Improved identification of peptides, cross-link sites, and modification sites by Target-enhanced Accurate Inclusion Mass Screening (TAlMS)

Chemical cross-linking of proteins coupled with mass spectrometry relies on the successful identification of cross-linked peptide pairs, or cross-links, to gain structural insights into proteins and protein complexes. As cross-links are typically of lower abundance than linear peptides, only a small fraction of tandem mass spectra (MS2) obtained by data-dependent acquisition (DDA) is informative for cross-link identification. To improve MS2 of low-abundance ions/species, we optimized a previously described targeted mass spectrometry method called Accurate Inclusion Mass Screening (AIMS) and named the modified method TAIMS for Target-enhanced AIMS. Compared to DDA, TAIMS significantly improved the quality of MS2 as indicated by enhanced fragment ion coverage, E-value, and seven other metrics. Of an E. coli lysate cross-linked with disuccinimidyl sulfoxide, the percentage of high-quality MS2 among identified cross-link precursor ions increased from 43% by DDA to 95% by TAIMS. Additionally, 43% of the inclusion-list entries generated from unidentified cross-link-spectrum matches gained identity through TAIMS, of which 76% turned out to be linear peptides and 14% being cross-links, including 13 inter-molecular cross-links missed entirely by DDA. Overall, TAIMS increased high-confidence cross-link identifications by 53%-129%, counting precursor ions. Additionally, TAIMS markedly improved the precision of cross-link site localization and prevented sensitivity loss in cross-link search against large databases. We also demonstrate that TAIMS is a general method for identification of low-abundance, post-translationally modified peptides. In a phosphoproteomics experiment, TAIMS increased the identification number of phosphopeptides with high-precision phosphosite localization by 67%. These results show that TAIMS has widespread use in proteomics.