Acquisition Performance Kit)). Prior to beginning a large analysis,
we ensure that optimum conditions of our technology are met by
monitoring several instrument-dependent quality parameters
[120]. Additionally, as mass drift can happen when operating
TOF-based instruments, we ensure that proper external calibrations are run after a predefined period that can vary upon lab
conditions or sample set. External calibrations are carried out utilizing PepCalMix standard from which at least seven peptides are
used to maintain calibration at MS level and seven fragment ions to
calibrate MS/MS (Tables 1 and 2).
Table 1
Peptides from PepCalMix used in Triple TOF MS calibration
Compound name
Precursor m/z
(Da)
Use for
MS/MS
CE for
MS/MS
DP for
MS/MS
Theorical retention
time (min)
1 AETSELHTSLK
408.5501
0
40
80
15.6
2 GAYVEVTAK
473.2602
0
40
80
16.5
3 IGNEQGVSR
485.253
0
40
80
12.7
4 LVGTPAEER
491.2656
0
40
80
15
5 LDSTSIPVAK
519.7997
0
40
80
18
6 AGLIVAEGVTK
533.3233
0
40
80
20.3
7 LGLDFDSFR
540.2734
0
40
80
24.2
8 GFTAYYIPR
549.2863
0
40
80
22.5
9 SGGLLWQLVR
569.8339
0
40
80
24.4
10 AVGANPEQLTR
583.3136
0
40
80
17.1
11 SAEGLDASASLR 593.8005
0
40
80
18.2
12 VFTPLEVDVAK
613.3495
0
40
80
23.6
13 VGNEIQYVALR
636.3527
0
40
80
21.6
14 YIELAPGVDNSK 657.345
0
40
80
20.4
15 DGTFAVDGPG
VIAK
677.8583
0
40
80
21.7
16 YDSINNTEVSGIR 739.3615
0
40
80
18.8
17 SPYVITGPGVVE
YK
758.9105
1
40
80
22.1
18 ALENDIGVPSDA
TVK
768.9034
0
40
80
20.4
19 AVYFYAPQIPL
YANK
883.4738
0
40
80
24.2
20 TVESLFPEEAE
TPGSAVR
964.9774
0
40
80
23.3
SWATH-MS Protocols in Human Diseases
129