Automated reduction and interpretation of high resolution electrospray mass spectra of large molecules

Here a fully automated computer algorithm is applied to complex mass spectr a of peptides and proteins. This method uses a subtractive peak finding rou tine to locate possible isotopic clusters in the spectrum, subjecting these to a combination of the previous Fourier transform/ Patterson method for p rimary charge determination and the method for least-squares fitting to a t heoretically derived isotopic abundance distribution for m/z determination of the most abundant isotopic peak, and the statistical reliability of this determination. If a predicted protein sequence is available, each such m/z value is checked for assignment as a sequence fragment. A new signal-to-no ise calculation procedure has been devised for accurate determination of ba seline and noise width for spectra with high peak density. In 2 h, the prog ram identified 824 isotopic clusters representing 581 mass values in the sp ectrum of a GluC digest of a 191 kDa protein; this is >50% more than the nu mber of mass values found by the extremely tedious operator-applied methodo logy used previously. The program should be generally applicable to classes of large molecules, including DNA and polymers, Thorough high resolution a nalysis of spectra by Horn (THRASH) is proposed as the program's verb. (J A m Soc Mass Spectrom 2000, 11, 320 -332) (C) 2000 American Society for Mass Spectrometry.