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MS-GF+ (aka MSGF+ or MSGFPlus) performs peptide identification by scoring MS/MS spectra against peptides derived from a protein sequence database.
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Why is my TMT ion intensity as same with each other #85

Open zlq978983092 opened 4 years ago

zlq978983092 commented 4 years ago

I use masic to run a TMT mzml.files. The sample is labled with TMT11(Tumor labeled with 127N, 128N, 129N, 130N and 131N; adjacent non-tumor liver tissue labeled with 127C, 128C, 129C, 130C and 131C)。But the ion intensity of the pairs are almost the same.Could anyone tell me why?

Ion_126.128 Ion_127.125 Ion_127.131 Ion_128.128 Ion_128.134 Ion_129.131 Ion_129.138
4789.06 10126.88 10126.88 8772.32 8772.32 19953.53 19953.53
0 0 0 0 0 0 0
0 0 0 797.6 797.6 0 0
0 0 0 860.02 860.02 0 0
0 767.81 767.81 776.82 776.82 0 0
0 0 0 663.34 663.34 0 0
0 0 0 0 0 0 0
3293.81 2931.59 2931.59 3170.81 3170.81 5620.08 5620.08
0 0 0 0 0 0 0
0 0 0 0 0 0 0
0 0 0 0 0 0 0
0 0 0 0 0 0 0
0 0 0 0 0 0 0
0 0 0 0 0 538.7 538.7
2743.13 5481.95 5481.95 7949.49 7949.49 9733.88 9733.88
0 0 0 0 0 0 0
3081.06 1001.36 1001.36 3266.14 3266.14 5401.92 5401.92
0 801.55 801.55 1027.26 1027.26 1175.86 1175.86
512.51 0 0 0 0 0 0
0 540.16 0 0 0 0 0
0 0 0 0 0 0 0
0 0 0 0 0 0 0
0 0 0 631.54 631.54 1059.93 1059.93
740.33 0 0 739.49 739.49 956.81 956.81
0 582.12 582.12 0 0 0 0
0 0 0 0 0 0 0
1702.59 936.13 936.13 2519.36 2519.36 2867.07 2867.07
0 0 0 0 0 0 0
0 570.27 570.27 0 0 0 0
2211.69 1969 1969 945.66 945.66 1174.08 1174.08
3944.25 9181.27 9181.27 8947.57 8947.57 17669.34 17669.34
0 0 0 0 0 0 0
0 0 0 0 0 0 0
995.6 0 0 0 0 940.38 940.38
0 0 0 0 0 0 0
0 0 0 0 0 0 0
0 0 0 0 0 0 0
0 0 0 0 0 607.69 607.69
0 0 0 0 0 0 0
alchemistmatt commented 4 years ago

TMT 11 ions are very closely spaced; you need to use a very tight reporter ion tolerance.
I suggest 0.003 Da

For an example parameter file, see https://github.com/PNNL-Comp-Mass-Spec/MASIC/blob/master/Docs/Parameter_Files/TMT11_LTQ-FT_10ppm_ReporterTol0.003Da_2017-03-17.xml

which has

<item key="ReporterIonToleranceDa" value="0.003" />
zlq978983092 commented 4 years ago

Thanks a lot. I use your parameter to run again and I think I got the proper result !

在 2019-12-18 14:20:49，"Matthew Monroe" notifications@github.com 写道：

TMT 11 ions are very closely spaced; you need to use a very tight reporter ion tolerance. I suggest 0.003 Da

For an example parameter file, see https://github.com/PNNL-Comp-Mass-Spec/MASIC/blob/master/Docs/Parameter_Files/TMT11_LTQ-FT_10ppm_ReporterTol0.003Da_2017-03-17.xml

which has

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