CH908, Problem set ? – Ion Sources

1. The following is an electrospray mass spectrum. Calculate the mass and charge state of each ion. Some of the peaks cannot be assigned. Why not? What are the possible sources of these peaks?

There's many ways to solve this problem, but this was my simple way: create a excel spreadsheet and guess the charge states until they all line up. Look at the standard deviation of the last column.

m/z / z = z + n / m = z*m/z - z*H
764.7936 / 36 / 27496.29 / 37 / 28260.07 / 38 / 29023.86
785.4459 / 35 / 27455.33 / 36 / 28239.77 / 37 / 29024.21
807.228 / 34 / 27411.49 / 35 / 28217.71 / 36 / 29023.93
830.2614 / 33 / 27365.37 / 34 / 28194.62 / 35 / 29023.88
854.6555 / 32 / 27316.73 / 33 / 28170.37 / 34 / 29024.02
880.5196 / 31 / 27264.87 / 32 / 28144.38 / 33 / 29023.89
908.0058 / 30 / 27209.94 / 31 / 28116.94 / 32 / 29023.94
937.2675 / 29 / 27151.53 / 30 / 28087.79 / 31 / 29024.05
968.4701 / 28 / 27088.94 / 29 / 28056.41 / 30 / 29023.87
1001.841 / 27 / 27022.5 / 28 / 28023.33 / 29 / 29024.17
1037.575 / 26 / 26950.73 / 27 / 27987.3 / 28 / 29023.87
1075.965 / 25 / 26873.92 / 26 / 27948.88 / 27 / 29023.84
1117.312 / 24 / 26791.3 / 25 / 27907.6 / 26 / 29023.91
1161.956 / 23 / 26701.8 / 24 / 27862.75 / 25 / 29023.7
1210.33 / 22 / 26605.08 / 23 / 27814.4 / 24 / 29023.72
1262.905 / 21 / 26499.83 / 22 / 27761.73 / 23 / 29023.63
1320.267 / 20 / 26385.19 / 21 / 27704.45 / 22 / 29023.71
1383.101 / 19 / 26259.78 / 20 / 27641.87 / 21 / 29023.97
1452.179 / 18 / 26121.07 / 19 / 27572.24 / 20 / 29023.41
1528.597 / 17 / 25969.01 / 18 / 27496.6 / 19 / 29024.18
1613.477 / 16 / 25799.51 / 17 / 27411.98 / 18 / 29024.45
σ / 512.6327 / σ / 256.3191 / σ / 0.225443
n / 15 / 16 / 17
H / 1.007825

Some of the small, interspersed peaks, like 714 and 659, and such cannot be assigned because we don't have the resolution to determine their charge state, and we don't know if there are more than one charge state of them.

They are almost certainly nozzle-skimmer (in source) CAD fragments from the main protein. However, they could also be contaminants or from a previous sample (carry-over).
2. Calculate the repeat unit mass and end group masses of the polymer in the following MALDI spectrum.

Again, there's many ways to solve this, but I used a simple excel spreadsheet:

MALDI TOF spectrum of a polymer
guestimate / residual mass
delta mass / dm/median / oligomer number
1053.586 / 44.04 / 1.000313734 / 23 / 40.9836875
1097.626 / 44.033 / 1.000154737 / 24 / 40.9975
1141.659 / 44.027 / 1.000018455 / 25 / 41.0043125
1185.686 / 44.023 / 0.9999276 / 26 / 41.005125
1229.709 / 44.026 / 0.999995741 / 27 / 41.0019375
1273.735 / 44.025 / 0.999973027 / 28 / 41.00175
1317.76 / 44.025 / 0.999973027 / 29 / 41.0005625
1361.785 / 44.027 / 1.000018455 / 30 / 40.999375
1405.812 / 176.102 / 3.999937537 / 31 / 41.0001875
1581.914 / 176.105 / 4.000005678 / 35 / 40.9974375
1758.019 / 44.03 / 1.000086596 / 39 / 40.9976875
1802.049 / 44.025 / 0.999973027 / 40 / 41.0015
1846.074 / 44.024 / 0.999950314 / 41 / 41.0003125
1890.098 / 44.026 / 0.999995741 / 42 / 40.998125
1934.124 / 44.019 / 0.999836745 / 43 / 40.9979375
1978.143 / 44.026 / 0.999995741 / 44 / 40.99075
2022.169 / 44.018 / 0.999814031 / 45 / 40.9905625
2066.187 / 44.025 / 0.999973027 / 46 / 40.982375
2110.212 / 87.833 / 1.99501717 / 47 / 40.9811875
2198.045 / 49 / 40.7618125
median / 44.0262 / average / 40.9847
guess oligomer number N = / 23.9308934

This spreadsheet says that the oligomer mass is 44.0262 (polyethylene glycol) with a residual mass of 40.9847. This residual will be the sum of the two endgroups plus the charge carrier. The sample is singly charged, so there's only one of the latter.

This is a strange value, but it corresponds to water (18.011) plus a sodium ion (22.989) = 41.000. This is an error of 15 millidaltons, which is not bad for a long extrapolation. It would be better with higher resolution data.

3. Using polyacrylamide gel electrophoresis, a silver-stained gel spot yields a dark band for a protein of about 40 kDa. Could you get a usable signal from ESI - FTMS? ESI – qTOF? MALDI – TOF?

A dark band on a silver stained gel will have something like 1-10 nanograms of material. At 40 kDa, that's 250 - 2500 femtomoles. If the sample is clean, and if you can extract most of that protein, that's plenty for detection on all three instruments. The FTMS will be the worst of the three, and will often struggle with 1-10 femtomoles of material.