Using the protein chip interface with quadrupole time-of-flight mass spectrometry to directly identify peaks in SELDI profiles--initial evaluation using low molecular weight serum peaks.

Mass spectrometric profiling, particularly in the form of SELDI, has been used in many studies, particularly in attempts to generate diagnostic serum profiles. Several studies have generated promising results but one of the limitations is the inability to identify easily potential discriminatory peaks. This may enable specific assays to be developed and increased biological insight. We describe the first systematic technical evaluation of the ProteinChip interface coupled to a tandem mass spectrometer which allows direct sequencing of peptides <6000 Da, and describe the direct sequence identification of 21 peaks commonly observed in serum samples. Additionally we describe for the first time the use of on-chip acetylation to assist in the validation of sequence identification.