Fundamental workflow

Schema of the fundamental workflow.

The SanXoT workflow consisting of three steps:

1. scan-to-peptide integration: peptide-level quantitative information is obtained by taking into account the information of all the scans where the same peptide is identified. Scan outliers are those that quantify in a statistically significant way compared to other scans pointing to the same peptide (since it is assumed that scans where the peptide is the same, all scans should quantify equally).
2. peptide-to-protein integration: protein-level quantitative information is obtained using data of all the peptides that have been identified and quantified for a certain protein. Peptide outliers are those that quantify differently from other peptides pointing to the same protein in the relations file (this might happen especially in non-unique peptides, that can be present in different proteins).
3. protein-to-all integration: to compare proteins between them, so proteins having statistically significant changes of expression are identified.

Each integration is performed by the GIA (the Generic Integration Algorithm) In each of these steps, the associated level variance can be calculated, giving detailed information about the experiment.

There are many possible variations of this workflow. For example, the last step (protein-to-all) can be removed to perform a peptide-level systems biology, or the peptide-to-protein integration can be modified to account for post-translational modifications, or extra levels can be added prior to the scan level (for example to integrate different features present in the same spectrum, as in the case of NeuCode).

See also

• The fundamental workflow at Exploring SanXoT features
• Unit test of the fundamental workflow
• General design of SanXoT