Table 1.

Common requirements for various aspects of proteomic and metabolomic sample analysis

	Proteomics	LC-MS based metabolomics
MS instrumentation	Ion trap, Q-TOF, QqQ, hybrid, Orbitrap	TOF, Q-TOF, QqQ, single-quad, Orbitrap
Ionisation	ESI, MALDI	ESI, APCI
Detector	MCP, electron multiplier, Orbitrap	MCP, electron multiplier, Orbitrap
Polarity	Positive	Positive/negative
High resolution	Required	Optional
High mass accuracy (MS1)	As high as possible	70 ppm or better
High scan speed	Required	Optional
High sensitivity	Required	Required/less critical
High dynamic range	Required	Required
MSn capability	Required	Optional (comparison to standards)
High mass accuracy (MSn)	Optional	Required
High resolution	Optional	Required
Chromatographic separation	Required	Required (screening)
Column chemistry	RP (HILIC)	RP, HILIC, others
Nano-flow	Required	Normal flow preferred
Injection volume	0.5–10 μL	1–100 μL
Long columns/gradients	Required	Optional
Low inter-day variability	Optional	Required
Software for analysis	Vendor-specific, commercial or free software	Vendor-specific and limited free software
MSMS analysis	Automated	Manual
Databases	Available for sequenced organisms	Incomplete
Identification of analyte	Required	Optional
Use of standards	Optional (absolute quantitation, SWATH)	Required