Novel DNA coding regions and protein arginylation reveal unexplored T. cruzi proteome and PTMs

Gilberto Santos de Oliveira, Rebeca Kawahara, Livia Rosa-Fernandes, Carla C. Avila, Martin R. Larsen, João Marcelo Pereira Alves, Giuseppe Palmisano*

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Publikation: Bidrag til tidsskriftTidsskriftartikelForskningpeer review

Resumé

Chagas disease, also known as American trypanosomiasis, is a neglected tropical disease caused by the Trypanosoma cruzi parasite. In order to develop diagnostic and therapeutic solutions, there has been an intense investigation on the parasite biology using omics technologies such as genomics, transcriptomics lipidomics and proteomics. In particular, large scale mass spectrometry-based proteomics studies have allowed the identification and quantification of proteins and selected PTMs in different biological conditions. In this study, we investigated the unassigned MS/MS spectra commonly observed in large scale bottom up proteomics experiments looking at the T. cruzi (Sylvio X10/1) proteome. A deep proteomics data analysis using proteogenomic and unrestrictive PTMs search approaches allowed us to annotate 30% more MS/MS spectra and identify novel DNA coding regions and uncharacterized PTMs in Trypanosomatids, such as protein arginylation. Overall, this study shows: (1) the importance of assigning protein modifications, analytical artefacts and PTMs, in large-scale mass spectrometry-based proteomics data to deeply profile the trypanosomatids proteome. (2) The need of a better characterization of the influence of sample preparation steps on the identification of proteins and protein modifications. (3) The identification of novel DNA coding regions in T. cruzi. (4) The discovery of protein arginylation in trypanosomatids.

OriginalsprogEngelsk
TidsskriftInternational Journal of Mass Spectrometry
Vol/bind418
Sider (fra-til)51-66
ISSN1387-3806
DOI
StatusUdgivet - 2017

Fingeraftryk

Pulse time modulation
Proteome
DNA
Proteins
Mass spectrometry
Proteomics

Citer dette

de Oliveira, G. S., Kawahara, R., Rosa-Fernandes, L., Avila, C. C., Larsen, M. R., Pereira Alves, J. M., & Palmisano, G. (2017). Novel DNA coding regions and protein arginylation reveal unexplored T. cruzi proteome and PTMs. International Journal of Mass Spectrometry, 418, 51-66. https://doi.org/10.1016/j.ijms.2016.11.020
de Oliveira, Gilberto Santos ; Kawahara, Rebeca ; Rosa-Fernandes, Livia ; Avila, Carla C. ; Larsen, Martin R. ; Pereira Alves, João Marcelo ; Palmisano, Giuseppe. / Novel DNA coding regions and protein arginylation reveal unexplored T. cruzi proteome and PTMs. I: International Journal of Mass Spectrometry. 2017 ; Bind 418. s. 51-66.
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title = "Novel DNA coding regions and protein arginylation reveal unexplored T. cruzi proteome and PTMs",
abstract = "Chagas disease, also known as American trypanosomiasis, is a neglected tropical disease caused by the Trypanosoma cruzi parasite. In order to develop diagnostic and therapeutic solutions, there has been an intense investigation on the parasite biology using omics technologies such as genomics, transcriptomics lipidomics and proteomics. In particular, large scale mass spectrometry-based proteomics studies have allowed the identification and quantification of proteins and selected PTMs in different biological conditions. In this study, we investigated the unassigned MS/MS spectra commonly observed in large scale bottom up proteomics experiments looking at the T. cruzi (Sylvio X10/1) proteome. A deep proteomics data analysis using proteogenomic and unrestrictive PTMs search approaches allowed us to annotate 30{\%} more MS/MS spectra and identify novel DNA coding regions and uncharacterized PTMs in Trypanosomatids, such as protein arginylation. Overall, this study shows: (1) the importance of assigning protein modifications, analytical artefacts and PTMs, in large-scale mass spectrometry-based proteomics data to deeply profile the trypanosomatids proteome. (2) The need of a better characterization of the influence of sample preparation steps on the identification of proteins and protein modifications. (3) The identification of novel DNA coding regions in T. cruzi. (4) The discovery of protein arginylation in trypanosomatids.",
keywords = "MS/MS spectra interpretation, Protein argynilation, Proteomics, PTMs, Trypanosoma cruzi",
author = "{de Oliveira}, {Gilberto Santos} and Rebeca Kawahara and Livia Rosa-Fernandes and Avila, {Carla C.} and Larsen, {Martin R.} and {Pereira Alves}, {Jo{\~a}o Marcelo} and Giuseppe Palmisano",
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Novel DNA coding regions and protein arginylation reveal unexplored T. cruzi proteome and PTMs. / de Oliveira, Gilberto Santos; Kawahara, Rebeca; Rosa-Fernandes, Livia; Avila, Carla C.; Larsen, Martin R.; Pereira Alves, João Marcelo; Palmisano, Giuseppe.

I: International Journal of Mass Spectrometry, Bind 418, 2017, s. 51-66.

Publikation: Bidrag til tidsskriftTidsskriftartikelForskningpeer review

TY - JOUR

T1 - Novel DNA coding regions and protein arginylation reveal unexplored T. cruzi proteome and PTMs

AU - de Oliveira, Gilberto Santos

AU - Kawahara, Rebeca

AU - Rosa-Fernandes, Livia

AU - Avila, Carla C.

AU - Larsen, Martin R.

AU - Pereira Alves, João Marcelo

AU - Palmisano, Giuseppe

PY - 2017

Y1 - 2017

N2 - Chagas disease, also known as American trypanosomiasis, is a neglected tropical disease caused by the Trypanosoma cruzi parasite. In order to develop diagnostic and therapeutic solutions, there has been an intense investigation on the parasite biology using omics technologies such as genomics, transcriptomics lipidomics and proteomics. In particular, large scale mass spectrometry-based proteomics studies have allowed the identification and quantification of proteins and selected PTMs in different biological conditions. In this study, we investigated the unassigned MS/MS spectra commonly observed in large scale bottom up proteomics experiments looking at the T. cruzi (Sylvio X10/1) proteome. A deep proteomics data analysis using proteogenomic and unrestrictive PTMs search approaches allowed us to annotate 30% more MS/MS spectra and identify novel DNA coding regions and uncharacterized PTMs in Trypanosomatids, such as protein arginylation. Overall, this study shows: (1) the importance of assigning protein modifications, analytical artefacts and PTMs, in large-scale mass spectrometry-based proteomics data to deeply profile the trypanosomatids proteome. (2) The need of a better characterization of the influence of sample preparation steps on the identification of proteins and protein modifications. (3) The identification of novel DNA coding regions in T. cruzi. (4) The discovery of protein arginylation in trypanosomatids.

AB - Chagas disease, also known as American trypanosomiasis, is a neglected tropical disease caused by the Trypanosoma cruzi parasite. In order to develop diagnostic and therapeutic solutions, there has been an intense investigation on the parasite biology using omics technologies such as genomics, transcriptomics lipidomics and proteomics. In particular, large scale mass spectrometry-based proteomics studies have allowed the identification and quantification of proteins and selected PTMs in different biological conditions. In this study, we investigated the unassigned MS/MS spectra commonly observed in large scale bottom up proteomics experiments looking at the T. cruzi (Sylvio X10/1) proteome. A deep proteomics data analysis using proteogenomic and unrestrictive PTMs search approaches allowed us to annotate 30% more MS/MS spectra and identify novel DNA coding regions and uncharacterized PTMs in Trypanosomatids, such as protein arginylation. Overall, this study shows: (1) the importance of assigning protein modifications, analytical artefacts and PTMs, in large-scale mass spectrometry-based proteomics data to deeply profile the trypanosomatids proteome. (2) The need of a better characterization of the influence of sample preparation steps on the identification of proteins and protein modifications. (3) The identification of novel DNA coding regions in T. cruzi. (4) The discovery of protein arginylation in trypanosomatids.

KW - MS/MS spectra interpretation

KW - Protein argynilation

KW - Proteomics

KW - PTMs

KW - Trypanosoma cruzi

U2 - 10.1016/j.ijms.2016.11.020

DO - 10.1016/j.ijms.2016.11.020

M3 - Journal article

VL - 418

SP - 51

EP - 66

JO - International Journal of Mass Spectrometry

JF - International Journal of Mass Spectrometry

SN - 1387-3806

ER -