文摘
A new algorithm is described for label-free quantitation of relative protein abundances across multiplecomplex proteomic samples. Q-MEND is based on the denoising and peak picking algorithm, MEND,previously developed in our laboratory. Q-MEND takes advantage of the high resolution and massaccuracy of the hybrid LTQ-FT MS mass spectrometer (or other high-resolution mass spectrometers,such as a Q-TOF MS). The strategy, termed "cross-assignment", is introduced to increase substantiallythe number of quantitated proteins. In this approach, all MS/MS identifications for the set of analyzedsamples are combined into a master ID list, and then each LC-MS run is searched for the features thatcan be assigned to a specific identification from that master list. The reliability of quantitation is enhancedby quantitating separately all peptide charge states, along with a scoring procedure to filter out lessreliable peptide abundance measurements. The effectiveness of Q-MEND is illustrated in the relativequantitative analysis of Escherichia coli samples spiked with known amounts of non-E. coli proteindigests. A mean quantitation accuracy of 7% and mean precision of 15% is demonstrated. Q-MENDcan perform relative quantitation of a set of LC-MS data sets without manual intervention and cangenerate files compatible with the Guidelines for Proteomic Data Publication.