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Mirror proteases of Ac-Trypsin and Ac-LysargiNase precisely improve novel event identifications in Mycolicibacterium smegmatis MC(2) 155 by proteogenomic analysis

Accurate identification of novel peptides remains challenging because of the lack of evaluation criteria in large-scale proteogenomic studies. Mirror proteases of trypsin and lysargiNase can generate complementary b/y ion series, providing the opportunity to efficiently assess authentic novel peptid...

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Autores principales: Jiang, Songhao, Shi, Jiahui, Li, Yanchang, Zhang, Zhenpeng, Chang, Lei, Wang, Guibin, Wu, Wenhui, Yu, Liyan, Dai, Erhei, Zhang, Lixia, Lyu, Zhitang, Xu, Ping, Zhang, Yao
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9597629/
https://www.ncbi.nlm.nih.gov/pubmed/36312923
http://dx.doi.org/10.3389/fmicb.2022.1015140
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author Jiang, Songhao
Shi, Jiahui
Li, Yanchang
Zhang, Zhenpeng
Chang, Lei
Wang, Guibin
Wu, Wenhui
Yu, Liyan
Dai, Erhei
Zhang, Lixia
Lyu, Zhitang
Xu, Ping
Zhang, Yao
author_facet Jiang, Songhao
Shi, Jiahui
Li, Yanchang
Zhang, Zhenpeng
Chang, Lei
Wang, Guibin
Wu, Wenhui
Yu, Liyan
Dai, Erhei
Zhang, Lixia
Lyu, Zhitang
Xu, Ping
Zhang, Yao
author_sort Jiang, Songhao
collection PubMed
description Accurate identification of novel peptides remains challenging because of the lack of evaluation criteria in large-scale proteogenomic studies. Mirror proteases of trypsin and lysargiNase can generate complementary b/y ion series, providing the opportunity to efficiently assess authentic novel peptides in experiments other than filter potential targets by different false discovery rates (FDRs) ranking. In this study, a pair of in-house developed acetylated mirror proteases, Ac-Trypsin and Ac-LysargiNase, were used in Mycolicibacterium smegmatis MC(2) 155 for proteogenomic analysis. The mirror proteases accurately identified 368 novel peptides, exhibiting 75–80% b and y ion coverages against 65–68% y or b ion coverages of Ac-Trypsin (38.9% b and 68.3% y) or Ac-LysargiNase (65.5% b and 39.6% y) as annotated peptides from M. smegmatis MC(2) 155. The complementary b and y ion series largely increased the reliability of overlapped sequences derived from novel peptides. Among these novel peptides, 311 peptides were annotated in other public M. smegmatis strains, and 57 novel peptides with more continuous b and y pairs were obtained for further analysis after spectral quality assessment. This enabled mirror proteases to successfully correct six annotated proteins' N-termini and detect 17 new coding open reading frames (ORFs). We believe that mirror proteases will be an effective strategy for novel peptide detection in both prokaryotic and eukaryotic proteogenomics.
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spelling pubmed-95976292022-10-27 Mirror proteases of Ac-Trypsin and Ac-LysargiNase precisely improve novel event identifications in Mycolicibacterium smegmatis MC(2) 155 by proteogenomic analysis Jiang, Songhao Shi, Jiahui Li, Yanchang Zhang, Zhenpeng Chang, Lei Wang, Guibin Wu, Wenhui Yu, Liyan Dai, Erhei Zhang, Lixia Lyu, Zhitang Xu, Ping Zhang, Yao Front Microbiol Microbiology Accurate identification of novel peptides remains challenging because of the lack of evaluation criteria in large-scale proteogenomic studies. Mirror proteases of trypsin and lysargiNase can generate complementary b/y ion series, providing the opportunity to efficiently assess authentic novel peptides in experiments other than filter potential targets by different false discovery rates (FDRs) ranking. In this study, a pair of in-house developed acetylated mirror proteases, Ac-Trypsin and Ac-LysargiNase, were used in Mycolicibacterium smegmatis MC(2) 155 for proteogenomic analysis. The mirror proteases accurately identified 368 novel peptides, exhibiting 75–80% b and y ion coverages against 65–68% y or b ion coverages of Ac-Trypsin (38.9% b and 68.3% y) or Ac-LysargiNase (65.5% b and 39.6% y) as annotated peptides from M. smegmatis MC(2) 155. The complementary b and y ion series largely increased the reliability of overlapped sequences derived from novel peptides. Among these novel peptides, 311 peptides were annotated in other public M. smegmatis strains, and 57 novel peptides with more continuous b and y pairs were obtained for further analysis after spectral quality assessment. This enabled mirror proteases to successfully correct six annotated proteins' N-termini and detect 17 new coding open reading frames (ORFs). We believe that mirror proteases will be an effective strategy for novel peptide detection in both prokaryotic and eukaryotic proteogenomics. Frontiers Media S.A. 2022-10-12 /pmc/articles/PMC9597629/ /pubmed/36312923 http://dx.doi.org/10.3389/fmicb.2022.1015140 Text en Copyright © 2022 Jiang, Shi, Li, Zhang, Chang, Wang, Wu, Yu, Dai, Zhang, Lyu, Xu and Zhang. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Microbiology
Jiang, Songhao
Shi, Jiahui
Li, Yanchang
Zhang, Zhenpeng
Chang, Lei
Wang, Guibin
Wu, Wenhui
Yu, Liyan
Dai, Erhei
Zhang, Lixia
Lyu, Zhitang
Xu, Ping
Zhang, Yao
Mirror proteases of Ac-Trypsin and Ac-LysargiNase precisely improve novel event identifications in Mycolicibacterium smegmatis MC(2) 155 by proteogenomic analysis
title Mirror proteases of Ac-Trypsin and Ac-LysargiNase precisely improve novel event identifications in Mycolicibacterium smegmatis MC(2) 155 by proteogenomic analysis
title_full Mirror proteases of Ac-Trypsin and Ac-LysargiNase precisely improve novel event identifications in Mycolicibacterium smegmatis MC(2) 155 by proteogenomic analysis
title_fullStr Mirror proteases of Ac-Trypsin and Ac-LysargiNase precisely improve novel event identifications in Mycolicibacterium smegmatis MC(2) 155 by proteogenomic analysis
title_full_unstemmed Mirror proteases of Ac-Trypsin and Ac-LysargiNase precisely improve novel event identifications in Mycolicibacterium smegmatis MC(2) 155 by proteogenomic analysis
title_short Mirror proteases of Ac-Trypsin and Ac-LysargiNase precisely improve novel event identifications in Mycolicibacterium smegmatis MC(2) 155 by proteogenomic analysis
title_sort mirror proteases of ac-trypsin and ac-lysarginase precisely improve novel event identifications in mycolicibacterium smegmatis mc(2) 155 by proteogenomic analysis
topic Microbiology
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9597629/
https://www.ncbi.nlm.nih.gov/pubmed/36312923
http://dx.doi.org/10.3389/fmicb.2022.1015140
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