Conference: ASMS 1998
Session Code: 	TPC 	Slot: 	099
Title: 	High mass accuracy peptide mapping using electrospray ionization time-of-flight mass
spectrometry with nozzle voltage fragmentation and database searching using MS Tag and MS Fit
Authors: 	*Whittal, Randy; Huang, Lan; Laiko, Victor; Clauser, Karl;
Baker, Peter; Baldwin, Michael; Burlingame, Alma;
Institutes: 	
Abstract: 	Orthoganol acceleration time-of-flight (TOF) mass spectrometers equipped with
electrospray ionization (ESI) sources provide mass spectra with good mass accuracy (10 ppm or
better) and relatively high resolution (5000 fwhm). This performance is especially valuable
for the analysis of peptides. ESI generated ions have low internal energy and thus production
of fragments requires energy input, thereby causing collision-induced dissociation (CID). The
PerSeptive Biosystems Mariner TOF does not have a collision cell, thus, to observe fragments
by CID requires increasing the potential difference in the interface region. Normally, this
approach is of limited utility due to the lack of parent ion selection. It will be shown that
the fragment ions generated in the orthoganol TOF have the same high mass accuracy and resolution
as the parent ion. This can allow more accurate sequencing information to be obtained on a peptide
since both the parent and fragment ion can be determined with high accuracy. Peptide identification
from a database is possible even for simple mixtures. The data base searching progam MS Fit
(prospector.ucsf.edu) provides peptide mapping for enzymatic digests. With information only
on the mass of the peptides, several possible alternative proteins may be identified. However,
combining high accuracy measurement of the fragment ions with data base searching using MS Tag
may unambiguously confirm the identity of the digest peptides and thus eliminate several false
candidate proteins from consideration. Coelution of two peptides frequently occurs during LCMS
analysis. However, high accuracy measurement of fragment ions combined with database searching
can allow peptide/protein identification from fragments of coeluting peaks. We will discuss the
utility of this method and its application to the identification of peptides from on-going problems
in protein biochemistry.