This document discusses current limitations and future directions in plant proteomics. It outlines several key challenges including the diversity of crop systems, limitations in tissue and cell isolations, difficulties in extracting and separating low abundant proteins, poor database annotation, and the need for improved validation and bioinformatics tools. Future work aims to address these issues through approaches like label-free proteomics, targeted assays, orthoproteomics, and large-scale comparative studies across genotypes.

1. CURREN
T
LIMITATI
ONS
CROP SYSTEMS
TISSUE AND
CELL
ISOLATIONS
PROTEIN
EXTRACTION
PROTEIN SEPARATION, DIGESTION &
QUANTITATION
DATABASE
SEARCH &
MAPPING TO
GENOME
DATA
VALIDATION
AND
INTERPRETAT
ION
metabolite profiling
High throughput
enzymatic assay
Bioinformatics tools
and databases
BIOMARKERS
DEVELOPMENT
CURRENT
LIMITATIONS
FUTURE DIRECTIONS
- Diversity of systems
Model crop species for
proteomics studies
- Selection of cell types
- Laser microdissection
- Fluorescent-activated
cell sorting (FACS)
- Highly abundant
proteins
- Detergent compatible
with 2-D gel & labelling
- Depletion by solvent,
antibody & fractionation
- Sequential extraction
- CPLLs
- Costs of DIGE and labelling approaches
- Detection & quantitation of low abundant proteins
- Characterization of protein modifications
- Label-free proteomics
- Peptide enrichment
- Selected reaction monitoring (SRM)
- High accuracy and sensitivity mass spectrometers
- Poor annotation
- High sequence
redundancy
- Curated databases
- Identification and
quantitation by unique
peptide
- Multihit and
normalization strategies
- Availability of
bioinformatics
tools
- Access to validation
tools
- High-throughput
enzymatic
assays
- Costs for large scale
proteomics
- Label-free proteomics
- Orthoproteomics
- Large scale
comparative
proteomics
- Targeted approach
(SRM)
in contrasting genotypes