title: Unrestrictive identification of post-translational modifications in the urine proteome without enrichment.
abstract: BACKGROUND
  Research on the human urine proteome may lay the foundation for the discovery of relevant disease biomarkers. Post-translational modifications (PTMs) have important effects on the functions of protein biomarkers. Identifying PTMs without enrichment adds no extra steps to conventional identification procedures for urine proteomics. The only difference is that this method requires software that can conduct unrestrictive identifications of PTMs. In this study, routine urine proteomics techniques were used to identify urine proteins. Unspecified PTMs were searched by MODa and PEAKS 6 automated software, followed by a manual search to screen out in vivo PTMs by removing all in vitro PTMs and amino acid substitutions.
  
  
  RESULTS
  There were 75 peptides with 6 in vivo PTMs that were found by both MODa and PEAKS 6. Of these, 34 peptides in 18 proteins have novel in vivo PTMs compared with the annotation information of these proteins on the Universal Protein Resource website. These new in vivo PTMs had undergone methylation, dehydration, oxidation, hydroxylation, phosphorylation, or dihydroxylation.
  
  
  CONCLUSIONS
  In this study, we identified PTMs of urine proteins without the need for enrichment. Our investigation may provide a useful reference for biomarker discovery in the future.
authors: National Key Laboratory of Medical Molecular Biology, Department of Physiology and Pathophysiology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences/School of Basic Medicine, 5 Dong Dan San Tiao, Beijing, China.
authors: Liu
authors: L
authors: Liu
authors: Department of Nephrology, Peking Union Medical College Hospital, 1 Dongcheng District Shuai Fu Yuan, Beijing, China.
authors: Xuejiao
authors: X
authors: Liu
authors: Department of Core Instrument Facility, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100005, China.
authors: Wei
authors: W
authors: Sun
authors: Department of Nephrology, Peking Union Medical College Hospital, 1 Dongcheng District Shuai Fu Yuan, Beijing, China.
authors: Mingxi
authors: M
authors: Li
authors: National Key Laboratory of Medical Molecular Biology, Department of Physiology and Pathophysiology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences/School of Basic Medicine, 5 Dong Dan San Tiao, Beijing, China.
authors: Youhe
authors: Y
authors: Gao