2DE	2 Dimensional Gel Electrophoresis
2D-DIGE	2 Dimensional Fluorescence Difference Gel Electrophoresis
AP-MS	Affinity Purification Mass Spectrometry
AQUA	Absolute Quantification
BiFC	Bimolecular Fluorescence Complementation
CAM	Crassulacean Acid Metabolism
CE	Capillary Electrophoresis
DDA	Data Dependent Acquisition
DEGs	Differentially Expressed Genes
DEPs	Differentially Expressed Proteins
DIA	Data Independent Acquisition
emPAI	Exponentially Modified Protein Abundance Index
FlexiQuant	Full-Length Expressed Stable Isotope-labeled Proteins for Quantification
FT-MS	Fourier Transform-Mass Spectrometry
ELISA	Enzyme-Linked Immunosorbent Assay
FRET	Förster Resonance Energy Transfer
GC	Gas Chromatography
GO	Gene Ontology
GRN	Gene Regulatory Network
GS	Gene Significance
GWAS	Genome Wide Association Study
HILIC	Hydrophilic Interaction Liquid Chromatography
HMDB	Human Metabolome Database
HPLC	High Performance Liquid Chromatography
ICAT	Isotope-Coded Affinity Tag
ICPL	Isotope-Coded Protein Label
kME	Eigengene-Based Connectivity
LC	Liquid Chromatography
MeRy-B	Metabolomic Repository Bordeaux
miRNA	microRNA
MRM	Multiple-Reaction Monitoring
mRNA	messenger RNA
MS	Mass Spectrometry
MS/MS	tandem mass spectra
MudPIT	Multidimensional Protein Identification Technology
MW	Molecular Weight
NGS	Next Generation Sequencing
NMR	Nuclear Magnetic Resonance
NSAF	Normalized spectral abundance factor
ODEs	Ordinary Differential Equations
PC	Pearson’s Correlation
PCS	Peptide-Concatenated Standards
pI	Isoelectric point
PMN	Plant Metabolic Network Database
PPI	Protein-Protein Interaction
PPIN	Plant-Pathogen Interaction Network
PRM	Parallel Reaction Monitoring
PTMs	Post Translational Modifications
PrEST	Protein Epitope Signature Tag
QconCAT	Quantification Concatemer
QTL	Quantitative Trait Locus
RNA-Seq	RNA Sequencing
siRNA	small interference RNA
SpC	Spectral Count
SEC	Size-Exclusion Chromatography
SNP	Single Nucleotide Polymorphism
SRM	Selected Reaction Monitoring
SVM	Support Vector Machine
SWATH	Sequential Windowed Acquisition of All Theoretical Fragment Ion Mass Spectra
SWIM	SWItchMiner
TAP-MS	Tandem Affinity Purification coupled with Mass Spectrometry
TMT	Tandem Mass Tags
WGCNA	Weighted Gene Co-expression Network Analysis
XICs	Extracted Ion Chromatogram
XL	Cross Linking
Y2H	Yeast Two Hybrid