Typic: A Practical and Robust Tool to Rank Proteotypic Peptides for Targeted Proteomics

Author(s)

Pauletti, Bianca A. ; Granato, Daniela C. ; Carnielli, Carolina M. ; Camara, Guilherme A. ; Normando, Ana Gabriela C. ; Telles, Guilherme P. ; Leme, Adriana F. Paes

• Document type: Journal article
• Source: JOURNAL OF PROTEOME RESEARCH; v. 22, n. 2, p. 7-pg., 2023-02-03.

Abstract

The selection of a suitable proteotypic peptide remains a challenge for designing a targeted quantitative proteomics assay. Although the criteria are well-established in the literature, the selection of these peptides is often performed in a subjective and time-consuming manner. Here, we have developed a practical and semiautomated workflow implemented in an open-source program named Typic. Typic is designed to run in a command line and a graphical interface to help selecting a list of proteotypic peptides for targeted quantitation. The tool combines the input data and downloads additional data from public repositories to produce a file per protein as output. Each output file includes relevant information to the selection of proteotypic peptides organized in a table, a colored ranking of peptides according to their potential value as targets for quantitation and auxiliary plots to assist users in the task of proteotypic peptides selection. Taken together, Typic leads to a practical and straightforward data extraction from multiple data sets, allowing the identification of most suitable proteotypic peptides based on established criteria, in an unbiased and standardized manner, ultimately leading to a more robust targeted proteomics assay. (AU)

• FAPESP's process: 19/09692-9 - Validation of target proteins associated with the progression of potentially malignant disorders into Oral Cancer
• Grantee: Ana Gabriela Costa Normando
• Support Opportunities: Scholarships in Brazil - Doctorate
• FAPESP's process: 18/02180-0 - Study of the glycoprotein composition in the surface of extracellular vesicles of plasma from patients with oral cancer and its correlation to prognosis
• Grantee: Carolina Moretto Carnielli
• Support Opportunities: Scholarships in Brazil - Post-Doctoral
• FAPESP's process: 19/14828-7 - Quantitative targeted proteomics by target LC-MS (SRM) to determine the ligands and interaction interface of cystatin B complex, a prognostic marker for oral cancer
• Grantee: Guilherme Araújo Câmara
• Support Opportunities: Scholarships in Brazil - Master
• FAPESP's process: 18/18496-6 - The role of alcohol treated-extracellular vesicles in oral cells transformation
• Grantee: Adriana Franco Paes Leme
• Support Opportunities: Research Projects - Thematic Grants
• FAPESP's process: 18/15535-0 - From discovery to validation of prognostic candidates for oral cancer in liquid biopsies
• Grantee: Daniela Campos Granato
• Support Opportunities: Research Grants - Young Investigators Grants
• FAPESP's process: 19/18751-9 - Discovery and validation of prognostic candidates for oral cancer in liquid biopsies.
• Grantee: Daniela Campos Granato
• Support Opportunities: Scholarships in Brazil - Young Researchers