2 research outputs found
Typic: A Practical and Robust Tool to Rank Proteotypic Peptides for Targeted Proteomics
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
Typic: A Practical and Robust Tool to Rank Proteotypic Peptides for Targeted Proteomics
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