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J Biomol Tech. 2003 June; 14(2): 156.
PMCID: PMC2279913


A 2-day short course on de novo sequence analysis of peptide MS/MS spectra was organized by the Proteomics Research Group (PRG) for the ABRF ’03 meeting in Denver. This short course was held the 2 days prior to the start of ABRF ’03 and was designed for the novice as well as more experienced participants. To insure the quality of the course, it was limited to 100 attendees and was filled to capacity. The course focused on the interpretation of peptide spectra generated by the combination of electrospray ionization and collision activated dissociation. Basic skills to interpret unknowns were emphasized and taught using tryptic peptides as the primary examples. The instructors provided a list of rules to follow for de novo interpretation and covered real-life samples in the class work. Homework problems were assigned the first day and provided a challenge as well as some hands-on experience at solving the intricate spectra. The correct interpretation of the homework spectra was reviewed in depth the next day in class. Because of the length of the course, post-translational modifications, data generated from different types of instruments, and database searches were covered only briefly.

The requested survey was returned by 81% of the class participants with 96% of the respondents rating the course either excellent or good. The most frequent negative response was the lack of cookies for the afternoon break followed by the request for more extensive refreshments in general. The instructors were Dr. Nicholas E. Sherman, director for W.M. Keck Biomedical Mass Spectrometry Laboratory at the University of Virginia and Dr. Robert E. Settlage, associated with the same laboratory. Both instructors earned their Ph.D.s in chemistry from the University of Virginia under Dr. Donald Hunt. Ninety-six percent of the respondents were satisfied with the choice of instructors and comments regarding the class size, when compared with other MS courses, were positive.

The overall positive response to the course and level of attendance implies that the interest in this area has not diminished in the 3 years since a similar course was offered by ABRF and taught by Dr. Hunt prior to the meeting in Durham, NC. This highly positive response suggests that the course should be repeated at some point in the future.

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