the PRIDE database and its related tools.

Authors:  Juan Antonio Vizcaíno; Attila Csordas; Noemi del-Toro; José A Dianes; Johannes Griss; Ilias Lavidas; Gerhard Mayer; Yasset Perez-Riverol; Florian Reisinger; Tobias Ternent; Qing-Wei Xu; Rui Wang; Henning Hermjakob
Journal:  Nucleic Acids Res       Date:  2015-11-02       Impact factor: 16.971

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  2 in total

1.  Moving translational mass spectrometry imaging towards transparent and reproducible data analyses: a case study of an urothelial cancer cohort analyzed in the Galaxy framework.

Authors:  Peter Bronsert; Oliver Schilling; Melanie Christine Föll; Veronika Volkmann; Kathrin Enderle-Ammour; Sylvia Timme; Konrad Wilhelm; Dan Guo; Olga Vitek
Journal:  Clin Proteomics       Date:  2022-04-19       Impact factor: 5.000

2.  Accessible and reproducible mass spectrometry imaging data analysis in Galaxy.

Authors:  Melanie Christine Föll; Lennart Moritz; Thomas Wollmann; Maren Nicole Stillger; Niklas Vockert; Martin Werner; Peter Bronsert; Karl Rohr; Björn Andreas Grüning; Oliver Schilling
Journal:  Gigascience       Date:  2019-12-01       Impact factor: 6.524

  2 in total

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