Changes between Version 10 and Version 11 of LabelFree


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Timestamp:
Jan 14, 2014, 11:02:16 AM (9 years ago)
Author:
Fredrik Levander
Comment:

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  • LabelFree

    v10 v11  
    1212  - 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.
    1313 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.]
    14   - When the alignment job is finished you can check the log file to asses the quality of the alignment.
     14  - When the alignment job is finished you can check the log file to assess the quality of the alignment.
    1515 1. A quantitative peptide report can then be generated by selecting 'Create Feature Report' at the bottom of the Feature Report.
    1616  - 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.
     
    1919 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.
    2020
    21 After these steps, results can be exported from the hits table or feature table for further analysis. It is also possible to compare two samples using the hits comparison report.
     21After these steps, results can be exported from the hits table or feature table for further analysis. It is also possible to compare two sample groups using the hits comparison report.
    2222
    23 In addition, there are old plugins that use msInspect alignement output as input, and will compare groups of samples. It is possible to generate inclusion lists using these plugins.
     23In addition, there are old plugins that use msInspect alignement output as input, and will compare groups of samples. It is possible to generate inclusion lists using these plugins, but they are not maintained.
    2424