Mercurial > repos > galaxyp > proteomiqon_peptidespectrummatching

comparison proteomiqon_peptidespectrummatching.xml @ 1:a79a24eb9e76 draft default tip

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching commit c36184e88da16842e748a19c2dfabaa30a1f6a15"
author galaxyp
date Sat, 24 Jul 2021 11:40:03 +0000
parents db6faafbf75b
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0:db6faafbf75b 1:a79a24eb9e76
177 177
178 Given raw a MS run in the mzite format, this tool iterates accross all recorded MS/MS scans and determines the charge state of precursor ions which were selected for fragmentation. 178 Given raw a MS run in the mzite format, this tool iterates accross all recorded MS/MS scans and determines the charge state of precursor ions which were selected for fragmentation.
179 With this it is possible to query the peptide data base for every precursor ion mass +/- a tolerance (which defines the so called 'search space') and retrieve peptides that are 179 With this it is possible to query the peptide data base for every precursor ion mass +/- a tolerance (which defines the so called 'search space') and retrieve peptides that are
180 theoretical candidates for a match. For each of the peptide candidates we create an theoretical spectrum in silico and compare it to the measured MS/MS scan. 180 theoretical candidates for a match. For each of the peptide candidates we create an theoretical spectrum in silico and compare it to the measured MS/MS scan.
181 181
182 .. image:: PSM.png 182 .. image:: $PATH_TO_IMAGES/PSM.png
183 :width: 768pt 183 :width: 768pt
184 :height: 563pt 184 :height: 563pt
185 185
186 To measure similarity we use our own implementations of three established search enginge scores: SEQUEST, Andromeda and XTandem. 186 To measure similarity we use our own implementations of three established search enginge scores: SEQUEST, Andromeda and XTandem.
187 The search space is extended by so called decoys. Decoys are reversed counterparts of peptides within the search space and allow 187 The search space is extended by so called decoys. Decoys are reversed counterparts of peptides within the search space and allow