The application uses the information about the grouping of samples in the data distribution maps to show which protein group, protein, or peptide was identified in which file, sample, and sample group. The color-coding refers to the confidence level of the identification—that is, the confidence of the best PSM found for the particular file, sample, or sample group.

Data distribution maps with color-coded identification confidence levels for proteins in sample groups, samples, and files

In precursor ion identification, there is frequently no confidence information from an identified MSn spectrum, but the application found a quantification value for a particular sample. For example, it identified only the light peptide in a SILAC experiment, but it also found an integrated extracted ion current (XIC) chromatogram for the heavy peptide. The application displays such cases in blue on the distribution map.

Procedure

  1. Create a study and an analysis as follows:
  2. Create a quantification processing workflow.
  3. Create a quantification consensus workflow.
  4. Set the appropriate parameters of the Reporter Ions Quantifier node or the Precursor Ions Quantifier node to display the appropriate columns in the output result file.
  5. To have the result report display the Found in Samples, Found in Sample Groups, Found in Files, and Found in Samples columns, drag the Data Distributions node to the to the Post-Processing area of the Workflow Editor.
  6. Select Run at the top right of the Analysis window.
  7. The job queue appears, displaying the status of your search as it progresses. For job queue information, refer to the Job queue Help topic.