PXD008088

PXD008088 is an original dataset announced via ProteomeXchange.

Title	Development of a Trypanosoma cruzi Strain Typing Assay using MS2 peptide spectral libraries (Tc-STAMS2)
Description	Chagas disease is one of the most important neglected diseases with an estimated number of 12 million infected individuals, the majority living in Central and South America. The Trypanosoma cruzi (T.cruzi) protozoan parasite is the etiological agent of Chagas disease. T.cruzi is highly genetically diverse and a new nomenclature assigned each strain to seven genetic groups (TcI-TcVI and Tcbat), named Discrete Typing Units (DTUs), based on their biochemical, immunological and phenotypical characteristics. T.cruzi DTUs have been correlated to diverse clinical outcomes highlighting the importance of molecular epidemiological screens. Despite the development of T.cruzi typing methods based on genetic signatures, each method presenting its own advantages and challenges. The work presented here shows the application of mass spectrometry for Trypanosoma cruzi Strain Typing Assay using MS2 peptide spectral libraries (Tc-STAMS2). The novelty of the method is based on the use of peptide fragmentation spectra as strain-specific fingerprints to classify and identify DTUs. Initially, a spectra library is generated from characterized T.cruzi strains. The library is subsequently inspected using MS/MS spectra from unknown strains and confidently assigned to a specific strain in an automated and computationally-driven approach. The Tc-STAMS2 method was challenged to test several variables such as sample type and preparation, instrument setup and identification platform. Tc-STAMS2 provided high confidence and robustness in T.cruzi strain typing. The Tc-STAMS2 method represents a proof-of-concept of a complementary strategy to the current DNA-based T. cruzi genotyping methods. Moreover, the method allows the identification of strain-specific features that could be related to the biology of T.cruzi strains and their clinical outcomes.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_04:41:26.067.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Gilberto Oliveira
SpeciesList	scientific name: Trypanosoma cruzi; NCBI TaxID: 5693;
ModificationList	No PTMs are included in the dataset
Instrument	LTQ Orbitrap

Revision	Datetime	Status	ChangeLog Entry
0	2017-10-31 06:32:33	ID requested
1	2018-03-19 02:18:08	announced
2	2018-04-25 06:33:23	announced	Updated publication reference for PubMed record(s): 29608573.
⏵ 3	2024-10-22 04:41:32	announced	2024-10-22: Updated project metadata.

de Oliveira GS, Kawahara R, Rosa-Fernandes L, Mule SN, Avila CC, Teixeira MMG, Larsen MR, Palmisano G, Development of a Trypanosoma cruzi strain typing assay using MS2 peptide spectral libraries (Tc-STAMS2). PLoS Negl Trop Dis, 12(4):e0006351(2018) [pubmed]

10.1371/journal.pntd.0006351;

curator keyword: Biological

submitter keyword: Trypanosoma cruzi

Discrete Typing Units (DTUs)

Mass spectrometry

Spectral matching

Strain typing methods

Giuseppe Palmisano
contact affiliation	Glycoproteomics Lab. Department of Parasitology Institute of Biomedical Sciences - University of São Paulo
contact email	palmisano.gp@gmail.com
lab head
Gilberto Oliveira
contact affiliation	University of São Paulo
contact email	gilberto_so@outlook.com
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2018/03/PXD008088

PRIDE project URI

• PRIDE
  1. PXD008088
     1. Label: PRIDE project
     2. Name: Development of a Trypanosoma cruzi Strain Typing Assay using MS2 peptide spectral libraries (Tc-STAMS2)