Simulate_Mass_SpectrPeptide_Sequence00 This is a peptide sequence in the one letter amino acid code. 2013-03-05 17:24:34.891 UTC PEPTIDE 2013-03-12 13:50:49.564 UTC Resolving_Power00 20000 2013-03-12 13:51:07.122 UTC This is the resolving power of the mass spectrometer 2013-03-12 13:50:58.238 UTC Distribution_Image This is a PNG image of the simulated mass spectrum, zoomed in to the region around the distribution. 2013-03-12 13:53:06.433 UTC Integer_Mass This is the peptide integer mass 2013-03-12 13:53:15.730 UTC Monoisotopic_Mass This is the peptide monoisotopic mass 2013-03-12 13:53:24.420 UTC Simulate_Mass_Spectrumelemental_composition1RP0distribution_image00int_mass00mi_mass00 This Rshell calculates the isotopic distribution (assuming singly protonated species) according to the FFT method by Rockwood et al. implemented in 1999 by Magnus Palmblad. See also http://www.ms-utils.org/isotop.r and http://www.ms-utils.org/isotop.html for more information and a MATLAB version of the same algorithm. The peak shape can easily be substituted for a Lorentzian for FT-MS. 2013-03-12 13:52:54.46 UTC net.sf.taverna.t2.activitiesrshell-activity1.4net.sf.taverna.t2.activities.rshell.RshellActivity elemental_composition 1 false RP 0 false distribution_image 0 0 mi_mass 0 0 int_mass 0 0 false localhost 6311 false false elemental_composition DOUBLE_LIST RP DOUBLE distribution_image PNG_FILE mi_mass DOUBLE int_mass DOUBLE net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeCalculate_Elemental_Compositionpeptide_sequence0elemental_composition11 This BeanShell takes an amino acid sequence in the one letter code and calculates the elemental composition of the five elements found in the 20 common amino acids. The algorithm can easily be extended to consider also phosphorylated or otherwise modified amino acids. 2013-03-05 17:23:32.180 UTC net.sf.taverna.t2.activitiesbeanshell-activity1.4net.sf.taverna.t2.activities.beanshell.BeanshellActivity peptide_sequence 0 text/plain java.lang.String true elemental_composition 1 1 workflow net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeSimulate_Mass_Spectrumelemental_compositionCalculate_Elemental_Compositionelemental_compositionSimulate_Mass_SpectrumRPResolving_PowerCalculate_Elemental_Compositionpeptide_sequencePeptide_SequenceDistribution_ImageSimulate_Mass_Spectrumdistribution_imageInteger_MassSimulate_Mass_Spectrumint_massMonoisotopic_MassSimulate_Mass_Spectrummi_mass 1d01d819-2734-437f-97fd-4431aaa92679 2012-02-20 17:37:40.904 UTC 4de29351-5394-417b-8dca-b1d1db1ec28c 2013-03-05 16:11:46.592 UTC 4e1eb5af-6e1d-4305-a2ed-94aa08f42d15 2013-03-05 16:44:38.821 UTC d6be9bcd-ceb8-41ea-b27e-2c47f71a32da 2013-03-05 16:36:54.201 UTC 44a689d5-340f-43e4-984f-395ad66ec1f6 2013-03-05 16:31:39.223 UTC cf3a5e18-65c0-4e6a-bfbc-db2ab180a710 2013-03-12 13:28:25.841 UTC 972e6d33-6e8b-4d34-ae4c-24662c635e76 2013-03-12 13:45:33.840 UTC d855ea33-775c-4235-afac-403f037bcc20 2013-03-05 16:15:50.256 UTC c46ba829-cb52-4c61-9d2f-0fda2c4b7b1d 2013-03-05 15:55:50.274 UTC This workflow takes as input a peptide sequence and calculates the elemental composition of the peptide (Calculate_Elemental_Composition). This is then transferred as a numerical vector to the Rshell Simulate_Mass_Spectrum, that calculates the isotopic distribution using the FFT method and convolutes the theoretical (infinite resolution) distribution with a Gaussian peak shape. The building blocks can be used in any other workflows using the isotopic distribution of peptides or other molecules as measured by mass spectrometry. The workflow is tested and works in R 2.15.2 with Rserve 0.6.8 for R 2.15. 2013-03-12 13:50:38.4 UTC 3b10a1d3-0936-46ab-919b-de87d0dbcac0 2013-03-05 16:34:22.934 UTC 536e2162-9c56-44e5-85a4-896302aa8f35 2012-02-20 17:42:16.589 UTC 9cb75551-86f5-495c-90c1-70926a10cf14 2013-03-04 16:16:40.843 UTC fa0389ef-2ecd-4109-9b4f-5fe8d5645105 2013-03-06 15:21:57.171 UTC 65cb4310-4786-4b3d-8f1d-24a6e13d69bb 2013-03-05 16:38:31.408 UTC a2d4df5d-d976-4bdc-8010-7d3e757a7ce4 2013-03-12 13:47:50.530 UTC 87c48586-3e62-475f-8105-5fa2ed7baaea 2013-03-12 09:50:52.495 UTC fc2ac688-cd2d-470c-8b8b-698d4e2a659d 2013-03-12 10:10:55.279 UTC 4d24bd15-0bfd-4589-8936-3858e3891981 2012-02-20 17:41:14.534 UTC c9ade8c4-800c-4d66-aa44-9039b03d0eca 2013-03-04 16:12:57.548 UTC 7244455d-1918-4418-a502-73a036aee26f 2013-03-12 09:16:48.323 UTC 8ae54fb9-8182-407f-8724-9f1e9b61d625 2013-03-05 16:58:11.708 UTC 36e1f9f5-bb5b-44ff-8e91-e8e7e4ea838c 2013-03-05 15:34:36.315 UTC 6085e57f-ab6a-4a14-96cb-1f43e97dfc34 2013-03-05 16:05:36.807 UTC 8600a640-9948-490e-8906-580d31e16b57 2013-03-12 09:18:48.555 UTC 5fc899d5-2525-4da4-b25c-709ac37e2909 2013-03-05 15:47:07.362 UTC 8ebd1acf-b9bd-4e7e-91cc-c2e4aef3ae34 2013-03-04 16:37:04.861 UTC 9414c1f6-8df5-4ee8-83e2-bca4337826a8 2013-03-12 13:43:31.314 UTC f2e2286e-dca5-43cf-803e-7049f059cdfb 2013-03-12 13:53:32.844 UTC 384a355c-4f59-45a3-ae55-7cf3a02bfe81 2013-03-04 16:37:00.241 UTC Simulate_Mass_Spectrum 2013-03-12 13:49:15.323 UTC 919e925b-6aeb-4502-a608-2fc846e57dad 2013-03-05 15:56:30.557 UTC 5d9e8184-45b8-462c-a93b-3c48c7ef3221 2013-03-05 15:34:12.533 UTC b409b222-639e-4b04-841c-53cf1684f84b 2013-03-05 15:53:20.655 UTC 7cd47926-5366-46b9-998f-331216c53f5e 2013-03-05 16:51:41.357 UTC d55524bc-0788-4a2d-a444-12394491e167 2013-03-05 16:37:56.865 UTC c6c42f3b-2bca-417c-908f-62c43b9dce75 2013-03-06 15:27:56.427 UTC 337d02be-4c5e-40e6-b22e-2dc55645363d 2013-03-05 16:36:45.429 UTC 1160cf02-b2b3-4902-91f1-3f7f28ec4012 2013-03-05 16:30:57.951 UTC e05ea583-7396-499f-a4cd-9e2a70d541d1 2013-03-04 16:10:43.454 UTC 6ea772ec-5aa1-4338-9845-e5061792bdea 2013-03-12 13:44:32.468 UTC bd246e6a-36bb-429c-acde-73cc36ad0082 2012-02-20 17:45:49.78 UTC 68efc44e-043b-4e35-a1ff-0ca1318a404e 2013-03-05 16:29:19.218 UTC 4ba4b076-e140-4c31-9200-d26ae4bed473 2012-02-20 17:31:21.413 UTC 11e61394-6cac-4449-b251-05a2cacc4634 2013-03-05 16:57:38.101 UTC d8404dd0-a258-4bcd-9005-495ab856dfb0 2013-03-05 15:37:39.579 UTC Magnus Palmblad 2013-03-05 17:13:38.785 UTC 01f43f7a-3263-46a2-ba19-54513f90cae6 2013-03-05 15:57:16.631 UTC 440cbb5c-c490-454c-a5ba-9ff491042fe4 2013-03-05 15:55:25.34 UTC 7817a5c4-42c6-41b9-a066-737c5e0b3a27 2013-03-05 15:58:00.522 UTC 7a2e2c06-a0ba-49cb-aa1c-58c73f40b331 2013-03-04 16:17:14.84 UTC fc5320b4-54db-4be1-8c08-d26dd95d407f 2013-03-05 17:07:56.921 UTC cb93ce10-6523-4993-b011-3f171c00d688 2013-03-05 15:31:37.419 UTC 3b770629-e652-433b-9309-2184a2a87c23 2013-03-05 16:07:36.359 UTC a4d37600-c620-4d25-91c9-020fc87328f0 2013-03-12 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