Feature Detection Techniques for Preprocessing Proteomic Data

Table 1

Comparison table of gel-based and non-gel-based methods for proteomic data analysis. This table highlights some benefits and drawbacks to many popular technological approaches in analyzing protein samples. GB and NGB, respectively, denote the associated technique as gel-based or non-gel-based.

Analysis Method	Benefits	Drawbacks
2-DE-MS and DIGE-MS (GB)	1. DIGE minimizes gel-to-gel variation	1. low-abundant protein identification
	2. DIGE produces better spot matching	2. sensitive to experimental and technological variation
	3. allows for study of protein change on large scale	3. laborious process
	4. strong resolving power	4. difficulties automating procedure
	5. high sensitivity	5. protein comigration
	6. low equipment cost	6. study replication may be prohibitive
LC-MS and LC-MS/MS (GB)	1. fast procedure	1. difficulty analyzing low-abundance proteins
	2. easily automated high resolution measurements	2. not quantitative
		3. Expensive machines
	3. MS/MS improves the detection limits for some compounds	4. MS/MS spectrum TIC decreased compared to MS spectrum TIC
	4. MS/MS improves S/N ratio relative to MS	5. Ion activation methods affect spectra efficiency, reproducibility, feature detection
ICAT (NGB)	1. accurate relative quantification	1. missed identification of proteins containing little to no cysteine residue (i.e., cysteine-content biased)
	2. reduces peptide mixture complexity
	3. compatible with various fractionation methods	2. posttranslational modifications missed
	4. at least as sensitive as DIGE	3. complex interpretation of MS/MS spectra when biotin group added
		4. noise impacts peak detection for ICAT peaks with low expression levels
		5. compounds may dilute through LC column at different speeds
iTRAQ (NGB)	1. greater sensitivity than DIGE and ICAT	1. occasional inherent problem due to timed-ion selector resolution of tandem mass spectrometer
	2. can perform relative or absolute quantification in four phenotypes	2. compounds may dilute through LC column at different speeds
MudPIT (NGB)	1. orthogonality of the chromatographic phases in the separation process	1. does not allow for identification of the site at which probe labeling occurs
	2. robust representation of separated proteins peptides, from complex peptides	2. since the proteins are broken down to their component, any information about modifications and isoforms is lost.
		3. large computing power required to complete database searching
		4. the approach is generally limited to use with organisms that have complete genome sequence data available for searching