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Biological Magnetic Resonance Data BankA Repository for Data from NMR Spectroscopy on Proteins, Peptides, Nucleic Acids, and other Biomolecules |
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Biological Magnetic Resonance Data BankA Repository for Data from NMR Spectroscopy on Proteins, Peptides, Nucleic Acids, and other Biomolecules |
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The page, "Heuristically Determined Formulas by Mass," is designed to be a tool for the Mass Spectrometry community. It is meant to be used for generating large lists of potential formulas with different isotopic labelings. The resulting files can then be compared using Mathematica scripts written by Adrian Hegeman. Because of this, there is a prefered format for the input files.
The software is designed to accept a file or list with one comparison per line, with each line containing an index number folowed by a retention time followed by the mass to be queried against.
For example:
1 38.378 211.1558 2 19.313 234.1112 3 52.042 191.1523 4 38.386 840.5971 5 54.5 243.1246 6 2.724 109.0015 7 4.045 108.1168 8 8.374 127.0994 9 8.375 174.1091 10 32.563 196.1336
It can also accept a file or list containing only masses. In this case, an index will be generated and the retention time will be set to '?'. Whichever format you choose, mark the appropriate 'Mass list type' radio button.
The results will be in a tab separated file that can be downloaded. The result lines will be of the form:
index-number retention-time input-mass matching-mass formula #C #H #N #O #P #SAn example of the results:
1 38.378 211.155800000 211.153693279 C9H19N2O1P1S0 9 19 2 1 1 0 1 38.378 211.155800000 211.153830135 C8H17N3O3P0S0 8 17 3 3 0 0 2 19.313 234.111200000 234.110630624 C14H8N2O1P0S0 14 8 2 1 0 0 2 19.313 234.111200000 234.111200340 C9H13N4O1P0S1 9 13 4 1 0 1 2 19.313 234.111200000 234.112102130 C5H12N9O0P1S0 5 12 9 0 1 0 2 19.313 234.111200000 234.112981554 C12H16N0O0P2S0 12 16 0 0 2 0 2 19.313 234.111200000 234.113118410 C11H14N1O2P1S0 11 14 1 2 1 0 2 19.313 234.111200000 234.113255266 C10H12N2O4P0S0 10 12 2 4 0 0 3 52.042 191.152300000 191.150916694 C5H14N8O0P0S0 5 14 8 0 0 0 3 52.042 191.152300000 191.151932974 C11H16N0O2P0S0 11 16 0 2 0 0
The formulas were generated as combinations of C, H, N, S, O, and P with natural abundance molecular masses of 2000 Da or less, and then rules for filtering the billions of possibilities down to around 400 million. These rules were obtained from the paper by Kind and Fiehn, "Seven Golden Rules for heuristic filtering of molecular formulas obtained by accurate mass spectrometry" (Kind T. and Fiehn O. BMC Bioinformatics. 2007 Mar 27;8:105.Click here to read)