title: On the scalability and requirements of whole protein mass spectrometry.
abstract: Top-down proteomics has improved over the past decade despite the significant challenges presented by the analysis of large protein ions. Here, the detection of these high mass species by electrospray-based mass spectrometry (MS) is examined from a theoretical perspective to understand the mass-dependent increases in the number of charge states, isotopic peaks, and interfering species present in typical protein mass spectra. Integrating these effects into a quantitative model captures the reduced ability to detect species over 25 kDa with the speed and sensitivity characteristic of proteomics based on <3 kDa peptide ions. The model quantifies the challenge that top-down proteomics faces with respect to current MS instrumentation and projects that depletion of (13)C and (15)N isotopes can improve detection at high mass by only <2-fold at 100 kDa whereas the effect is up to 5-fold at 10 kDa. Further, we find that supercharging electrosprayed proteins to the point of producing <5 charge states at high mass would improve detection by more than 20-fold.
authors: Department of Chemistry, Northwestern University, Evanston, Illinois 60208, USA.
authors: Philip D
authors: PD
authors: Compton
authors: Leonid
authors: L
authors: Zamdborg
authors: Paul M
authors: PM
authors: Thomas
authors: Neil L
authors: NL
authors: Kelleher
mesh_terms: D002247:Carbon Isotopes / Q000737:chemistry; D007553:Isotope Labeling; D009587:Nitrogen Isotopes / Q000737:chemistry; D011506:Proteins / Q000032:analysis*; D040901:Proteomics; D021241:Spectrometry, Mass, Electrospray Ionization / Q000379:methods*
chemical_list: D002247:Carbon Isotopes; D009587:Nitrogen Isotopes; D011506:Proteins