Accurate Mass Tag Retention Time Database for Urine Proteome Analysis by Chromatography–Mass Spectrometry

---

I. A. Agron^1,2, D. M. Avtonomov^1,2,3, A. S. Kononikhin^1,3, I. A. Popov^1,2,3, S. A. Moshkovskii², and E. N. Nikolaev^1,2,3*

¹Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, Leninsky pr. 38, 119334 Moscow, Russia; fax: (499) 137-8258; E-mail: nvduh@chph.ras.ru

²Orekhovich Institute of Biomedical Chemistry, Russian Academy of Medical Sciences, ul. Pogodinskaya 10, 119121 Moscow, Russia; fax: (499) 246-3423; E-mail: inst@ibmc.msk.ru; ennikolaev@rambler.ru

³Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, ul. Kosygina 4, 119334 Moscow, Russia; fax: (495) 137-4101; E-mail: ibcp@sky.chph.ras.ru

^* To whom correspondence should be addressed.

Received August 25, 2009; Revision received October 23, 2009

---

Information about peptides and proteins in urine can be used to search for biomarkers of early stages of various diseases. The main technology currently used for identification of peptides and proteins is tandem mass spectrometry, in which peptides are identified by mass spectra of their fragmentation products. However, the presence of the fragmentation stage decreases sensitivity of analysis and increases its duration. We have developed a method for identification of human urinary proteins and peptides. This method based on the accurate mass and time tag (AMT) method does not use tandem mass spectrometry. The database of AMT tags containing more than 1381 AMT tags of peptides has been constructed. The software for database filling with AMT tags, normalizing the chromatograms, database application for identification of proteins and peptides, and their quantitative estimation has been developed. The new procedures for peptide identification by tandem mass spectra and the AMT tag database are proposed. The paper also lists novel proteins that have been identified in human urine for the first time.

---

KEY WORDS: proteomics, ion cyclotron resonance mass spectrometry, accurate mass time tags, urine

DOI: 10.1134/S0006297910050147

---