biostudies-literatureWong CCNIDCR NIH HHSNCRR NIH HHSNIMH NIH HHSNIGMS NIH HHS1405-14https://www.ebi.ac.uk/biostudies/studies/S-EPMC2946190biostudies-literatureUnknown20(8)We evaluate the effect of ion-abundance threshold settings for data-dependent acquisition on a hybrid LTQ-Orbitrap mass spectrometer, analyzing features such as the total number of spectra collected, the signal to noise ratio of the full MS scans, the spectral quality of the tandem mass spectra acquired, and the number of peptides and proteins identified from a complex mixture. We find that increasing the threshold for data-dependent acquisition generally decreases the quantity but increases the quality of the spectra acquired. This is especially true when the threshold setting is set above the noise level of the full MS scan. We compare two distinct experimental configurations: one where full MS scans are acquired in the Orbitrap analyzer while tandem MS scans are acquired in the LTQ analJournal of the American Society for Mass SpectrometryComparison of different signal thresholds on data dependent sampling in Orbitrap and LTQ mass spectrometry for the identification of peptides and proteins in complex mixtures.PMC2946190R01 MH067880-09U01 DE016267P41 RR011823-10RR011823P41 RR011823F32 GM071278-02R01 MH0678805R01-MH067880DE016267U01 DE016267-04Venable JDYates JRXu TWong CCCociorva DfalseComparison of different signal thresholds on data dependent sampling in Orbitrap and LTQ mass spectrometry for the identification of peptides and proteins in complex mixtures.We evaluate the effect of ion-abundance threshold settings for data-dependent acquisition on a hybrid LTQ-Orbitrap mass spectrometer, analyzing features such as the total number of spectra collected, the signal to noise ratio of the full MS scans, the spectral quality of the tandem mass spectra acquired, and the number of peptides and proteins identified from a complex mixture. We find that increasing the threshold for data-dependent acquisition generally decreases the quantity but increases the quality of the spectra acquired. This is especially true when the threshold setting is set above the noise level of the full MS scan. We compare two distinct experimental configurations: one where full MS scans are acquired in the Orbitrap analyzer while tandem MS scans are acquired in the LTQ anal2009-01-01T00:00:00Z2009 Aug2025-05-29T20:25:22.326Z2025-05-29T20:25:22.326ZS-EPMC29461901946788310.1016/j.jasms.2009.04.007