title: Assessing the dynamic range and peak capacity of nanoflow LC-FAIMS-MS on an ion trap mass spectrometer for proteomics.
abstract: Proteomics experiments on complex mixtures have benefited greatly from the advent of fast-scanning ion trap mass spectrometers. However, the complexity and dynamic range of mixtures analyzed using shotgun proteomics is still beyond what can be sampled by data-dependent acquisition. Furthermore, the total liquid chromatography-mass spectrometry (LC-MS) peak capacity is not sufficient to resolve the precursors within these mixtures, let alone acquire tandem mass spectra on all of them. Here we describe the application of a high-field asymmetric waveform ion mobility spectrometry (FAIMS) device as an interface to an ion trap mass spectrometer. The dynamic range and peak capacity of the nanoflow LC-FAIMS-MS analysis was assessed using a complex tryptic digest of S. cerevisiae proteins. By adding this relatively simple device to the front of the mass spectrometer, we obtain an increase in peak capacity >8-fold and an increase in dynamic range of >5-fold, without increasing the length of the LC-MS analysis. Thus, the addition of FAIMS to the front of a table-top mass spectrometer can obtain the peak capacity of multidimensional protein identification technology (MudPIT) while increasing the throughput by a factor of 12.
authors.affiliation: Department of Genome Sciences, University of Washington, Box 355065, Seattle, Washington 98195-5065, USA.
authors.forename: Jesse D
authors.initials: JD
authors.lastname: Canterbury
authors.forename: Xianhua
authors.initials: X
authors.lastname: Yi
authors.forename: Michael R
authors.initials: MR
authors.lastname: Hoopmann
authors.forename: Michael J
authors.initials: MJ
authors.lastname: MacCoss
mesh_terms: D002853:Chromatography, Liquid / Q000379:methods*; D005656:Fungal Proteins / Q000032:analysis; D013058:Mass Spectrometry / Q000379:methods*; D036103:Nanotechnology / Q000379:methods*; D010455:Peptides / Q000032:analysis; D040901:Proteomics / Q000379:methods*; D015203:Reproducibility of Results
chemical_list: D005656:Fungal Proteins; D010455:Peptides