1. Which sample preparation? Identification/ quantitation?
4 h gradient
1h gradient
Protocol 2
Protocol 5
Protocol 4
Protocol 3
Protocol 1
Which sample type?
Cells/tissues
Body fluids
IP/AP/purified proteins/gel slices
Fractionation?
YES NO
Which sample preparation?
In-gel
In-solution
MARS-14 depletion
Length of LC method?
UHR-QTOF
(maXis 4G+)
MS instrument
ID+LFQ
Identification/ quantitation? ID
Ion trap
(amaZon Speed)
MaxQuant
Data analysis
Mascot
Analysis C
Analysis A
Choice of analysis
Analysis B