DigDig

Kód výsledku v IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F61388971%3A_____%2F25%3A00638573" target="_blank" >RIV/61388971:_____/25:00638573 - isvavai.cz</a>

Výsledek na webu

<a href="https://peterslab.org/DigDig/doc/" target="_blank" >https://peterslab.org/DigDig/doc/</a>

DOI - Digital Object Identifier

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Jazyk výsledku

angličtina

Název v původním jazyce

DigDig

Popis výsledku v původním jazyce

Anotace v jazyce prácenProteolysis is a crucial step in both bottom-up and structural proteomics workflows, directly influencing peptide identification and sequence coverage in mass spectrometry-based analyses. While classical proteomics typically relies on highly specific enzymes with well-defined cleavage patterns, structural MS approaches such as hydrogen/deuterium exchange mass spectrometry (HDX-MS) often employ non-specific or semi-specific proteases, producing complex peptide mixtures that require more detailed digestion analysis. To address these needs and streamline the entire process, we developed DigDig, a standalone, Java-based software tool for evaluating and comparing proteolytic digestion across diverse experimental conditions. DigDig processes output files from common search engines and provides customizable visualizations of key digestion metrics, including sequence coverage, reproducibility, peptide redundancy, cleavage site preferences, and peptide length distributions. A distinguishing feature is its ability to detect and report repetitive peptide sequences, which are frequently missed by standard tools. We demonstrate its capabilities using datasets from both specific and non-specific digestions, highlighting its utility in digestion quality control, protease characterization, and method development, particularly in HDX-MS workflows.n

Název v anglickém jazyce

DigDig

Popis výsledku anglicky

Anotace v jazyce prácenProteolysis is a crucial step in both bottom-up and structural proteomics workflows, directly influencing peptide identification and sequence coverage in mass spectrometry-based analyses. While classical proteomics typically relies on highly specific enzymes with well-defined cleavage patterns, structural MS approaches such as hydrogen/deuterium exchange mass spectrometry (HDX-MS) often employ non-specific or semi-specific proteases, producing complex peptide mixtures that require more detailed digestion analysis. To address these needs and streamline the entire process, we developed DigDig, a standalone, Java-based software tool for evaluating and comparing proteolytic digestion across diverse experimental conditions. DigDig processes output files from common search engines and provides customizable visualizations of key digestion metrics, including sequence coverage, reproducibility, peptide redundancy, cleavage site preferences, and peptide length distributions. A distinguishing feature is its ability to detect and report repetitive peptide sequences, which are frequently missed by standard tools. We demonstrate its capabilities using datasets from both specific and non-specific digestions, highlighting its utility in digestion quality control, protease characterization, and method development, particularly in HDX-MS workflows.n

Druh

R - Software

CEP obor

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OECD FORD obor

10608 - Biochemistry and molecular biology

Projekt

Výsledek vznikl pri realizaci vícero projektů. Více informací v záložce Projekty.

Návaznosti

P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)

Rok uplatnění

2025

Kód důvěrnosti údajů

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Interní identifikační kód produktu

DigDig2025

Technické parametry

Samostatný program sestavený v jazyce Java fungující na běžných výpočetních strojích pod systémy Unix/Linux, Windows a MAC OS

Ekonomické parametry

Detailní analýza LC-MS/MS s důrazem na parametrizaci proteolytického štěpení a extrakci štěpných preferencí

IČO vlastníka výsledku

61388971

Název vlastníka

Mikrobiologický ústav AV ČR, v. v. i.