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Ion Mobility Tandem Mass Spectrometry Enhances Performance of Bottom-up Proteomics

2014; Elsevier BV; Volume: 13; Issue: 12 Linguagem: Inglês

10.1074/mcp.m114.041038

1535-9484

Dominic Helm, Johannes P.C. Vissers, Chris Hughes, Hannes Hahne, Benjamin Ruprecht, Fiona Pachl, Arkadiusz Grzyb, Keith Richardson, Jason Wildgoose, Stefan K. Maier, Harald Marx, Mathias Wilhelm, Isabelle Becher, Simone Lemeer, Marcus Bantscheff, James Langridge, Bernhard Küster,

Molecular Biology Techniques and Applications

One of the limiting factors in determining the sensitivity of tandem mass spectrometry using hybrid quadrupole orthogonal acceleration time-of-flight instruments is the duty cycle of the orthogonal ion injection system. As a consequence, only a fraction of the generated fragment ion beam is collected by the time-of-flight analyzer. Here we describe a method utilizing postfragmentation ion mobility spectrometry of peptide fragment ions in conjunction with mobility time synchronized orthogonal ion injection leading to a substantially improved duty cycle and a concomitant improvement in sensitivity of up to 10-fold for bottom-up proteomic experiments. This enabled the identification of 7500 human proteins within 1 day and 8600 phosphorylation sites within 5 h of LC-MS/MS time. The method also proved powerful for multiplexed quantification experiments using tandem mass tags exemplified by the chemoproteomic interaction analysis of histone deacetylases with Trichostatin A.