userguide:pride_inspector
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userguide:pride_inspector [2011/03/08 14:15] 132.168.74.230 |
userguide:pride_inspector [2012/03/14 12:03] 132.168.73.124 |
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| ====== PRIDE Inspector ====== | ====== PRIDE Inspector ====== | ||
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| + | PRIDE Inspector is an application to visualize and perform a first quality assessment of MS data. \\ | ||
| + | With PRIDE Inspector users can have a close look at their own data before the actual submission, or access data already in PRIDE for data mining purposes. | ||
| + | |||
| + | ===== Download ===== | ||
| PRIDE Inspector is available at [[http://code.google.com/p/pride-toolsuite/wiki/PRIDEInspector]]\\ | PRIDE Inspector is available at [[http://code.google.com/p/pride-toolsuite/wiki/PRIDEInspector]]\\ | ||
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| * Dowload the pride-inspector-X.Y.Z.zip file, then unzip.\\ | * Dowload the pride-inspector-X.Y.Z.zip file, then unzip.\\ | ||
| * To execute PRIDE Inspector, double-click on pride-inspector-X.Y.Z.jar\\ | * To execute PRIDE Inspector, double-click on pride-inspector-X.Y.Z.jar\\ | ||
| + | * To open a PRIDE XML file, select the ''File->Open File...'' menu and browse to an PRIDE XML file | ||
| + | {{:userguide:prideinspector_1.png|}} | ||
| + | ===== FAQ ===== | ||
| - | PRIDE Inspector is an application to visualize and perform a first quality assessment of MS data. With PRIDE Inspector users can have a close look at their own data before the actual submission, or access data already in PRIDE for data mining purposes. | + | ==== Why do I not get the same number of peptides between hEIDI & Pride Inspector ? ==== |
| - | * To open a PRIDE XML file, select the ''File->Open File...'' menu and browse to an PRIDE XML file | + | {{:userguide:pride_peptidecountinprideinspectorandheidi.png|}} |
| - | * Check especially experiment details | + | |
| - | {{:userguide:prideinspector_1.png|}} | + | Peptide unicity in an hEIDI context is based on sequence & calculated mass.\\ |
| + | For example, the peptide ''FASFIDKVR'' is represented by one peptide node in the ''Peptide View''. \\ | ||
| + | This peptide matches on 15 master proteins (see the ''Protein Group(s) match(es)'' column) but 7 other proteins as well (information not visible in hEIDI)\\ | ||
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| + | {{:userguide:pride_onepeptideinheidi.png|}} | ||
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| + | In Pride Inspector, a row exists for each peptide-protein match.\\ | ||
| + | For example, the peptide ''FASFIDKVR'' appears 22 times: one row for each protein match. | ||
| + | |||
| + | {{:userguide:pride_onepeptideinprideinspector.png|}} | ||
| + | |||
| + | So, the number of peptides in Pride Inspector is generally bigger than the peptide count in a User context. | ||
| {{:userguide:prideinspector_2.png|}} | {{:userguide:prideinspector_2.png|}} | ||
userguide/pride_inspector.txt · Last modified: 2012/03/14 12:06 by 132.168.73.124
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