On the benefits of acquiring peptide fragment ions at high measured mass accuracy.

Journal of the American Society for Mass Spectrometry
Alexander ScherlDavid R Goodlett

Abstract

The advantages and disadvantages of acquiring tandem mass spectra by collision-induced dissociation (CID) of peptides in linear ion trap Fourier-transform hybrid instruments are described. These instruments offer the possibility to transfer fragment ions from the linear ion trap to the FT-based analyzer for analysis with both high resolution and high mass accuracy. In addition, performing CID during the transfer of ions from the linear ion trap (LTQ) to the FT analyzer is also possible in instruments containing an additional collision cell (i.e., the "C-trap" in the LTQ-Orbitrap), resulting in tandem mass spectra over the full m/z range and not limited by the ejection q value of the LTQ. Our results show that these scan modes have lower duty cycles than tandem mass spectra acquired in the LTQ with nominal mass resolution, and typically result in fewer peptide identifications during data-dependent analysis of complex samples. However, the higher measured mass accuracy and resolution provides more specificity and hence provides a lower false positive ratio for the same number of true positives during database search of peptide tandem mass spectra. In addition, the search for modified and unexpected peptides is greatly facilitated...Continue Reading

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Citations

Nov 16, 2011·Journal of the American Society for Mass Spectrometry·Gene Hart-Smith, Mark J Raftery
Aug 15, 2013·Journal of the American Society for Mass Spectrometry·Alex G Harrison
Aug 7, 2013·Journal of the American Society for Mass Spectrometry·Alex G HarrisonTalat Yalcin
Dec 17, 2008·Journal of the American Society for Mass Spectrometry·Shawna M HengelDavid R Goodlett
Sep 24, 2009·Journal of the American Society for Mass Spectrometry·Yihsuan S TsaiDavid R Goodlett
Aug 7, 2010·Journal of the American Society for Mass Spectrometry·Dominic WinterWolf D Lehmann
Apr 7, 2010·Analytical Chemistry·Scott R HeronJonathan M Cooper
Jun 3, 2011·Analytical Chemistry·Feliciano Priego-CapoteJean-Charles Sanchez
Sep 22, 2011·Analytical Chemistry·Long YuNick C Polfer
Jul 4, 2009·Analytical Chemistry·Alexandre PanchaudDavid R Goodlett
Mar 19, 2011·Journal of Proteome Research·Long YuNick C Polfer
Dec 5, 2008·Journal of Proteome Research·Michael T BoyneNeil L Kelleher
Mar 5, 2009·Journal of Proteome Research·Michael R HoopmannMichael J MacCoss
Dec 4, 2009·Molecular & Cellular Proteomics : MCP·Feliciano Priego-CapoteJean-Charles Sanchez
Dec 24, 2009·Proteomics·Erik AhrnéFrederique Lisacek
Jan 28, 2014·Journal of Mass Spectrometry : JMS·Alex G Harrison
Sep 7, 2016·Rapid Communications in Mass Spectrometry : RCM·Adelina E Acosta-MartinPierre Lescuyer
Jul 12, 2011·Molecular & Cellular Proteomics : MCP·Michaela ScigelovaAlexander Makarov
Nov 28, 2013·Mass Spectrometry Reviews·John D ChapmanChristophe D Masselon
Jun 21, 2021·Experimental Eye Research·Kevin L ScheyRoger J W Truscott
Mar 27, 2018·Journal of Proteome Research·Stefan K SolntsevLloyd M Smith

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