ISSN 1607-6729, Doklady Biochemistry and Biophysics, 2011, Vol. 437, pp. 90–93. © Pleiades Publishing, Ltd., 2011. Original Russian Text © A.L. Chernobrovkin, V.A. Mitkevich, I.A. Popov, M.I. Indeikina, E.V. Ilgisonis, A.V. Lisitsa, A.I. Archakov, 2011, published in Doklady Akademii Nauk, 2011, Vol. 437, No. 4, pp. 561–564. 90 Modern technologies of full genome sequencing and resequencing make it possible to identify many individual features of organisms at the genomic level—single nucleotide polymorphisms (SNPs). Among them, nonsynonymous polymorphisms are of the greatest interest, because they lead to changes in the primary structure of proteins [1]. Such mutations, if their translation is detected in a protein sequence, are called single amino acid polymorphisms (SAPs). It is assumed that SAPs are responsible for the pheno- type of an individual, including predisposition to dis- eases [2] and susceptibility to drugs [3, 4]. For exam- ple, approximately 100 SAPs are known for tran- sthyretin, 85 of which lead to intensification of formation of amyloid fibrils and cause hereditary sys- temic amyloidosis [2]. High-performance methods of mass-spectrometric analysis make it possible to accurately determine the amino acid sequence of proteins. Using proteomic methods, it is possible to identify modified variants of proteins [5, 6], in particular, to perform proteotyping (i.e., to identify SAPs and other protein modifications by mass-spectrometric procedure [7]). The author of [5], population proteotyping was performed by the hybrid immunoaffinity–mass-spectrometry (IA-MS) technique. In total, during the analysis of 1000 blood plasma samples, 27 modifications in five analyzed pro- teins were detected, including 20 posttranslational modifications and seven SAPs. Amino acid polymor- phisms occurred in 87% protein; the highest frequency of mutations was found in transthyretin. Proteotyping can be used to determine the relative level of expression of alleles in heterozygous genes. Roth et al., who used the top–down method of protein identification, showed heterozygous expression of glu- cose-6-phosphatase and confirmed their results by using genotyping [6]. IA-MS and top–down approaches are not com- monly used because of technical or methodological difficulties. However, there are methods for identifica- tion of SAPs using the widely used bottom–up mass- spectrometric analysis. These methods are based on the use of databases containing numerous ample of protein sequences. Variants are added to the standard databases by including sequences that carry docu- mented SAPs [8]. In addition, the expressed sequence tags (EST) database can also be used as such a data- base. [9]. In this paper, we propose an iterative method for analyzing mass spectrometry data that allows targeted search for SAPs in identified proteins. Identification is performed in two iterations. In the first iteration, pro- tein identification involves using a protein database containing one amino acid sequence of protein for each protein-coding gene. Then, the second iteration involves searching polymorphisms in preliminarily identified proteins in open information sources. METHODS Mass spectra. Mass-spectrometric data for two pro- teomic experiments were loaded in the mzData format from the PRIDE database (www.ebi.ac.uk/pride/) [10] (for accession numbers, see the table). The first of the downloaded data sets refers to the HUPO Plasma Proteome Project. We used the results of an experi- ment in which the fraction of major blood plasma pro- teins was removed on an immunoaffinity column, after which the proteins were further fractionated using a solid-phase sorbent specific for cysteine-con- taining peptides and N-glycopeptides. Data of this experiment included two mass spectra files (accession numbers 8275 and 8277 in the table), which were obtained by fragmentation of peptide ions using an Identification of Single Amino Acid Polymorphisms in MS/MS Spectra of Peptides A. L. Chernobrovkin a , V. A. Mitkevich b , I. A. Popov b , M. I. Indeikina b , E. V. Ilgisonis b , A. V. Lisitsa a , and A. I. Archakov a Presented by Academician A.A. Makarov November 12, 2010 Received November 12, 2010 DOI: 10.1134/S1607672911020098 a Orekhovich Institute of Biomedical Chemistry, Russian Academy of Medical Sciences, Pogodinskaya ul. 10, Moscow, 119832 Russia b Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, ul. Vavilova 32, Moscow, 119991 Russia BIOCHEMISTRY, BIOPHYSICS AND MOLECULAR BIOLOGY