Scientific standards and MIAPEs in plant proteomics research and publications

摘要

“ I suspect that the authors are capable of doing a much better job of preparing a scientific Ms., and I wish that they had applied more effort with this one. If the writing and Ms. preparation are this sloppy and amateurish, can the research be trusted? The authors simply list quantitative results, and make some broad, generalized, pedestrian comments. Hardly a Discussion .” (Anonymous referee) In this opinion paper it is my intent to briefly discuss some key issues related to scientific standards in plant proteomics research and the “Minimal Information About a Proteomics Experiment” (MIAPEs) requested for derived publications. It is mainly aimed at beginners rather than scientists who have established a long trajectory and experience within the field, trying to rationally connect proteomics and plant biology. The content was presented at the “1st INPPO World Congress on Plant Proteomics: Methodology to Biology,” September 2014, and has been discussed in reviews published by the author, with the most recent referenced herein (Jorrin Novo et al., 2009 ; Jorrin Novo et al., 2014 , 2015 ; Valledor and Jorrin, 2011 ). As an opinion paper it should be, what else!?, subjected to comments, disagreements, or criticisms, but at the very least open discussion. It reflects 12 years of active research, as an author (who has had some experience with rejected manuscripts), a reviewer, and an editor who has handled around 400 manuscripts (about 50% of which were ultimately accepted). MS-based Proteomics, as an analytical tool, has developed to an unanticipated level in a very short period of time. Even so, its potential remains far from being fully exploited especially as a component of plant biology in comparison with other organisms (i.e., humans, yeast, bacteria). Some areas (PTMs, interactomics) or techniques (targeted, arrays, imaging) are minimally represented in the current plant literature, while others (protein trafficking, degradation, protein function at the –omics level) remain absent or anecdotal. Despite being a powerful technique, it has limitations (quantitation, orphan organisms). As my friend Juan Pablo Albar (recently deceased) used to say, “Jesus, real proteomics is only possible when studying organisms with a sequenced genome as we should pretend to identify gene products.” It is not a panacea, or a miracle. By itself it is almost impossible to unravel biological processes. Results must be validated, and contrasted with those obtained by using biochemical, molecular (classical, other –omics), or cellular biology approaches. We now appreciate that the protein world is much more complex from a structural and functional point of view than ever imagined. It is increasingly clear that in its present state, proteomics is mostly descriptive and to a great extent speculative. While description is valuable by itself, it is not always adequate to support biological speculations or support speculative conclusions. While this opinion might be considered controversial by some, it is shared by others and is well presented in the last review by Paola Picotti (Boersema et al., 2015 ). Because of this evolution in the nature of (plant) proteomics, we have chosen to present a philosophical rather than data-based contribution. For those with limited prior experience, but with a well-designed biological project, it is important to remember that proteomic analysis is much more than just sending samples to a Proteomics Service (you should not pretend that mass spectrometists are knowledgeable about plant biology), then blindly accepting the results, and preparing a more or less confident protein identification and quantification table. Only if one understands both the experimental system and the proteomics techniques applied can we understand the results well enough to speculate about how, why, and what insight the results provide? Proteomics has innate limitations which must be taken into account; data must be critically evaluated, correctly validated and interpreted, and finally, submitted manuscripts should fit into the general scientific and particular proteomics standards or MIAPEs (Minimum Information About a Proteomics Experiment). Such a MIAPEs have been translated to a number of documents elaborated by the Proteomics Standard Initiative within the Human Proteomics Organization (HUPO; http://www.psidev.info/node/91 ); they are related to “community standards for data representation in proteomics to facilitate data comparison, exchange and verification” (Orchard et al., 2003 ; http://www.psidev.info/ ), making reference to each of the steps in a standard proteomics workflow (gel electrophoresis, gel informatics, MS general, MS informatics, MS quantitation, column chromatography, capillary electrophoresis, molecular interaction). These standards are requested by the four top-ranking journals in the field (by year of appearance, Proteomics, Molecular, and Cellular Proteomics, Journal of Proteome Research, and Journ