A promising trend in the quantitative analysis and identification of proteins by chromatography-mass-spec- trometry (HPLC/MS) is an approach based on the use of databases of accurate mass and chromatography retention times of peptide markers (or tag) of proteins. Databases of such markers have been called Accurate Mass and Time tag (AMT) [1-4]. Their use makes it possible to signifi- cantly increase the throughput of protein identification due to the possibility of carrying out the analysis without involving methods of tandem mass spectrometry (MS/MS). However, a number of fundamental problems inter- fered with the development and wide application of AMT tags. Inaccuracies of genomic databases and low efficien- cy of tandem mass spectrometry used for peptide identifi- cation are “translated” into errors in generated AMT databases. Besides, chromatography data depend on spe- cific experimental conditions of separation and used instrumental platforms. As a result, AMT databases com- piled by a certain proteomic center cannot be used by other researchers having different experimental systems ISSN 0006-2979, Biochemistry (Moscow), 2009, Vol. 74, No. 11, pp. 1195-1202. © Pleiades Publishing, Ltd., 2009. Original Russian Text © M. L. Pridatchenko, I. A. Tarasova, V. Guryca, A. S. Kononikhin, C. Adams, D. A. Tolmachev, A. Yu. Agapov, V. V. Evreinov, I. A. Popov, E. N. Nikolaev, R. A. Zubarev, A. V. Gorshkov, C. D. Masselon, M. V. Gorshkov, 2009, published in Biokhimiya, 2009, Vol. 74, No. 11, pp. 1469-1478. Originally published in Biochemistry (Moscow) On-Line Papers in Press, as Manuscript BM09-039, July 5, 2009. 1195 Abbreviations: AMT, accurate mass and time; BioLCCC, liquid chromatography of biomacromolecules under critical condi- tions; LSS, Linear Solvent Strength theory proposed by Snyder; MPN, multi-point normalization; MS/MS, tandem mass spec- trometry; SSRCalc, Sequence Specific Retention Calculator. * To whom correspondence should be addressed. Use of Models of Biomacromolecule Separation in AMT Database Generation for Shotgun Proteomics M. L. Pridatchenko 1 , I. A. Tarasova 1 , V. Guryca 2 , A. S. Kononikhin 1 , C. Adams 3 , D. A. Tolmachev 1 , A. Yu. Agapov 1 , V. V. Evreinov 4 , I. A. Popov 5 , E. N. Nikolaev 5 , R. A. Zubarev 3 , A. V. Gorshkov 4 , C. D. Masselon 2 , and M. V. Gorshkov 1 * 1 Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, Leninsky pr. 38, 119334 Moscow, Russia; fax: (499) 137-8258; E-mail: mike.gorshkov@gmail.com 2 CEA, Universite Joseph Fourier, 17 Avenue des Martyrs, Bat. C3, 38054 Grenoble Cedex 9, France; fax: +33 (43) 878-5051 3 Uppsala University, Institute for Cell and Molecular Biology, Box 596, BMC, SE 75 124, Uppsala, Sweden; fax: +46 (18) 471-7209 4 Semenov Institute of Chemical Physics, Russian Academy of Sciences, ul. Kosygina 4, 119991 Moscow, Russia; fax: (495) 137-8247 5 Emmanuel Institute of Biochemical Physics, Russian Academy of Sciences, ul. Kosygina 4, 119334 Moscow, Russia; fax: (495) 137-4101 Received February 5, 2009 Revision received April 20, 2009 Abstract—Generation of a complex proteome database requires use of powerful analytical methods capable of following rapid changes in the proteome due to changing physiological and pathological states of the organism under study. One of the promising technologies with this regard is the use of so-called Accurate Mass and Time (AMT) tag peptide databases. Generation of an AMT database for a complex proteome requires combined efforts by many research groups and laborato- ries, but the chromatography data resulting from these efforts are tied to the particular experimental conditions and, in gen- eral, are not transferable from one platform to another. In this work, we consider an approach to solve this problem that is based on the generation of a universal scale for the chromatography data using a multiple-point normalization method. The method follows from the concept of linear correlation between chromatography data obtained over a wide range of separa- tion parameters. The method is further tested for tryptic peptide mixtures with experimental data collected from mutual studies by different independent research groups using different separation protocols and mass spectrometry data process- ing tools. DOI: 10.1134/S0006297909110030 Key words: high performance liquid chromatography, proteomics, mass spectrometry