Library

By DIA-NN (> v1.9, recommended)

1. Generate the predicted library with the .predicted.speclib suffix based on sequence databases in UniProt format (see instructions).

2. Convert the .predicted.speclib file to .parquet format (see instructions).

By others

In this way, the .tsv or .parquet library should contain these columns:

• Precursor.Id - peptide seq + precursor charge.

• Modified.Sequence - peptide seq with modifications, only supporting C(UniMod:4) and M(UniMod:35).

• Stripped.Sequence - peptide seq.

• Precursor.Charge - the charge of the precursor.

• Proteotypic - whether the peptide is proteotypic (i.e., uniquely mapping to a single protein).

• Decoy - 0. Full-DIA will generate the decoys itself.

• N.Term - N-terminal enzymatic specificity of the peptide.

• C.Term - C-terminal enzymatic specificity of the peptide.

• RT - retention time or iRT or predicted RT of the peptide.

• IM - ion mobility or predicted ion mobility of the precursor.

• Q.Value - 0.

• Peptidoform.Q.Value - 0.

• PTM.Site.Confidence - 0.

• PG.Q.Value - 0.

• Precursor.Mz - m/z of the precursor.

• Product.Mz - m/z of the fragment ion.

• Relative.Intensity - relative intensity of the fragment ion.

• Fragment.Type - “b” or “y”.

• Fragment.Charge - 1 or 2.

• Fragment.Series.Number - the number of aas of the fragment ion.

• Fragment.Loss.Type - “noloss”

• Exclude.From.Quant - 0.

• Protein.Ids - all UniProt Ids of proteins matched to the peptides in the library.

• Protein.Group - None.

• Protein.Names - all UniProt names of proteins matched to the peptides in the library.