I

N D E X

Calibrating mass, automatic (Mariner data only) (continued)

reverting to instrument calibration 5-22

troubleshooting 9-9turning on 5-34when to use 5-28

Calibrating mass, manual

see also Calibration constants baseline correcting and deisotoping

to optimize mass accuracy 7-14

calibration reference file (REF) 5-17

commands dimmed on menu 9-11constants, applying A and B to new

file 5-16

error, fit 5-12error, initial 5-12

fit outliers, eliminating 5-12importing, Voyager

requirements 5-25multi-point calibration 5-8overview 5-5

peak matches, clearing list 5-13peak matches, sorting 5-11peak matching, automatic 5-6peak matching, manual 5-6peak weighting factor 5-10procedure 5-8

results 5-13

reverting to instrument calibration 5-22

single-point calibration 5-8troubleshooting 9-9when to use 5-6

Calibrating mass, PSD (Voyager data only)

all segment masses considered 8-15

calibration reference file (REF) 8-21

constants, applying A and B to new file 8-20

error message when selecting calibration reference file 8-14

internal calibration using known monoamino acid fragment ions 8-10

internal calibration, values used 8-7

multi-point calibration 8-10peak detection, checking before

calibrating 8-10

peak matches, clearing list 8-15peak matching, automatic 8-15peak matching, manual 8-16peak weighting factor 8-14Precursor mass, changing 8-23procedure 8-12

results 8-18

reverting to instrument calibration 5-22

selecting peaks for optimum mass accuracy 8-19

selecting peaks near Max Stitch Mass 8-19

single-point calibration 8-10 Calibration, see Calibrating mass

Index-4 Applied Biosystems