Spectral Libraries and DIA Library Generation — Hands-on

Understand how spectral libraries connect LC–MS/MS identifications to DIA-based quantification. This module focuses on the concepts behind spectral libraries, how DDA experiments feed library building, the role of retention time anchoring and formats, and how to plan DIA-ready libraries for reproducible proteome coverage.

Spectral Libraries and DIA Library Generation

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Session Index

Session 1 — Spectral Library Concepts & Content Session 2 — DDA-Based Library Building Logic Session 3 — DIA-Focused Libraries & Formats Session 4 — Planning DIA Studies Around Libraries

Session 1

Fee: Rs 8800

Spectral Library Concepts & Content

What a spectral library represents in proteomics

linking peptide IDs to reference spectra fragment m/z and intensity patterns retention time annotations

Key fields stored for each library entry (conceptual)

peptide sequence and charge modification state quality and confidence tags

Types of spectral libraries and their roles

project specific vs public organism or tissue focused general vs targeted panels

Session 2

Fee: Rs 11800

DDA-Based Library Building Logic

Using DDA runs as input to libraries

sample selection ideas fractionation to gain coverage importance of high confidence IDs

Filtering and curating candidate peptides for a library

FDR and quality thresholds charge state and length ranges handling modifications conceptually

Retention time and iRT anchoring concepts

normalizing retention times using reference peptides transfer between gradients idea

Session 3

Fee: Rs 14800

DIA-Focused Libraries & Formats

How DIA engines use spectral libraries conceptually

matching DIA fragments to library entries scoring of candidate matches role of RT and fragment patterns

Library formats and practical considerations (high level)

generic vs tool specific formats embedded vs external RT scales managing versions of libraries

Predicted spectral and hybrid libraries (conceptual)

motivation for predicted libraries combining experimental and predicted content coverage vs confidence tradeoffs

Session 4

Fee: Rs 18800

Planning DIA Studies Around Libraries

Designing a DIA experiment with library needs in mind

theory plus planning worksheet

Library maintenance, extension and documentation

adding new peptides over time tracking provenance and parameters linking library versions to studies

Reporting library generation workflows in studies

summaries for methods sections tables describing coverage and content exporting library subsets for sharing

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Spectral Libraries and DIA Library Generation Training | DIA-Ready Proteomics Workflows

Spectral Libraries and DIA Library Generation — Hands-on