SwathXtend

SwathXtend integrates spectral libraries and performs statistical analyses to improve peptide and protein identification and quantification from SWATH-MS (Sequential Windowed Acquisition of All Theoretical Mass Spectra) proteomics data.

Key Features:

• Integration of Spectral Libraries: Generates extended peptide MS/MS assay libraries by combining local seed libraries with external community-derived assay libraries.
• Enhanced SWATH-MS Performance: Demonstrates that combining local and external libraries increases the number of identified peptides and proteins and improves specificity for detecting differentially abundant proteins.
• Statistical Analysis and Multiple Testing Correction: Implements statistical analyses including multiple testing corrections to support rigorous quantitative comparisons when searching large extended assay libraries.

Scientific Applications:

• Differential abundance analysis: Detects changes in protein abundance with improved specificity in SWATH-MS-based proteomic studies.
• Comprehensive proteome characterization: Enhances peptide and protein identification in complex proteome compositions by expanding assay library coverage.
• SWATH-MS benchmarking and evaluation: Facilitates assessment of SWATH-MS performance across varying protein abundance scenarios using extended assay libraries.

Methodology:

Integrates local seed and external peptide MS/MS assay libraries and assesses SWATH-MS performance using test samples such as yeast extract peptides spiked into human K562 cell lysates at varying ratios.