The Proteome Discoverer application validates an analysis' setup before it starts processing. If the application detects any issues with the setup, it displays a message for each issue. These messages are either warnings messages, which you do not need to resolve before processing, or error messages, which you must resolve before processing. The following figure shows one of each type of message.
The validation cannot detect every problem, but it can check for these specific problems or inconsistencies:
- The set workflows have major errors because of missing mandatory node types, such as:
- validator nodes
- missing connections
- missing parameters
NOTE
These errors typically prevent the Run button from being available.
NOTE
CHIMERYS also checks your account capacity on the service as part of analysis validation. If the predicted time to analyze all the files in the submitted analysis is larger than the capacity, the analysis validation fails and the workflows do not start. In this case, consider first searching a subset of files for the analysis and then search the remaining files when the analysis time on the account is large enough to successfully search the remaining files.
- When you use quantification nodes or have assigned quantification methods to your input files, the validation makes sure that the following conditions are met:
- All quantification nodes used in the workflow of a particular processing step have the same kind of quantification method; for example, you cannot have mixed precursor and reporter ion quantification nodes in a workflow.
- Not all input files of a particular processing step have the same quantification method assigned; for example, you have mixed precursor and reporter ion quantification files in a processing step.
- The kind of quantification node used in the workflow of a particular processing step is not compatible with the quantification method set for the input files of this step; for example, you try to process reporter quantification files with a precursor quantification node or vice versa.
- All input files have a quantification method set, but no quantification node is used in the workflow of the processing step.
- A quantification node is used in the workflow of a processing step, but none of the input files have a quantification method set.
- You have not selected any of the study variables for grouping on the Grouping & Quantification page. If you use only one file, you usually do not want to group. However, you can create biological replicates using different channels of a quantification method such as TMT in an experiment on a single raw data file in which you want to group by tissue, matrix, or experimental condition.
- Some of the processing steps provide quantification values, but the workflow of the consensus step does not contain any node that processes quantification values.
- The quantification method used for the input files of a particular processing step is not valid.
The application validates the analysis. If there are no errors, the application begins processing. The job queue opens so that you can monitor the progress of the job.
The job is done when Completed appears in the Execution State column for the processing and consensus workflows.
The application uses the name of the first raw data file or sample as the default name of the results file as a whole.
The job queue view opens. Use the job queue to check the status of your search as the search progresses. For information about the job queue, see Job queue.
The application creates one or more MSF and result files, depending on whether the data files to be analyzed are batch-processed. It might reuse MSF files to produce a new result file if a different report for the given data is required.
The result file has the same name as the input file but with a .pdResult extension. The Analysis Results page displays the name of the result file.