Precision in reports when using the command line

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Precision in reports when using the command line Will Thompson  2025-07-25 12:38
 

Hi Nick, Brendan and team

What is the methodology to retrieve either full precision or a set scientific notation when calling reports from the command line? An example below of a report where we would love to be able to get better precision for start and end time for the peaks, and for concentration, but the default behavior seems to be 2 decimals for retention time and unpredictable for concentration. Is there a way to specify the export precision in the report xml, so that it can be done reproducibly between Skyline installs?

Cheers,

Will


<?xml version="1.0"?>

<views> <view name="MoveKitCE_PeakIntegration" rowsource="pwiz.Skyline.Model.Databinding.Entities.Transition" sublist="Results!*" uimode="small_molecules"> <column name="Results!*.Value.PrecursorResult.PeptideResult.ResultFile.FileName" caption="file_name" /> <column name="Results!*.Value.PrecursorResult.PeptideResult.ResultFile.Replicate.Name" caption="replicate_id" /> <column name="Precursor.Peptide.Protein.Name" caption="molecule_group" /> <column name="Precursor.Peptide.MoleculeName" caption="molecule_name" /> <column name="Precursor.Adduct" caption="adduct" /> <column name="Precursor.Peptide.RetentionTimeCalculatorScore" caption="retention_time_calculator_score" /> <column name="Results!*.Value.Chromatogram.ChromatogramPrecursorMz" caption="precursor_mz" /> <column name="Results!*.Value.Chromatogram.ChromatogramProductMz" caption="ion_mz" /> <column name="Results!*.Value.PrecursorResult.MinStartTime" caption="start_time" /> <column name="Results!*.Value.PrecursorResult.MaxEndTime" caption="end_time" /> <column name="Results!*.Value.PrecursorResult.PeptideResult.PeptideRetentionTime" caption="peak_max_time" /> <column name="Results!*.Value.PrecursorResult.PeptideResult.PredictedResultRetentionTime" caption="predicted_peak_max_time" /> <column name="Results!*.Value.UserSetPeak" caption="is_modified_from_skyline_peak" /> <column name="Results!*.Value.PrecursorResult.PeptideResult.Quantification.CalculatedConcentration" caption="calculated_concentration" /> </view> </views>

 
 
Nick Shulman responded:  2025-07-25 12:47
If you include the command-line argument:
--report-invariant
then the numbers will be formatted to full precision.
Also, the column names will always be in English and will not have spaces in them.
-- Nick
 
Will Thompson responded:  2025-07-28 08:16
Thank you Nick! Exactly what we needed.

Cheers

Will