Changes between Version 7 and Version 8 of LabelFree

Timestamp:

Mar 15, 2013, 11:28:52 AM (10 years ago)

Author:

Fredrik Levander

Comment:

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LabelFree

@@ -9 +9 @@
  1. Upload the .peptides.tsv files, and the mzML or mzXML files used for feature finding. In the case of mzML files, they can be used both for the peptide identification and the quantification. Check all the .peptides.tsv files and extensions->import file[s]->msInspect feature importer. 
  1. Open up the Feature report (PROJECT_NAME->reports->Features
- 1. Match features with identifications. Press the 'Match-Feature-Hits' button at the bottom of the report.
- 1. Now MS/MS identifications in the Hits report will contain precursor quantity values, and the features will have sequence information where available. There is a log file generated with information about the matching of features and MS/MS identifications.
- 1. Optionally, to align features and propagate identifications between files: Run the 'Propagate Feature Sequences' plug-in, which is located at the bottom of the Feature report. 
+ 1. Match features with identifications. Press the 'Match-Feature-Hits' button at the bottom of the report. [[BR]]
+  - When the job is done MS/MS identifications in the Hits report will contain precursor quantity values, and the features will have sequence information where available. There is a log file generated with information about the matching of features and MS/MS identifications.
+ 1. Optionally, but advised! Align features and propagate identifications between files: Run the 'Propagate Feature Sequences' plug-in, which is located at the bottom of the Feature report. This will run the alignment method described in [http://www.ncbi.nlm.nih.gov/pubmed/23306530 Sandin et al 2013]
  1. A quantitative peptide report can then be generated by selecting 'Create Feature Report' at the bottom of the Feature Report.
  1. Optionally run Proteios Protein Assembly