Add software information of DIANN into OLS.

vdemichev / DiaNN

DIA-NN - a universal automated software suite for DIA proteomics data analysis.

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Add software information of DIANN into OLS. #362

Open WangHong007 opened 2 years ago

WangHong007 commented 2 years ago

Hi, Thanks for providing such a fantastic tool. We are going to add DIANN's information to OLS @ypriverol, please confirm whether the following information is correct:

Name of the main score at the PSM level: Lib.Q.Value
Name of the main score at Peptide level: Q.Value
Name of the main score at Protein Level: Protein.Q.Value

By the way, is it normal that all the values in the Lib.Q.Value column in report.tsv are 0?

Best, Hong

ypriverol commented 2 years ago

@vdemichev Some background about this issue. In order to generate the mzTab from DIA-NN output we will need to add the tool and some scores, and statistical metrics to an ontology vocabulary in OLS in this case PSI-MS.

vdemichev commented 2 years ago

Hi both,

Run specific: 'main PSM score' - Q.Value main score at the peptide level - does not exist, the user can however use the maximum of the q-values for the respective precursors main score at the protein level - PG.Q.Value

Global (without MBR and if the library is not filtered based on global q-values already): PSM: Global.Q.Value Protein: Global.PG.Q.Value

Global (if MBR or if the library is filtered based on global q-values already): PSM: Lib.Q.Value Protein: Lib.PG.Q.Value

Best, Vadim

ypriverol commented 2 years ago

@WangHong007 you can use:

Hi both,

Run specific: 'main PSM score' -

PSM-level q-value https://www.ebi.ac.uk/ols/ontologies/ms/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FMS_1002354&viewMode=All&siblings=false

Q.Value main score at the peptide level - does not exist, the user can however use the maximum of the q-values for the respective precursors main score at the protein level - PG.Q.Value

protein-level q-value https://www.ebi.ac.uk/ols/ontologies/ms/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FMS_1001869&viewMode=All&siblings=false

Global (without MBR and if the library is not filtered based on global q-values already): PSM: Global.Q.Value Protein: Global.PG.Q.Value

Global (if MBR or if the library is filtered based on global q-values already): PSM: Lib.Q.Value Protein: Lib.PG.Q.Value

Best, Vadim

WangHong007 commented 2 years ago

The scores at the three levels in the DIANN report are confirmed as follows(in this case): Protein level: Global.PG.Q.Value(without MBR) Peptide level: the minimum of the respective precursor q-values (minimum of Q.Value per group) PSM level: Q.Value

Dia-NN in the ontology vocabulary of OLS: MS:1003253 Cite Dia-NN in SDRF: NT=DIA-NN;AC=MS:1003253

ypriverol commented 2 years ago

Yes.

vdemichev commented 2 years ago

Comment:

Many prefer global protein q-values only, which give better data completeness: this is Lib.PG.Q.Value with MBR and Global.PG.Q.Value without MBR
Likewise, might want to filter based on global precursor q-values
Peptide-level q-value should be rather be the minimum of the respective precursor q-values

ypriverol commented 2 years ago

As you said @WangHong007 we have added DIA-NN to OLS, here the term:

[Term]
id: MS:1003253
name: DIA-NN
def: "A universal software for data-independent acquisition (DIA) proteomics data processing" [PMID:31768060, https://github.com/vdemichev/DiaNN]
is_a: MS:1001139 ! quantitation software name
is_a: MS:1001456 ! analysis software