Managing expectations when publishing tools and methods for computational proteomics

Journal of Proteome Research
Lennart MartensSusan T Weintraub

Abstract

Computational tools are pivotal in proteomics because they are crucial for identification, quantification, and statistical assessment of data. The gateway to finding the best choice of a tool or approach for a particular problem is frequently journal articles, yet there is often an overwhelming variety of options that makes it hard to decide on the best solution. This is particularly difficult for nonexperts in bioinformatics. The maturity, reliability, and performance of tools can vary widely because publications may appear at different stages of development. A novel idea might merit early publication despite only offering proof-of-principle, while it may take years before a tool can be considered mature, and by that time it might be difficult for a new publication to be accepted because of a perceived lack of novelty. After discussions with members of the computational mass spectrometry community, we describe here proposed recommendations for organization of informatics manuscripts as a way to set the expectations of readers (and reviewers) through three different manuscript types that are based on existing journal designations. Brief Communications are short reports describing novel computational approaches where the impleme...Continue Reading

References

Jul 31, 2012·PLoS Computational Biology·Andrew MorinPiotr Sliz

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Citations

Nov 10, 2015·Journal of Proteome Research·Laurent GattoAndreas Beyer
May 26, 2016·Journal of Proteome Research·Johan TelemanJohan Malmström
Apr 19, 2016·Journal of Proteome Research·Kenneth BryanDavid J Lynn
Jul 2, 2019·Journal of Proteome Research·Salvador Martínez-BartoloméJohn R Yates

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