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Table 1 Strengths and weaknesses of -omic techniques

From: A comprehensive multi-omics approach uncovers adaptations for growth and survival of Pseudomonas aeruginosa on n-alkanes

Technique Advantages Disadvantages
RNA-seq - Established protocols
- Many commercially available kits
- Captures both translated and non-translated regions of RNA
- mRNA abundance does not always correlate with protein abundance
- Expense and turn around time
Ribosome Footprinting (Ribo-seq) - Global view of all translated mRNA
- Nucleotide/codon-level resolution
- Identifies unique genomic sites: frameshifts, splice isoforms, ribosome pause sites
- Technically more difficult
- Time-consuming post-sequencing analysis
- Expense
Proteomic LC-MS - Represents net result of transcriptional and translational regulation
- Deconvolutes complex protein mixtures
- Simple to gather intra- and extracellular protein data
- Typically identifies fewer genes than nucleic acid-based tools
- No individual method to separate all proteins
Small Molecule LC-MS - Measures end product of enzymatic activity
- Standards can be used for simple quantitation
- Prior knowledge of elution time and exact mass helpful
- Different separation techniques for classes of molecules
  1. LC-MS liquid chromatography-mass spectrometry