Changes between Version 8 and Version 9 of LabelFree

Timestamp:

Mar 15, 2013, 11:38:38 AM (10 years ago)

Author:

Fredrik Levander

Comment:

--

LabelFree

@@ -10 +10 @@
  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. [[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]
+  - 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.]
+  - When the alignment job is finished you can check the log file to asses the quality of the alignment.
  1. A quantitative peptide report can then be generated by selecting 'Create Feature Report' at the bottom of the Feature Report.
+  - The generated report is tab separated and can be used for differential expression anaysis in external software. The report contains headers with sample name, fraction and replicate information where applicable. If you which to conduct differential expression analysis at the peptide level, the following steps are not needed.
  1. Optionally run Proteios Protein Assembly
+  - During the protein assembly process, the generated proteins will get a precursor intensity which is the sum of the precursor intensities of the included peptides. Note that which peptides will be included is based on the settings selected for protein assembly.
  1. Run Hits comparison report (with quantitative option checked) to generate report where peptides or proteins (Protein Assembly required for the latter) are compared between sample groups based on precursor quantities.