EuPA Open Proteomics最新文献

Proceedings of the EuBIC-MS 2020 Developers’ Meeting EuBIC-MS 2020开发者会议纪要

EuPA Open Proteomics Pub Date : 2020-12-01 DOI: 10.1016/j.euprot.2020.11.001

Christopher Ashwood , Wout Bittremieux , Eric W. Deutsch , Nadezhda T. Doncheva , Viktoria Dorfer , Ralf Gabriels , Vladimir Gorshkov , Surya Gupta , Andrew R. Jones , Lukas Käll , Dominik Kopczynski , Lydie Lane , Ludwig Lautenbacher , Marc Legeay , Marie Locard-Paulet , Bart Mesuere , Yasset Perez-Riverol , Eugen Netz , Julianus Pfeuffer , Timo Sachsenberg , Sander Willems

{"title":"Proceedings of the EuBIC-MS 2020 Developers’ Meeting","authors":"Christopher Ashwood , Wout Bittremieux , Eric W. Deutsch , Nadezhda T. Doncheva , Viktoria Dorfer , Ralf Gabriels , Vladimir Gorshkov , Surya Gupta , Andrew R. Jones , Lukas Käll , Dominik Kopczynski , Lydie Lane , Ludwig Lautenbacher , Marc Legeay , Marie Locard-Paulet , Bart Mesuere , Yasset Perez-Riverol , Eugen Netz , Julianus Pfeuffer , Timo Sachsenberg , Sander Willems","doi":"10.1016/j.euprot.2020.11.001","DOIUrl":"10.1016/j.euprot.2020.11.001","url":null,"abstract":"<div><p>The 2020 European Bioinformatics Community for Mass Spectrometry (EuBIC-MS) Developers’ meeting was held from January 13<sup>th</sup> to January 17<sup>th</sup> 2020 in Nyborg, Denmark. Among the participants were scientists as well as developers working in the field of computational mass spectrometry (MS) and proteomics. The 4-day program was split between introductory keynote lectures and parallel hackathon sessions. During the latter, the participants developed bioinformatics tools and resources addressing outstanding needs in the community. The hackathons allowed less experienced participants to learn from more advanced computational MS experts, and to actively contribute to highly relevant research projects. We successfully produced several new tools that will be useful to the proteomics community by improving data analysis as well as facilitating future research. All keynote recordings are available on <span>https://doi.org/10.5281/zenodo.3890181</span><svg><path></path></svg>.</p></div>","PeriodicalId":38260,"journal":{"name":"EuPA Open Proteomics","volume":"24 ","pages":"Pages 1-6"},"PeriodicalIF":0.0,"publicationDate":"2020-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.euprot.2020.11.001","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"47619132","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 3

English lessons for E. coli 大肠杆菌的英语课

EuPA Open Proteomics Pub Date : 2019-03-01 DOI: 10.1016/j.euprot.2019.07.008

Helene Klug, Florian Christoph Sigloch

引用次数: 1

Sweet google O’ mine—The importance of online search engines for MS-facilitated, database-independent identification of peptide-encoded book prefaces 甜蜜的谷歌O ' mine -在线搜索引擎的重要性，为ms便利，数据库独立识别肽编码的书籍序言

EuPA Open Proteomics Pub Date : 2019-03-01 DOI: 10.1016/j.euprot.2019.07.012

Alexander Hogrebe, Rosa R. Jersie-Christensen

{"title":"Sweet google O’ mine—The importance of online search engines for MS-facilitated, database-independent identification of peptide-encoded book prefaces","authors":"Alexander Hogrebe, Rosa R. Jersie-Christensen","doi":"10.1016/j.euprot.2019.07.012","DOIUrl":"10.1016/j.euprot.2019.07.012","url":null,"abstract":"<div><p>In the recent year, we felt like we were not truly showing our full potential in our PhD projects, and so we were very happy and excited when YPIC announced the ultimate proteomics challenge. This gave us the opportunity of showing off and procrastinating at the same time:) The challenge was to identify the amino acid sequence of 19 synthetic peptides made up from an English text and then find the book that it came from. For this task we chose to run on an Orbitrap Fusion™ Lumos™ Tribrid™ Mass Spectrometer with two different sensitive MS2 resolutions, each with both HCD and CID fragmentation consecutively. This strategy was chosen because we speculated that multiple MS2 scans at high quality would be beneficial over lower resolution, speed and quantity in the relatively sparse sample. The resulting chromatogram did not reveal 19 sharp distinct peaks and it was not clear to us where to start a manual spectra interpretation. We instead used the de novo option in the MaxQuant software and the resulting output gave us two phrases with words that were specific enough to be searched in the magic Google search engine. Google gave us the name of a very famous physicist, namely Sir Joseph John Thomson, and a reference to his book “Rays of positive electricity” from 1913. We then converted the paragraph we believed to be the right one into a FASTA format and used it with MaxQuant to do a database search. This resulted in 16 perfectly FASTA search-identified peptide sequences, one with a missing PTM and one found as a truncated version. The remaining one was identified within the MaxQuant de novo sequencing results. We thus show in this study that our workflow combining de novo spectra analysis algorithms with an online search engine is ideally suited for all applications where users want to decipher peptide-encoded prefaces of 20th century science books.</p></div>","PeriodicalId":38260,"journal":{"name":"EuPA Open Proteomics","volume":"22 ","pages":"Pages 14-18"},"PeriodicalIF":0.0,"publicationDate":"2019-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.euprot.2019.07.012","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37502635","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

YPIC Challenge YPIC挑战

EuPA Open Proteomics Pub Date : 2019-03-01 DOI: 10.1016/j.euprot.2019.07.006

Bernhard Blank-Landeshammer

引用次数: 0

Aims & scope 目标及范围

EuPA Open Proteomics Pub Date : 2019-03-01 DOI: 10.1016/j.euprot.2019.07.005

Maarten Dhaenens

引用次数: 0

Proceedings of the EuBIC Winter School 2019 2019年冬季学校会议纪要

EuPA Open Proteomics Pub Date : 2019-03-01 DOI: 10.1016/j.euprot.2019.07.002

Dominik Kopczynski , Wout Bittremieux , David Bouyssié , Viktoria Dorfer , Marie Locard-Paulet , Bart Van Puyvelde , Veit Schwämmle , Alessio Soggiu , Sander Willems , Julian Uszkoreit

引用次数: 2

Quick and clean: Cracking sentences encoded in E. coli by LC–MS/MS, de novo sequencing, and dictionary search 快速清洁:通过LC-MS /MS, de novo测序和字典搜索破解大肠杆菌编码的句子

EuPA Open Proteomics Pub Date : 2019-03-01 DOI: 10.1016/j.euprot.2019.07.010

Lili Niu , Matthias Mann

{"title":"Quick and clean: Cracking sentences encoded in E. coli by LC–MS/MS, de novo sequencing, and dictionary search","authors":"Lili Niu , Matthias Mann","doi":"10.1016/j.euprot.2019.07.010","DOIUrl":"10.1016/j.euprot.2019.07.010","url":null,"abstract":"<div><p>In this study, we faced the challenge of deciphering a protein that has been designed and expressed by <em>E. coli</em> in such a way that the amino acid sequence encodes two concatenated English sentences. The letters ‘O’ and ‘U’ in the sentence are both replaced by ‘K’ in the protein. The sequence cannot be found online and carried to-be-discovered modifications. With limited information in hand, to solve the challenge, we developed a workflow consisting of bottom-up proteomics, de novo sequencing and a bioinformatics pipeline for data processing and searching for frequently appearing words. We assembled a complete first question: “Have you ever wondered what the most fundamental limitations in life are?” and validated the result by sequence database search against a customized FASTA file. We also searched the spectra against an <em>E. coli</em> proteome database and found close to 600 endogenous, co-purified <em>E. coli</em> proteins and contaminants introduced during sample handling, which made the inference of the sentence very challenging. We conclude that <em>E. coli</em> can express English sentences, and that de novo sequencing combined with clever sequence database search strategies is a promising tool for the identification of uncharacterized proteins.</p></div>","PeriodicalId":38260,"journal":{"name":"EuPA Open Proteomics","volume":"22 ","pages":"Pages 30-35"},"PeriodicalIF":0.0,"publicationDate":"2019-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.euprot.2019.07.010","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37502640","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 2

Let me infuse this for you – A way to solve the first YPIC challenge 让我为你灌输这个——解决第一个YPIC挑战的方法

EuPA Open Proteomics Pub Date : 2019-03-01 DOI: 10.1016/j.euprot.2019.07.007

Britta Eggers, Sandra Pacharra, Martin Eisenacher, Katrin Marcus, Julian Uszkoreit Dr.

引用次数: 0

Editorial: The next generation in (EuPA Open) Proteomics 编辑:下一代(EuPA Open)蛋白质组学

EuPA Open Proteomics Pub Date : 2019-03-01 DOI: 10.1016/j.euprot.2019.07.001

Maarten Dhaenens

引用次数: 0

Introducing the YPIC challenge 介绍YPIC挑战

EuPA Open Proteomics Pub Date : 2019-03-01 DOI: 10.1016/j.euprot.2019.07.004

Maarten Dhaenens

引用次数: 1