Analysis data Ferries et al.: parsing of search results from MaxQuant

Select my path and filters

Load data

Path to the search results parsed with this script: ~/Documents/Boulot/CPR/Projets/PhosphoLocalisations/Data_C.Eyers/MQ/.

Add information to the table

I manually add the information of which search engine has been used for the search.

Filters

I keep only the phosphorylated ions.

I remove reverse and potential contaminants.

I keep only the files corresponding to the following acquisition methods: HCDOT.

Parse the localisation scores:

Distribution of the scores:

apply the threshold of localisation score : above 0.75. The data are not filtered yet, I indicate if the localisation score passes the threshold in the field LocalisationsFilter.

NOTE: In the field Modified.sequence of the input tables, there are two ways the phosphorylation site localisation can be indicated:

• “(ph)” after the phosphorylated residue.
• “p” before the phosphoryalated residue.

This is weird and I take these two possible options in to consideration when parsing the localisations.

Create a phospho-peptide ID in the MQ table

For all the different inputs, I create IDs of the phospho-peptides:

• PhosphopeptideID: concatenation of pool, sequence and localisation of the phosphorylation (seperated with "_").
• PhosphosequenceID: concatenation of pool, sequence and number of phosphorylations on the peptide (seperated with "_").

When there are several scores for the phosphorylations localisations, I create one ID for each scoring. I define the scorings as “ptmRS” when it is the phosphoRS algorithm, or “SearchEngine” when it is the default localisation score of the pipeline.

Save data

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References