Cross-correlation algorithm for calculation of peptide molecular weight from tandem mass spectra

Analytical Chemistry
John D VenableJohn R Yates

Abstract

We have developed an approach to identify the molecular weight of a peptide ion directly from its corresponding tandem mass spectrum using a cross-correlation function. We have shown that the monoisotopic molecular weight can be calculated for approximately 90% of tandem mass spectra identified from tryptic digests of complex protein mixtures. The accuracy of the calculated monoisotopic masses was dependent on the resolution and mass accuracy of the spectra analyzed, but was typically <0.25 amu for linear ion trap mass spectra. The ability to calculate accurate monoisotopic molecular weights for low-resolution ion trap data should significantly improve both the speed and performance of database searches for which typical mass accuracies of approximately 3 amu are employed. In addition, this strategy can also be used to identify the precursor ion for tandem mass spectra acquired using large ion selection windows in data-independent collision-activated dissociation and has the potential to identify multiplexed tandem mass spectra.

References

Dec 3, 1999·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·V DancíkP A Pevzner
Jun 13, 2002·Proceedings of the National Academy of Sciences of the United States of America·Michael J MacCossJohn R Yates
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Dec 13, 2003·Analytical Chemistry·Michael J MacCossJohn R Yates

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Citations

Sep 6, 2013·Journal of the American Society for Mass Spectrometry·Huisong PakMarkus Muller
May 30, 2012·Journal of Proteome Research·Jeffrey A MilloyScott A Gerber
Jun 20, 2008·Journal of Proteome Research·Samuel H PayneVineet Bafna
Aug 4, 2009·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Ritendra Datta, Marshall Bern
Jul 18, 2014·Analytical Chemistry·Nai-ping DongWei Fan
Oct 27, 2015·Analytical Chemistry·Lin HeJohn R Yates
Aug 20, 2015·Journal of the American Society for Mass Spectrometry·John R Yates
Oct 2, 2014·Molecular Neurobiology·Wei-Chieh ChiangJonathan H Lin
Dec 3, 2014·Biotechnology Advances·Lunzhao YiYizeng Liang
May 18, 2016·Analytical and Bioanalytical Chemistry·Anton Kaufmann, Stephan Walker
Dec 3, 2013·Journal of Proteome Research·Angelito I NepomucenoDavid C Muddiman
Jun 8, 2011·PloS One·Mary Kate BonnerAhna R Skop
Dec 1, 2006·Journal of Mass Spectrometry : JMS
Feb 12, 2021·Journal of the American Society for Mass Spectrometry·Jean-Francois GreischAlbert J R Heck
Aug 8, 2009·Journal of Proteome Research·Seungjin Na, Eunok Paek

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