A new algorithm using cross-assignment for label-free quantitation with LC-LTQ-FT MS

作者：Andreev Victor P; Li Lingyun; Cao Lei; Gu Ye; Rejtar Tomas; Wu Shiaw Lin; Karger Barry L^*

来源：Journal of Proteome Research, 2007, 6(6): 2186-2194.

DOI：10.1021/pr0606880

• label-free
• quantitation
• cross-assignment
• LC-MS
• LTQ-PT

A new algorithm is described for label-free quantitation of relative protein abundances across multiple complex 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 mass accuracy 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 substantially the number of quantitated proteins. In this approach, all MS/MS identifications for the set of analyzed samples are combined into a master ID list, and then each LC-MS run is searched for the features that can be assigned to a specific identification from that master list. The reliability of quantitation is enhanced by quantitating separately all peptide charge states, along with a scoring procedure to filter out less reliable peptide abundance measurements. The effectiveness of Q-MEND is illustrated in the relative quantitative analysis of Escherichia coli samples spiked with known amounts of non-E. coli protein digests. A mean quantitation accuracy of 7% and mean precision of 15% is demonstrated. Q-MEND can perform relative quantitation of a set of LC-MS data sets without manual intervention and can generate files compatible with the Guidelines for Proteomic Data Publication.

• 出版日期2007
• 单位东北大学