title: Absorption mode Fourier transform mass spectrometry with no baseline correction using a novel asymmetric apodization function.
abstract: BACKGROUND
  Absorption mode Fourier transform ion cyclotron resonance (FTICR) mass spectra offer significant benefits in terms of spectral resolution, signal-to-noise (S/N) ratio and measured mass accuracy. However, to date, methods for producing absorption mode spectra have created an undesirable baseline deviation as a consequence of FFT artifacts, resulting in interference of the frequency side-lobes of intense peaks. Methods for fitting and removing this deviation have been developed, but these are computationally intensive, slow and can be unreliable in practice.
  
  
  METHODS
  We have developed an approach for producing FTICR mass spectra which uses a new apodization approach to produce spectra which do not exhibit baseline deviation, whilst maintaining all the normal absorption mode benefits. This method involves the use of 'full' apodization function, replacing the more common Hann or half Hann functions, and where the user can control the position of the function maximum expressed as a fraction (F) of the transient length.
  
  
  RESULTS
  Absorption mode spectra produced using the new apodization function we propose provide all the normal benefits but do not exhibit baseline deviation that must be corrected prior to spectral interpretation. Additionally, varying the value of the F parameter allows users additional control over the compromise between the spectral resolving power and the S/N ratio. This is particularly beneficial in spectra with pronounced amplitude changes during the recording of the transient (detection).
  
  
  CONCLUSIONS
  The use of a 'full' apodization function, which may be asymmetric, prior to zero-padding and Fourier transformation, allows the production of absorption mode spectra which do not suffer from baseline deviation. Hence, it is no longer necessary to apply a baseline deviation correction in post processing, providing a significant performance advantage.
authors.affiliation: Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland Baltimore, MD, USA.
authors.forename: David P A
authors.initials: DP
authors.lastname: Kilgour
authors.affiliation: Bruker Daltonics Inc, Billerica, MA, USA.
authors.forename: Steven L
authors.initials: SL
authors.lastname: Van Orden
mesh_terms: D002138:Calibration; D005583:Fourier Analysis; D007136:Immunoglobulins / Q000737:chemistry*; D013058:Mass Spectrometry / Q000295:instrumentation / Q000379:methods / Q000592:standards*; D009211:Myoglobin / Q000737:chemistry*; D012015:Reference Standards
chemical_list: D007136:Immunoglobulins; D009211:Myoglobin