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spectral-libraries

separate

Builds and manages DIA spectral libraries as peptide query parameters (precursor m/z, a few fragment m/z plus relative intensities, normalized RT, optional CCS), covering experimental DDA, chromatogram, and in-silico predicted libraries via Koina-served Prosit, AlphaPeptDeep, MS2PIP, and DeepLC, with iRT/CiRT RT calibration, NCE tuning, format conversion (DIA-NN tsv/speclib/parquet, OpenSWATH pqp/TraML, Spectronaut, blib/dlib/elib), and library QC/merge. Use when generating, calibrating, converting, or merging a spectral library to drive a DIA search. Running the actual DIA search is dia-analysis; building from DDA identifications depends on peptide-identification; modified-peptide libraries route to ptm-analysis; quantifying the result is quantification.

When to use

• generating spectral libraries
• calibrating RT/CCS/NCE
• converting library formats
• merging spectral libraries
• library QC
• building from DDA identifications
• in-silico predicted libraries
• empirical chromatogram libraries

When not to use

• running the actual DIA search
• acquisition-window design
• demultiplexing
• modified-peptide libraries
• quantifying the result

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