H2020Индивидуална стипендия2019–2021

BiT-XLMS · Development of comprehensive and user-friendly bioinformatics tools to study protein structures and interactions in mass spectrometry-based chemical cross-linking

„Хоризонт 2020“ — Действия „Мария Склодовска-Кюри“

Период: 2019-09-01 → 2021-12-31
Финансиране от ЕС: 171 461 €
Участници: 1
Схема: MSCA-IF-EF-ST

Линиите свързват координатора с партньорите.

Накратко на български

Биоинформатичните инструменти за химическо кръстосане и мас-спектрометрия помагат за определяне на структурата и взаимодействията между протеините. Създаденият софтуер MaxLynx позволява на биолозите да анализират тези данни самостоятелно и бързо, без да се нуждаят от експерти по програмиране.

Този кратък обзор е генериран от изкуствен интелект

Кратко обяснение, генерирано от езиков модел по текста на CORDIS. Оригиналът е по-долу.

Резултати накратко

Development of comprehensive and user-friendly bioinformatics tools to study protein structures and interactions in mass spectrometry-based chemical cross-linking

Crosslinking combined with mass spectrometry (XLMS) provides information about protein structures, conformations as well as protein interactions. In recent years, the field has undergone remarkable developments both experimentally with a variety of novel crosslinkers, a chemical agent to capture spatially close residues on proteins, as well as computationally, to extend searching capabilities from a couple of proteins to a proteome-wide. Despite this, comprehensive and user-friendly tools which also quickly and efficiently address new MS technologies were limited thus preventing widespread application of XLMS. This project aimed to develop comprehensive and user-friendly bioinformatics tools in XLMS and resulted in introducing MaxLynx (Yılmaz, et al., 2022), a novel computational proteomics workflow for XLMS integrated into the MaxQuant environment (Cox, et al., 2008). It can identify MS/MS spectra generated by two different crosslinker types: either non-cleavable or MS-cleavable crosslinkers. MaxLynx can be easily configured to search datasets generated by any novel chemical crosslinkers. It is user-friendly, fully automated and freely available. MaxLynx can run on Windows and Linux. It provides an interactive viewer to display annotated cross-linked spectra. Scientists from mass spectrometry or structural biology laboratories can analyze their XLMS data efficiently by using MaxLynx, without any assistance of bioinformatics experts. MaxLynx now will play an important role to make cross-linking one of the routine tools in structural biology.

Текст от CORDIS, на английски · Данни: CORDIS, © Европейски съюз

Цел на проекта

Mass spectrometry-based chemical cross-linking (XL-MS) is an emerging field to study protein structures, conformations and interactions. Despite its great potential, the data analysis part hinders its widespread applications for a variety of reasons. First, an arduous manual validation is still used in many laboratories. Second, most of the available bioinformatics tools are limited to conventional cross-linkers and not the new type of cross-linkers: MS-cleavable cross-linkers which are key to study protein interactions. Besides, almost every tool has been developed for identification but not quantification, which provides valuable information for changes in protein conformations. Above all, these tools are not user-friendly and requires an assistance of an expert bioinformatician for analysis. I therefore plan to develop fully-automated, comprehensive, user-friendly and free bioinformatics tools for XL-MS studies. This will be a part of one of the most commonly used proteomics software, MaxQuant, developed in the Cox group. MaxQuant software has already well-established preprocessing steps and a solid background. These will facilitate developing specialized tools in XL-MS effectively. I will build these bioinformatics tools which will be introduced as a module for MaxQuant software. My fellowship will cover the following three tasks: i) the identification of the protein samples by conventional cross-linkers, ii) a complete identification workflow for the analysis with MS-cleavable cross-linker and iii) performing relative quantification of over many samples. The extended version of MaxQuant will allow scientists from mass spectrometry or structural biology laboratories to analyze their XL-MS data efficiently without any assistance of bioinformatics expert. Moreover, the fully-automated and user-friendly feature of the tool will make cross-linking as one of the routine tools in structural biology.

Оригинален текст от CORDIS (на английски).

Участници

MAX-PLANCK-GESELLSCHAFT ZUR FORDERUNG DER WISSENSCHAFTEN EV · MUNCHENКоординаторГермания