Table 2.

The advantages and disadvantages of strategies used to study drug resistance.

	Techniques	Advantages	Disadvantages	References
Genomics	Southern blot, microarray, northern blot, sequencing, PFGE, FIGE	(a) Genetic basis of observed phenotype (b) Large genome coverage (22–97.5%) (c) Easy to perform and interpret (d) Reproducible	(a) Not much differences amongst species at genome level (b) Not much informative (c) Gene functions for most genes still unknown.	[7, 8, 14, 15, 22, 37, 41, 42, 44, 47, 51, 62]
Proteomics	2DE, MALDI-TOF, LC-MS/MS, LC-ESI-MS/MS, western blot, immunoblot	(a) Functional output of the cell (b) Posttranslational changes visualised (c) Mostly automated (d) Good indicator of protein abundance and expression	(a) Number of proteins lack annotated functions (b) Less abundant proteins hard to detect (c) Results from in vivo amastigotes difficult to interpret (d) Not reproducible in some cases	[6, 20, 23, 29, 30, 40, 49, 51, 51]
Metabolomics	CE-ESI-TOF-MS, HPLC, MALDI-TOF, flow cytometry, GC-MS	(a) Closest correlation to phenotype (b) Rapid visualisation and prediction of biological impact (c) High mass accuracy (d) Highly specific	(a) Unable to quantify most of the metabolites. (b) Analyte derivatives make data complex (c) Data hard to analyse (d) Complicated bioinformatics tools needed (e) Costly instrumentation	[4, 5, 22, 24, 32, 35, 41, 43, 48, 51]

PFGE: pulsed field gel electrophoresis; FIGE: field inversion gel electrophoresis; 2DE: two-dimensional gel electrophoresis; MALDI-TOF MS: matrix assisted laser desorption/ionisation time of flight mass spectrometry; LC-MS/MS: liquid chromatography mass spectra/mass spectrometry; LC-ESI-MS/MS: liquid chromatography electrospray ionisation tandem mass spectrometry; CE-ESI-TOF-MS: capillary electrophoresis mass spectrometry coupled with electrospray ionisation mass spectrometry; HPLC: high performance liquid chromatography; GC-MS: gas chromatography mass spectrometry.