Scope

Plant Proteomics and Protein Structural Biology section publishes significant findings and major advances in the field of protein-based regulation of biological processes, specifically focusing on proteome-wide and structural biology studies that examine the dynamics, functions, and interactions of proteins from plant systems.

Topics covered by this section include, but are not limited to:

• Comparative proteomic studies employing 2-DE, labeling, or unlabeled strategies
• Characterization of subcellular, cellular, or plant organ proteomes
• Characterization of protein modifications by mass spectrometry
• Protein-protein interactions and protein networks
• Protein cross-linking studies using mass spectrometry
• Bioinformatic analysis of proteomic data, including new online resources and tools
• Novel or improved methods involving mass spectrometry
• Structural characterization and analysis of proteins, using secondary structure determination techniques, small-angle scattering techniques, X-ray crystallography, NMR spectroscopy, and electron microscopy to explore molecular structure and dynamics of proteins and how alterations in their structure affect their function
• Protein modeling if validated by experimental data
• In-depth phylogenetic studies, i.e. studying the evolutionary relationships between species, that focus on protein classes related to signal transduction, such as those regulating phosphorylation, ubiquitination, sumoylation, etc.
• Large-scale bio-informatic surveys comparing (evolutionarily conserved) sites for regulatory PTMs across species

Data sets also welcomed in the section are:

• extensive comparative data sets (e.g. mutant versus wild-type or different treatments)
• data sets that are not exhaustively validated, but have reproducible and ideally validated results (minimal number of replicates and stringent statistics).
• data sets which go beyond a list of what can be detected (even if not straightforward to fully validate observations in non-model plants). Extensive speculation merely based on a list is discouraged.

Validation can be broadly interpreted (e.g. direct validation of differential candidates through another biochemical approach or genetics, but this can also be with respect to a particular pathway that stands out and that can be validated through simple experiments).

These submission types will not be accepted in the section:

• Descriptive studies that only present a list of detected proteins (cataloging) in a given species, unless they are extended to elaborate on a new pathway or biological process related to the treatment or to the species presented or address difficult to obtain plant tissues or cells
• Phylogenetic studies or large-scale bio-informatic surveys should not only catalog a protein family in a few (exotic) species but should provide a thorough analysis within (at least) the Viridiplantae.
• For experimental studies, the following content and quality requirements are criteria for exclusion:
1. Quantitative omics analyses (e.g. transcriptomics, proteomics, metabolomics) must be performed on a minimum number of 3 biological replicates in order to enable an assessment of significance. Studies that do not comply will not be considered for review.
2. Studies falling into the categories below will not be considered for review unless they are expanded and provide insight into the biological system or process being studied:
   • Purely descriptive collections of transcripts, proteins or metabolites, including a limited number of comparative sets as a result of different conditions or treatments;
   • Descriptive studies that define gene families using basic phylogenetics and the assignment of cursory functional attributions (e.g. expression profiles, hormone or metabolite levels, promoter analysis, informatic parameters).
3. Studies using transgenic or mutant plants should be based on data from multiple independent alleles (at least 2) displaying a common and stable phenotype. Examples include T-DNA, transposon, RNAi, CRISPR/Cas9, chemically induced, overexpressors, reporter fusions (GUS, FPs, LUC) etc.
• Qualitative data can be presented from a single allele but should be indicative of observations from multiple alleles which should be explicitly stated in the text.
• Quantitative data should be derived from multiple alleles (at least 2) and should be displayed separately for each allele (with at least 3 independent replications for each allele).
• Studies reporting single alleles may be considered acceptable when:
• i) Complementation via transformation is used for confirmation
• ii) The allele has been previously characterized and published and is representative of multiple independent lines;
• iii) Systems where genetic transformation is difficult or not yet possible, alternative evidence should be presented supporting the reported allele.

These submission requirements must be met:

• Submissions to the section should comply with the technical requirements for proteomics studies as indicated in the author guidelines (here).
• All proteomics datasets (even if only a small portion of the data is being discussed) must be submitted to an online repository (e.g. Figshare, PRIDE) before submission and the identifier (and reviewer access) needs to be included in the manuscript.

Submission

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