Reporter report not containing per-sample ratios following demultiplexing

[steve-lefever]

Hi,

We're running the following Reporter commands to obtain a report containing the individual sample ratios using a TMT 11-plex pool

java -cp Reporter-0.12.0/Reporter-0.12.0.jar eu.isas.reporter.cli.ReporterCLI -method 'TMT 11-plex' -id sample.psdb -out sample_reporter.psdb -temp_folder /var/tmp

java -cp Reporter-0.12.0/Reporter-0.12.0.jar eu.isas.reporter.cli.ReportCLI -in sample_reporter.psdb -out ./ -report_prefix Reporter_ -reports 6,12 -temp_folder /var/tmp

However, this results in the default peptide report not containing any per-sample ratios. It only has the following columns, of which the 'Raw Ratios' and 'Normalized Ratios' columns are empty

Protein(s)
Unique Protein Group
Protein Group(s)
#Validated Protein Group(s)
Position
AAs Before
Sequence
AAs After
Modified Sequence
Fixed Modifications
Variable Modifications
Localization Confidence
#Validated PSMs
#PSMs
Confidence [%]
Validation
Raw Ratios
Normalized Ratios

What command do we need to run to obtain a report containing values for each individual label?

Thanks in advance, Steve

[hbarsnes]

Hi Steve,

I would recommend merging the two command lines into:

java -cp Reporter-0.12.0/Reporter-0.12.0.jar eu.isas.reporter.cli.ReporterCLI -method 'TMT 11-plex' -id sample.psdb -out sample_reporter.psdb -temp_folder /var/tmp -reports 6,12

This will be faster (as there is no need to load the data a second time) and should ensure that the quantification data is included.

Note however that Reporter is still in beta and that especially the command line support has not yet been fully tested.

Best regards, Harald