Software is being developed to account for error in peptide assignments in semiquantitative analysis. Currently, it is assumed that the amount of collisions in the spectrometer accurately indicates the amount of peptides in the sample, but peptides of low abundance in a complex sample often are underrepresented. This also is a problem for relative quantification based on differential stable isotope labeling.The authors describe several software programs for relative quantification based on isotope labeling, including Applied Biosystems’ ProQuant and ProteinPilot, Thermo Fisher Scientific’s XPress in its BioWorks package and Bruker Daltonics’ Warp-LC as well as free programs Multi-Q, iTracker, iTraq reporter ion counter, ZoomQuant and Stem.Label-free mass spectrometry is becoming popular. The authors emphasize that the technique requires a precise spectrometer. Free programs for label-free detection include SpecArray, MsInspect, MSight, Topp, PeppeR and SuperHirn. Commercial programs include Waters’ QuanLynx, Thermo Fisher Scientific’s Sieve, Rosetta Biosoftware’s Elucidator and Genedata’s Expressionist. The authors note that it is important to correct for errors in peptide intensity values and chromatographic fluctuations in label-free analysis. They also detail a proposed solution for peptide assignment when using label-free mass spectrometry. In this solution, the alignment of peptide signals from several liquid-chromatography mass spectrometry runs would be normalized. These normalized peptide signals then would be subjected to comparison against several additional runs or a large repository of mass spectrometry data. (Journal of Proteome Research, January 2008, pp. 51-61.)