Proceedings of the EuBIC-MS 2020 Developers’ Meeting
Publication date: Available online 24 November 2020Source: EuPA Open ProteomicsAuthor(s): 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 (Source: EuPA Open Proteomics)
Source: EuPA Open Proteomics - November 26, 2020 Category: Bioinformatics Source Type: research
Sweet google O’ mine—The importance of online search engines for MS-facilitated, database-independent identification of peptide-encoded book prefaces: A EUPA YPIC challenge entry
Publication date: Available online 6 October 2019Source: EuPA Open ProteomicsAuthor(s): Alexander Hogrebe, Rosa R. Jersie-ChristensenAbstractIn 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™ ...
Source: EuPA Open Proteomics - November 6, 2019 Category: Bioinformatics Source Type: research
Team COUNCIL OF RICKS submission for EUPA YPIC 2017
Publication date: Available online 16 October 2019Source: EuPA Open ProteomicsAuthor(s): Lindsay K. Pino, Brian C Searle, Han-Yin YangABSTRACTUsing primarily LC-MS/MS de novo sequencing techniques, we concluded that the peptides form the following sentence from Sir JJ Thomson’s (1914) preface to Rays of Positive Electricity and Their Application to Chemical Analyses:“I feel sure that there are many problems in chemistry which could be solved with far greater ease by this than by any other method. The method is surprisingly sensitive, more so even than that of spectrum analysis, requires an infinitesimal amount of mater...
Source: EuPA Open Proteomics - October 19, 2019 Category: Bioinformatics Source Type: research
Sweet Google O’ Mine - The Importance of Online Search Engines for MS-facilitated, Database-independent Identification of Peptide-encoded Book Prefaces: A EUPA YPIC challenge entry
Publication date: Available online 6 October 2019Source: EuPA Open ProteomicsAuthor(s): Alexander Hogrebe, Rosa R. Jersie-Christensen, Axl RoseAbstractIn 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...
Source: EuPA Open Proteomics - October 6, 2019 Category: Bioinformatics Source Type: research
The Young Proteomics Investigator Club turns three!
Publication date: Available online 25 September 2019Source: EuPA Open ProteomicsAuthor(s): (Source: EuPA Open Proteomics)
Source: EuPA Open Proteomics - September 26, 2019 Category: Bioinformatics Source Type: research
YPIC Challenge
Publication date: Available online 29 August 2019Source: EuPA Open ProteomicsAuthor(s): Maarten Dhaenens (Source: EuPA Open Proteomics)
Source: EuPA Open Proteomics - August 29, 2019 Category: Bioinformatics Source Type: research
Math, science, history, unraveling the mystery—That all started with de novo!
Publication date: Available online 17 August 2019Source: EuPA Open ProteomicsAuthor(s): Ekaterina Ilgisonis, Olga Kiseleva, Ksenia KuznetsovaAbstractThis work on solving the mystery of words encoded by amino acids in peptides was derived by the YPIC-EuPA Challenge. We received a dry synthetic peptide sample and performed a mass spectrometric analysis followed by de novo peptide sequencing. As a result, a part of “Rays of positive electricity and their application to chemical analyses” by J.J.Tomson was found to be encoded in the peptides of the sample. The words were first revealed from the peptides, that matched by Go...
Source: EuPA Open Proteomics - August 25, 2019 Category: Bioinformatics Source Type: research
Proceedings of the EuBIC Winter School 2019
Publication date: Available online 17 August 2019Source: EuPA Open ProteomicsAuthor(s): Dominik Kopczynski, Wout Bittremieux, David Bouyssié, Viktoria Dorfer, Marie Locard- Paulet, Bart Van Puyvelde, Veit Schwämmle, Alessio Soggiu, Sander Willems, Julian UszkoreitAbstractThe 2019 European Bioinformatics Community (EuBIC) Winter School was held from January 15th to January 18th 2019 in Zakopane, Poland. This year’s meeting was the third of its kind and gathered international researchers in the field of (computational) proteomics to discuss (mainly) challenges in proteomics quantification and data independent acquisition...
Source: EuPA Open Proteomics - August 19, 2019 Category: Bioinformatics Source Type: research
Math, Science, History, Unraveling the mystery. That all started with the de novo!
Publication date: Available online 17 August 2019Source: EuPA Open ProteomicsAuthor(s): Ekaterina Ilgisonis, Olga Kiseleva, Ksenia Kuznetsova, Maarten DhaenensAbstractThis work on solving the mystery of words encoded by amino acids in peptides was derived by the YPIC-EuPA Challenge. We received a dry synthetic peptide sample and performed a mass spectrometric analysis followed by de novo peptide sequencing. As a result, a part of “Rays of positive electricity and their application to chemical analyses” by J.J.Tomson was found to be encoded in the peptides of the sample. The words were first revealed from the peptides, ...
Source: EuPA Open Proteomics - August 19, 2019 Category: Bioinformatics Source Type: research
Let me infuse this for you – a way to solve the first YPIC challenge
Publication date: Available online 16 August 2019Source: EuPA Open ProteomicsAuthor(s): Britta Eggers, Sandra Pacharra, Martin Eisenacher, Katrin Marcus, Julian Uszkoreit, Maarten DhaenensAbstractIn a common proteomics analysis today, the origins of our sample in the vial are known and therefore a database dependent approach to identify the containing peptides can be used. The first YPIC challenge though provided us with 19 synthetic peptides, which together formed an English sentence. For the identification of these peptides, a de-novo approach was used, which brought us together with an internet search engine to the hidd...
Source: EuPA Open Proteomics - August 17, 2019 Category: Bioinformatics Source Type: research
Introducing the YPIC Challenge
Publication date: Available online 14 August 2019Source: EuPA Open ProteomicsAuthor(s): Maarten Dhaenens (Source: EuPA Open Proteomics)
Source: EuPA Open Proteomics - August 16, 2019 Category: Bioinformatics Source Type: research
Aims & Scope
Publication date: Available online 13 August 2019Source: EuPA Open ProteomicsAuthor(s): Maarten Dhaenens (Source: EuPA Open Proteomics)
Source: EuPA Open Proteomics - August 14, 2019 Category: Bioinformatics Source Type: research
Editorial: The next generation in (EuPA Open) Proteomics
Publication date: Available online 25 July 2019Source: EuPA Open ProteomicsAuthor(s): Maarten Dhaenens (Source: EuPA Open Proteomics)
Source: EuPA Open Proteomics - August 3, 2019 Category: Bioinformatics Source Type: research
English lessons for E. coli
Publication date: Available online 2 August 2019Source: EuPA Open ProteomicsAuthor(s): Helene Klug, Florian Christoph Sigloch (Source: EuPA Open Proteomics)
Source: EuPA Open Proteomics - August 3, 2019 Category: Bioinformatics Source Type: research
Quick and clean: Cracking sentences encoded in E. coli by LC–MS/MS, de novo sequencing, and dictionary search
In this study, we faced the challenge of deciphering a protein that has been designed and expressed by E. coli 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 fi...
Source: EuPA Open Proteomics - July 30, 2019 Category: Bioinformatics Source Type: research
