SwathXtend

SwathXtend is a software tool to improve the performance of SWATH-MS (Sequential Window Acquisition of All Theoretical Mass Spectra) proteomics experiments by integrating locally generated peptide assay libraries with external, repository-based libraries. The software generates extended peptide assay libraries and analyzes SWATH-quantitative comparisons statistically.

The developers of SwathXtend conducted a systematic evaluation of how different assay libraries affect SWATH performance. They used test samples containing peptides from yeast extract spiked into human K562 cell lysate peptides at various ratios to simulate protein abundance changes. The performance of SWATH-MS was assessed using local and external assay libraries with varying complexities and proteome compositions.

The experiments showed that integrating local seed libraries with external assay libraries performs better than using local ones alone. This improvement was observed in terms of the number of identified peptides and proteins and the specificity in detecting differentially abundant proteins. The extended assay libraries' performance was influenced by the similarity of MS/MS features between the seed and external libraries. Additionally, the authors emphasized the importance of using multiple testing corrections during statistical analysis when searching against large extended assay libraries to maintain statistical rigor.