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[[File:Fig1 fundamentalWorkflow.PNG|thumb|450px|Schema of the fundamental workflow.]]

The SanXoT workflow consisting of three steps:

# '''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).
# '''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).
# '''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<ref name=garciamarques2016>Garcia-Marques, F., et al., ''A Novel Systems-Biology Algorithm for the Analysis of Coordinated Protein Responses Using Quantitative Proteomics''. Mol Cell Proteomics, 2016. 15(5): p. 1740-60.</ref>) In each of these steps, the associated level variance can be calculated, giving detailed information about the experiment<ref name=navarro2014>Navarro, P., et al., ''General statistical framework for quantitative proteomics by stable isotope labeling''. J Proteome Res, 2014. 13(3): p. 1234-47.</ref>.

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<ref name=bagwan2018>Bagwan, N., et al. ''Comprehensive Quantification of the Modified Proteome Reveals Oxidative Heart Damage in Mitochondrial Heteroplasmy''. Cell Reports, 2018</ref>, 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<ref name=herbert2013>Herbert, A., et al., ''Neutron-encoded mass signatures for multiplexed proteome quantification''. Nature Methods, 2013</ref>).

== See also ==

* [[Exploring SanXoT features#Test 1: The fundamental workflow|The fundamental workflow at Exploring SanXoT features]]
* [[Unit tests for SanXoT#Test 1: The fundamental workflow|Unit test of the fundamental workflow]]
* [[How to use SanXoT#General design|General design of SanXoT]]

== References ==
<references/>

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Mtrevisan: Created page with "Schema of the fundamental workflow. The SanXoT workflow consisting of three steps: # '''scan-to-peptide integration''': pep..."