Gel-Based and Gel-Free Quantitative Proteomics Approaches at a Glance

Table 2

An overview of the latest MS-based quantitative proteomic studies on plant systems. The table shows the implemented quantitative approaches, plant species, biological questions, and reference of the corresponding paper.

Quantitative approach	Plant	Biological study	Authors
^18O labelling	Arabidopsis thaliana	Quantification of the degree of plasma membrane protein enrichment	[56]
ICAT	Arabidopsis thaliana	Localization of integral membrane proteins by using the localization of organelle proteins by isotope tagging (LOPIT)	[60]
ICAT	Hordeum vulgare	Identification of specific disulfide targets of barley thioredoxin in proteins released from barley aleurone layers	[63]
ICAT	Arabidopsis thaliana	Understanding of AtMPK6 role in transducing ozone-derived signals	[64]
ICAT	Arabidopsis thaliana	Functional information about S-nitrosylation sites in plants	[65]
ICAT	Triticum aestivum	Identification of wheat seed proteins and their related expression to chromosome deletion	[66]
ICAT, 2-DE, label-free	Zea mays	Quantitative comparative proteome analysis of purified mesophyll and bundle sheath chloroplast stroma in maize	[67]
ICAT	Oryza sativa	Protein profiling of uninucleate stage rice anther and identification of the CMS-HL-related proteins	[90]
ICAT	Arabidopsis thaliana	ProCoDeS (proteomic complex detection using sedimentation) for profiling the sedimentation of a large number of proteins	[91]
ICPL, iTRAQ	Ricinus communis	Quantitative proteomic comparison of ICPL versus iTRAQ on ricinus communis seeds	[71]
iTRAQ	Solanum tuberosum	Comparative proteomic approach of potato tubers after 0 and 5 months of storage at 5°C	[45]
iTRAQ	Arabidopsis thaliana	Quantitative study of the secreted proteins from Arabidopsis cells in response to Pseudomonas syringae	[76]
iTRAQ	Vitis vinifera	Comparative proteomic study of dynamic changes in control and infected Vitis vinifera	[77]
iTRAQ	Vitis vinifera	Comparative analysis of differentially expressed proteins in Erysiphe necator infected grape	[78]
iTRAQ	Citrus sinensis	Comparative proteomic approach of the pathogenic process of HLB in affected sweet orange leaves	[79]
iTRAQ	Zea mays	Proteomic approach of two maize inbreds in the early infection by Fusarium graminearum	[80]
iTRAQ	Arabidopsis thaliana	Changes tack of the Arabidopsis phosphoproteome during the defence response to Pseudomonas syringae	[81]
iTRAQ	Arabidopsis thaliana	Investigation of the proteomic changes in the chloroplasts of clpr2-1	[82]
iTRAQ	Hordeum vulgare	Comparative proteomic study of boron-tolerant and -intolerant barley	[83]
iTRAQ	Hordeum vulgare	Quantitative proteomic approach to unravel the contribution of vacuolar transporters to Cd^2+ detoxification	[84]
iTRAQ, 2D-DIGE	Brassica juncea	Quantitative proteomic approaches to understand the effect of cadmium on Brassica juncea roots	[85]
iTRAQ, label-free	Oryza sativa	Quantitative proteomic response of rice seedling to 48, 72, and 96 h of cold stress	[86]
iTRAQ, BN-PAGE, label-free	Zea mays	Comparative analysis of protein abundance in chloroplast thylakoid and envelope membrane proteomes in maize	[87]
Cys-TMT	Solanum lycopersicum	Study of the redox proteomic analysis of the Pseudomonas syringae tomato DC3000 treated tomato leaves	[89]
SILAC	Chlamydomonas reinhardtii	Dynamic changes of proteome turnover under salt stress	[92]
SILAC	Ostreococcus tauri	Quantitative proteomics on synthesis and degradation rate constants of individual proteins in autotrophic organisms	[93]
SILAC	Chlamydomonas reinhardtii	Comparative proteomics on the iron deficiency impact in Chlamydomonas reinhardtii	[94]
^14N/^15N labelling	Solanum tuberosum	Effectiveness of fully label a plant with ^15N isotopes	[95]
^14N/^15N labelling	Arabidopsis thaliana	Demonstration of plant ^15N labelling as a powerful comparative quantitative proteomic approach	[96]
^14N/^15N labelling	Arabidopsis thaliana	Comparative analysis of Arabidopsis cells following a cadmium exposure	[97]
^14N/^15N labelling	Nicotiana tabacum	Quantitative proteomic approach of the detergent-resistant membranes of tobacco cells in response to cryptogenin	[98]
^14N/^15N labelling	Arabidopsis thaliana	Quantitative approach of phosphorylated sites in signaling and protein response in flg22 or xylanase Arabidopsis-treated cells	[99]
HILEP	Arabidopsis thaliana	Demonstration of HILEP suitability for relative plant quantitative proteomic subjected to oxidative stress	[100]
SILIP	Solanum lycopersicum	SILIP development for homogeneously ^15N incorporation within the whole plant proteome	[101]
^14N/^15N labelling	Arabidopsis thaliana	Investigation of both partial and full ^15N labelling effect on quantitative analysis in a complex mixture	[102]
Spectral counting	Arabidopsis thaliana	Proteome map of Arabidopsis  thaliana	[103]
Spectral counting	Arabidopsis thaliana	Comprehensive Arabidopsis chloroplast proteome analysis	[104]
Spectral counting	Glycine max	Evaluation of the suitability of spectral counting to quantitative soybean proteome study	[105]
Spectral counting	Oryza sativa	Differential proteomic response of rice leaves exposed to high- and low-temperature stress	[106]
Peak ion intensity	Arabidopsis thaliana	Sucrose-induced phosphorylation changes of plasma membrane proteins in Arabidopsis	[107]
Peak ion intensity	Solanum lycopersicum	Quantitative proteomics of phosphoproteins in tomato hypersensitive response	[108]
Peak ion intensity, 2-DE	Glycine max	Investigation of the soybean plasma membrane function in response to flooding stress	[109]
Spectral counting + peak ion intensity	Medicago truncatula	Comparison of two label-free quantitative approaches on nodule protein extracts from Medicago truncatula	[110]
Spectral counting + peak ion intensity	Arachis hypogaea	Investigation of major allergens in transgenic peanut lines	[111]
MS^E	Apium graveolens	Analysis of the Apium graveolens protein response to salicylic acid	[112]
MS^E	Zea mays	Proteomic approach assessment of the transition from dark to light in maize seedlings	[113]
MS^E	Arabidopsis thaliana	Proteomic changes in the cell wall proteome in response to salicylic acid	[114]
MS^E	Hordeum vulgare	Study of the UV-B irradiation effect on the barley proteome	[115]