Fourteen years of plant proteomics reflected in Proteomics: Moving from model species and 2DE‐based approaches to orphan species and gel‐free platforms

Abstract

In this article, the topic of plant proteomics is reviewed based on related papers published in the journal Proteomics since publication of the first issue in 2001. In total, around 300 original papers and 41 reviews published in Proteomics between 2000 and 2014 have been surveyed. Our main objective for this review is to help bridge the gap between plant biologists and proteomics technologists, two often very separate groups. Over the past years a number of reviews on plant proteomics have been published . To avoid repetition we have focused on more recent literature published after 2010, and have chosen to rather make continuous reference to older publications. The use of the latest proteomics techniques and their integration with other approaches in the "systems biology" direction are discussed more in detail. Finally we comment on the recent history, state of the art, and future directions of plant proteomics, using publications in Proteomics to illustrate the progress in the field. The review is organized into two major blocks, the first devoted to provide an overview of experimental systems (plants, plant organs, biological processes) and the second one to the methodology.

De novo peptide sequencing by deep learning

“…deep learning | MS | de novo sequencing P roteomics research focuses on large-scale studies to characterize the proteome, the entire set of proteins, in a living organism (1)(2)(3)(4)(5). In proteomics, de novo peptide sequencing from tandem MS data plays the key role in the characterization of novel protein sequences.…”

Advances in proteomic technologies and their scope of application in understanding plant–pathogen interactions

“…Therefore, for high precision and accurate quantification of biologically important samples, the strategy of isotope dilution is implemented with SRM/MRM/PRM techniques, wherein the samples are spiked with defined amounts of isotope-labelled analogues (Jorrin-Novo et al 2015). After isotope labelling, the true and precise abundance of each protein or peptide is determined by standards such as Absolute Quantification (AQUA), Quantification Concatamers (QconCAT) and Protein Standard Absolute Quantification (PSAQ).…”

“…Although, the application of genomics and transcriptomics has revolutionized the fundamental concept of plant-pathogen interactions, the application of proteomics that could complement genomics is relatively under-utilized or not exploited to its full potential in most of the crops. For many years, proteomics was viewed as an intricate field, because of variable physical and chemical properties of proteins at different physiological conditions, and difficulties in separation and identification of proteins (Gonzalez-Fernandez et al 2010;Jorrin-Novo et al 2015). However, the accumulating genome information of plants and pathogens coupled with the advances in protein/peptide separation technologies and mass spectrometry (MS) analyses, reduced the complexity of proteome analysis and identification of individual proteins.…”

Mecanismos de defesa do trigo contra a ferrugem da folha por genes e proteínas

“…Porém, as informações obtidas pela análise de transcriptoma podem ser incompletas pelo fato de ocorrerem muitas modificações pós-traducionais, assim como interações entre as proteínas. Portanto, a correlação entre mRNA e níveis de proteínas é baixa (36). A proteômica encarrega-se do estudo sistemático de um proteoma e permite avaliações quantitativas e qualitativas de proteínas que atuam no metabolismo celular (51,16).…”