TY - JOUR
T1 - Novel DNA coding regions and protein arginylation reveal unexplored T. cruzi proteome and PTMs
AU - de Oliveira, Gilberto Santos
AU - Kawahara Sakuma, Rebeca
AU - Rosa-Fernandes, Livia
AU - Avilac, Carla C.
AU - Larsen, Martin R.
AU - Pereira Alvesc, 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 - Proteomics
KW - PTMs
KW - Trypanosoma cruzi
KW - MS/MS spectra interpretation
KW - Protein argynilation
UR - http://www.scopus.com/inward/record.url?scp=85009250512&partnerID=8YFLogxK
U2 - 10.1016/j.ijms.2016.11.020
DO - 10.1016/j.ijms.2016.11.020
M3 - Article
SN - 1387-3806
VL - 418
SP - 51
EP - 66
JO - International Journal of Mass Spectrometry
JF - International Journal of Mass Spectrometry
ER -