DigDig: A Software for In-Depth Analysis and Comparison of Proteolytic Digestion

Kód výsledku v IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F61388971%3A_____%2F25%3A00639921" target="_blank" >RIV/61388971:_____/25:00639921 - isvavai.cz</a>

Nalezeny alternativní kódy

RIV/00216208:11310/25:10508011

Výsledek na webu

<a href="https://pubs.acs.org/doi/10.1021/acs.analchem.5c04217" target="_blank" >https://pubs.acs.org/doi/10.1021/acs.analchem.5c04217</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1021/acs.analchem.5c04217" target="_blank" >10.1021/acs.analchem.5c04217</a>

Jazyk výsledku

angličtina

Název v původním jazyce

DigDig: A Software for In-Depth Analysis and Comparison of Proteolytic Digestion

Popis výsledku v původním jazyce

Proteolysis 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 nonspecific or semispecific 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 data sets from both specific and nonspecific digestions, highlighting its utility in digestion quality control, protease characterization, and method development, particularly in HDX-MS workflows. DigDig is freely available at https://peterslab.org/DigDig/.

Název v anglickém jazyce

DigDig: A Software for In-Depth Analysis and Comparison of Proteolytic Digestion

Popis výsledku anglicky

Proteolysis 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 nonspecific or semispecific 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 data sets from both specific and nonspecific digestions, highlighting its utility in digestion quality control, protease characterization, and method development, particularly in HDX-MS workflows. DigDig is freely available at https://peterslab.org/DigDig/.

Druh

J_imp - Článek v periodiku v databázi Web of Science

CEP obor

—

OECD FORD obor

10606 - Microbiology

Projekt

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

Návaznosti

I - Institucionalni podpora na dlouhodoby koncepcni rozvoj vyzkumne organizace

Rok uplatnění

2025

Kód důvěrnosti údajů

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

Název periodika

Analytical Chemistry

ISSN

0003-2700

e-ISSN

1520-6882

Svazek periodika

97

Číslo periodika v rámci svazku

39

Stát vydavatele periodika

US - Spojené státy americké

Počet stran výsledku

6

Strana od-do

21205-21210

Kód UT WoS článku

001582712600001

EID výsledku v databázi Scopus

2-s2.0-105018459768