Our lab also has a ThermoFinnigan LCQ Deca XP ion trap mass spectrometer equipped with with a Hill Instrument Co. nanospray source. Like the Q-TOF, it is able to obtain peptide sequence information by fragmenting peptides followed by measurement of the fragment ion mass/charge ratios. While the mass accuracy of this instrument is not as good as that of the Q-TOF instrument, it is more sensitive. The LCQ is coupled directly to an LC Packings (Dionex) Ultimate nanoflow HPLC system. With this configuration we are able to obtain approximately 30% sequence coverage of a mixture containing 10 fmols of 4 standard protein digests injected onto the column at a flow rate of 1 uL/min. Several hundred peptides can be sequenced in a single LC-MS/MS experiment. The sensitivity and reliability of these instruments makes it the method of choice for most protein identification problems where de novo sequencing is not required.

For protein identification by ion trap LC-MS/MS analysis, contact:

Chongfeng Xu, Ph.D.
Skirball Institute of Biomolecular Medicineæ
NYU School of Medicine
540 First Avenue, 5th Floor
New York, NY 10016
(212) 263-7266 (Tel.)
(212) 263-8214 (Fax)
xucf@saturn.med.nyu.edu