NP³ MS Workflow version 1.3.0

• A new command called pca_plot was implemented to create a PCA using the NP³ reference chemical space (UNPD+DrugBank+Allosteric datasets). The NP³ and other external tables may be used to create a new PCA in the NP³ chemical space.
• Now the PCA creation in the final reports procedure removes any blanks or beds before plotting; and also creates a PCA plot with only the putative protonated m/z.
• Bug fix in the join_jobs command, Step 7 to join IVAMNs (fixed the removal of invalid connections).
• In the test command, added a new output_path parameter to allow running and storing the NP³ test results in a different folder (not in the repository folder).

NP³ MS Workflow version 1.2.2

The join_jobs command was updated to maintain the msclusterID from the reference job and to accept duplicated sample codes among different jobs. These compose new approaches towards a better integrative clustering.
Now, only the results of the jobs being joined are needed for the join_jobs command. Step 7 was updated to use the IVAMNs of the provided jobs. There is no more dependency on the results of the original jobs. This will ease consecutive executions of join_jobs.

A final report was implemented, but is still being tested and will be documented in next releases.

The conda environment was updated with new dependencies of the final reports. The environment must be updated and the setup command must be executed again.

NP³ MS Workflow v1.2.1

The quantification grouping is now performed by the corr command (Step 9) and before every biocorrelation computation. This allows adding extra groupings to a job a posteriori its processing.

The quantification grouping is defined in the metadata with the column 'GR_'.

This modification was necessary to allow adding groups to a joined job.

NP³ MS Workflow v1.2.0

A new command called join_jobs was created and added to the NP³ MS Workflow! The join_jobs command is used to join NP³ jobs (results of the run or the join_jobs commands) into a single united job. Concatenate different jobs without the need of running them all together again. It uses the clean results from the provided NP³ jobs and execute the main pipeline from Step 3 to 10 with some modifications and adaptations. The join_jobs can be used to join the results from multiple original jobs and also from previous joined jobs with a new original or joined job.

The join_jobs command may be useful for processing growing libraries, which will have new datasets being included from time to time; or for processing very large jobs, which may be divided into smaller jobs and then joined by chunks with a smaller memory footprint (divide and conquer strategy).

This new command is properly documented in the workflow Manual, which describes the data organization to execute it, the new expected format of the metadata_join table and details on its methods!

NP³ MS Workflow v1.1.6

The spec2vec function can now be used for the spectra similarity comparison in step 5, using model trained on UniqueInchikey subset (12,797 spectra). The user may select to use spec2vec or NP3 shifted cosine function using the similarity_function parameter.

NP³ MS Workflow v1.1.5

The SSMN and IVAMN [M+H]+ are now automatically created by the workflow. The network files receive a suffix in their names equal to 'protonated' to indicate the new [M+H]+ networks.

NP³ MS Workflow v1.1.4

NP³ MS Workflow version used in the paper.