Scientific standards and MIAPEs in plant proteomics research and publications

Novo, Jesús V. Jorrín; Jesús,

doi:10.3389/fpls.2015.00473

Cited by 8 publications

(5 citation statements)

References 10 publications

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“…Furthermore, our research has been focused on studying plant responses to abiotic and biotic stresses related to decline syndrome, mainly drought and P. cinnamomi infestation, as well as differences among Q. ilex provenances from Andalusia combining proteomics, morphometry, and physiological analysis [17,20,21,22,23]. This manuscript does not intend to be a review of the field of proteomics, because there are already a high number of publications available in the literature [24,25,26,27,28,29,30,31,32], or discuss terminology or scientific standards mandated by the corresponding Minimum Information about Proteomics Experiment (MIAPE) guidelines [33]. On the other hand, the application of proteomics in forest tree research has also been the subject of some previous reviews, with a quite descriptive point of view [34,35].…”

Section: Introductionmentioning

confidence: 99%

Proteomics, Holm Oak (Quercus ilex L.) and Other Recalcitrant and Orphan Forest Tree Species: How do They See Each Other?

Rey

Castillejo

Sánchez-Lucas

et al. 2019

IJMS

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Proteomics has had a big impact on plant biology, considered as a valuable tool for several forest species, such as Quercus, Pines, Poplars, and Eucalyptus. This review assesses the potential and limitations of the proteomics approaches and is focused on Quercus ilex as a model species and other forest tree species. Proteomics has been used with Q. ilex since 2003 with the main aim of examining natural variability, developmental processes, and responses to biotic and abiotic stresses as in other species of the genus Quercus or Pinus. As with the progress in techniques in proteomics in other plant species, the research in Q. ilex moved from 2-DE based strategy to the latest gel-free shotgun workflows. Experimental design, protein extraction, mass spectrometric analysis, confidence levels of qualitative and quantitative proteomics data, and their interpretation are a true challenge with relation to forest tree species due to their extreme orphan and recalcitrant (non-orthodox) nature. Implementing a systems biology approach, it is time to validate proteomics data using complementary techniques and integrate it with the -omics and classical approaches. The full potential of the protein field in plant research is quite far from being entirely exploited. However, despite the methodological limitations present in proteomics, there is no doubt that this discipline has contributed to deeper knowledge of plant biology and, currently, is increasingly employed for translational purposes.

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Section: Introductionmentioning

confidence: 99%

Proteomics, Holm Oak (Quercus ilex L.) and Other Recalcitrant and Orphan Forest Tree Species: How do They See Each Other?

Rey

Castillejo

Sánchez-Lucas

et al. 2019

IJMS

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“…These leaf papers can be divided by experimental conditions: nine papers on abiotic stress, 15 on biotic stress, and eight on non-challenged plants (Figure 2B). To extract the same type of information on the proteins described in the papers we faced the difficulty of the insufficient descriptions of datasets and different terminologies used by the several authors, problems already reported by Jorrin-Novo [42]. For this reason we were not able to perform a bioinformatic functional annotation of the proteins (e.g., BLAST2GO) but, instead, we did a manual inspection of the data.…”

Section: Bibliographic Search (Description Of the Paper Dataset Ofmentioning

confidence: 99%

Protein Dynamics in the Plant Extracellular Space

et al. 2016

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The extracellular space (ECS or apoplast) is the plant cell compartment external to the plasma membrane, which includes the cell walls, the intercellular space and the apoplastic fluid (APF). The present review is focused on APF proteomics papers and intends to draw information on the metabolic processes occurring in the ECS under abiotic and biotic stresses, as well as under non-challenged conditions. The large majority of the proteins detected are involved in “cell wall organization and biogenesis”, “response to stimulus” and “protein metabolism”. It becomes apparent that some proteins are always detected, irrespective of the experimental conditions, although with different relative contribution. This fact suggests that non-challenged plants have intrinsic constitutive metabolic processes of stress/defense in the ECS. In addition to the multiple functions ascribed to the ECS proteins, should be considered the interactions established between themselves and with the plasma membrane and its components. These interactions are crucial in connecting exterior and interior of the cell, and even simple protein actions in the ECS can have profound effects on plant performance. The proteins of the ECS are permanently contributing to the high dynamic nature of this plant compartment, which seems fundamental to plant development and adaptation to the environmental conditions.

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“…Recently, Jorrin‐Novo published an opinion article in which scientific standards and MIAPE were discussed in the context of proteomics work and publications. From his experience, the failure to meet proper scientific standards and those requested for a proteomics paper is the most obvious and immediate reason for rejection.…”

Section: Introductionmentioning

confidence: 99%

“…From his experience, the failure to meet proper scientific standards and those requested for a proteomics paper is the most obvious and immediate reason for rejection. As just a simple example, the general terminology employed in the literature included terms such as protein expression, when proteomics approaches actually determine abundance . Abundance is the result not only of gene expression (transcription and translation) but also of protein degradation and PTMs.…”

Section: Introductionmentioning

confidence: 99%

A year (2014–2015) of plants in Proteomics journal. Progress in wet and dry methodologies, moving from protein catalogs, and the view of classic plant biochemists

et al. 2016

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The present review is an update of the previous one published in Proteomics 2015 Reviews special issue [Jorrin-Novo, J. V. et al., Proteomics 2015, 15, 1089-1112] covering the July 2014-2015 period. It has been written on the bases of the publications that appeared in Proteomics journal during that period and the most relevant ones that have been published in other high-impact journals. Methodological advances and the contribution of the field to the knowledge of plant biology processes and its translation to agroforestry and environmental sectors will be discussed. This review has been organized in four blocks, with a starting general introduction (literature survey) followed by sections focusing on the methodology (in vitro, in vivo, wet, and dry), proteomics integration with other approaches (systems biology and proteogenomics), biological information, and knowledge (cell communication, receptors, and signaling), ending with a brief mention of some other biological and translational topics to which proteomics has made some contribution.

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Scientific standards and MIAPEs in plant proteomics research and publications

Cited by 8 publications

References 10 publications

Proteomics, Holm Oak (Quercus ilex L.) and Other Recalcitrant and Orphan Forest Tree Species: How do They See Each Other?

Proteomics, Holm Oak (Quercus ilex L.) and Other Recalcitrant and Orphan Forest Tree Species: How do They See Each Other?

Protein Dynamics in the Plant Extracellular Space

A year (2014–2015) of plants in Proteomics journal. Progress in wet and dry methodologies, moving from protein catalogs, and the view of classic plant biochemists

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