Annotation refers to the assignment of observed peaks in a spectrum to the fragment ions responsible for them, and can be obtained manually or computationally. The peak annotations (or lack thereof) provide the best indication of whether the observed spectrum is of high quality and can be adequately explained by the analyte identification. For example, a spectrum with a large number of unannotated peaks is a telltale sign that the spectrum may be incorrectly identified or contaminated with another analyte. Some peaks in a spectrum, such as those resulting from cleavages of isobaric labeling reagents for quantifications, have special uses and should be clearly marked. Additionally, spectral library search engines can assign different weights to the matching of fragment ion peaks of different types due to their different information content. However, since each spectrum may have hundreds of peaks, peak annotations can account for a large fraction of the storage space and parsing time of a spectral library. Therefore, encoding peak annotations compactly but unambiguously is a highly desirable feature of any spectral library format.