MatrixAssisted Laser Desorption TimeofFlight Mass Spectrometry MALDITOF

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Matrix-Assisted Laser Desorption Time-of-Flight
Mass Spectrometry (MALDI-TOF)
Ions
Laser pulse irradiation
Sample
Matrix
Sample plate
Sample plate
Laser
Detector
Acceleration grids
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In-Gel Tryptic Digestion
FAP
MW
Add trypsin
Cut and wash gel slice
Extract peptides
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MALDI-TOF of FAP 3 Tryptic Digest
762.457
100
MW Std
MW Std
1296.686
2751.646
1265.674
Relative Intensity

1692.849
2750.654
763.472
1314.638
3637.783
1781.032
1144.528
1978.006
2842.411
3635.850
1019.480
848.439
3017.641
2145.132
2274.163
2557.281
3079.554
0
800
1000
1200
1400
1600
1800
2000
2200
2400
2600
2800
3000
3200
3400
3600
m/z
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Isotopic Resolution of Singly- and Doubly-Charged
Peptides
m/z785.865 (z2) m(m/z) x z mass of ion1571.73
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MALDI-TOF Peak List 1 (Peptide m/z list)
687.8751 699.3557 703.8684 711.1545 718.2427 719.8
397 730.2529 731.3375 791.4318 805.3564 839.2354 8
48.2219 896.5079 914.4462 925.5188
945.4449 989.5048 1009.6805 1054.4341 1063.4326 10
96.4844 1119.5581 1146.5930 1157.5448 1170.5892 11
88.5544 1217.5513 1245.6525 1267.6544 1276.5752
1303.6635 1304.7330 1342.6917 1346.6853 1396.5658
1473.8118 1572.8462 1629.8423 1671.9592 1677.7692
1699.8380 1715.7720 1742.9373 1773.9910 1783.0117

1857.0665 1940.9438 2198.2708 2269.0132 2328.1521
2746.4456 2806.4028 2993.6172 3712.7993 3798.9075
3960.8984 4019.6890
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Quadrupole Time-of-Flight (Q-TOF) Mass
Spectrometer
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1-D SDS PAGE of Urothelial Membrane Protein
Complex
100
875.08
66 K
Selected as precursor ions for MS/MS sequencing
C
1082.69
45 K
B
36 K
A

29 K
772.00
24 K
Cut and in-gel digested
21 K
14 K
0
1400
1000
1200
600
800
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Liquid chromatography - mass spectrometry (LC-MS)
Data-dependent nanoLC/ESI-MS/MS
autosampler
75?m I.D. ? 15cm, C18
Waters CapLC system
Q-TOF mass spectrometer
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MS/MS Sequencing of the m/z 875 Tryptic Fragment
A
T
Y
A
I/L
E
N
V
I/L
S
Q
N
G
I/L
V
R
y11
y9
y8
100
MH
1236.56
937.40
1036.46
y14
y10
1535.68
1149.53

y5
y12
y6
y4
581.26
1364.60
y7
510.23
694.34
y3
823.36
347.18
y13
y15
y2
y1
0
m/z
200
400
600
800
1000
1200
1400
1600
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A single DTA file (ms/ms of one peptide)
842.5046 2 142.9491 19.9629 143.9460
0.2450 170.9861 205.8167 183.0936 0.3334 224.0933
0.0136 228.0909 2.3326 268.1267 0.4691 272.1439
62.7571 273.1343 0.9928 288.1571 1.5253 298.1678
0.2026 323.1713 3.7294 325.2136 82.8106 328.2051
3.5819 341.1862 5.1490 343.2254 12.6910 344.9998
22.1723 353.2261 101.0716
364.9312 0.4143 371.2211 9.7322 385.2668
25.8953 386.2694 0.9792 394.1730 0.2044 395.2623
0.3770 401.0884 20.7589 403.1064 0.7991 422.2049
1.7898 423.2179 0.5638 436.2427 2.2053 453.1835
5.1715 454.3121 2.6212 458.3101 1.8438 461.2626
0.7628 472.3110 1494.9565 507.2370
11.3854 509.2536 3.0693 535.2925 0.8461 543.3054
12.8232
553.3311 2.6431 571.3781 60.9543 575.3595
0.4238 636.3104 0.4753 654.4095 110.9284 655.3958
6.6614 672.4235 1759.5968 673.3980
115.6948 682.4263 6.3140 705.4057 8.0873 725.4510
100.6408 726.1937 8.9482 743.4511
319.9946 769.5033 9.8461 781.4910
18.6391 824.5270 904.2136 842.5189
21.8975 861.6154 3.5977 878.5598 0.7447 879.5229
13.1704
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Some Important URL's
http//www.matrixscience.com/search_form_select.ht
ml http//saturn.med.nyu.edu/research/sb/PSB03/We
ek13.html
Key Search Parameters Data format is SEQUEST
(.dta) Instrument for MS/MS is ESI QUAD-TOF