Proteomics & personalized medicine Issue in Proteomics
A new issue in Proteomics was recently edited and published by René P. Zahedi et al. regarding proteomics and personalized medicine. This Focus Issue comprises a total of eight valuable contributions...
View ArticleNew Release of Spectronaut™ 6.0 from Biognosys
Biognosys releases Spectronaut™ 6.0 Every researcher with access to high-resolution mass spectrometer can now benefit from the Spectronaut™ software September 10, 2014 – Zurich-Schlieren (CH) –...
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ProteoWizard: The chosen one in RAW file conversion
I'm the chosen one.After five years in proteomics and a quick walk through different computational proteomics topics such as: database analysis, proteomics repositories and databases or identification...
View ArticleInstalling standalone SpectraST in linux
Some tips to install SpectraST in linux in standalone:1. - Download TTP latest version.2. - go to SpectraST folder and run make: cd TPP-x.x.x/trans_proteomic_pipeline/src/Search/SpectraST...
View ArticleWho is a senior developer anyway?
Who is a senior developer anyway?Originally posted in Java Code Geeksby David Green on October 28th, 2013 | Filed in: Software DevelopmentWhat makes you a “senior developer”? Everyone and their dog...
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Analysis of histone modifications with PEAKS 7: A respond to Search Engines...
Recently we posted a comparison of different search engines for PTMs studies (Evaluation of Proteomic Search Engines for PTMs Identification). After some discussion of the mentioned results in our post...
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Which journals release more public proteomics data!!!
I'm a big fan of data and the -omics family. Also, I like the idea of make more & more our data public available for others, not only for reuse, but also to guarantee the reproducibility and...
View ArticleOntologies versus controlled vocabularies.
While the minimum data standards describe the types of data elements to be captured, the use of standard vocabularies as values to populate the information about these data elements is also important...
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What is BioHackathon 2014?
In a week BioHackathon 2014 will start (http://www.biohackathon.org/). It will be my first time ins this kind of "meeting". I will give a talk about PRIDE and ProteomeXchange and future developments of...
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QC metrics into Progenesis QI for proteomics
Originally posted NonLinearProteomics as a field is rapidly maturing; there is a real sense that established techniques are being improved, and excitement at emerging techniques for quantitation....
View ArticlePRIDE and ProteomeXchange – Making proteomics data accessible and reusable
Slides Presentation: Youtube Presentation:
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HUPO-PSI Meeting 2014: Rookie’s Notes
Standardisation: the most difficult flower to grow.The PSI (Proteomics Standard Initiative) 2014 Meeting was held this year in Frankfurt (13-17 of April) and I can say I’m now part of this history....
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Trends in Mass Spec Instruments
I'm not doing marketing for any of the mass spec producers. Here a recently statistic I got about the use of different mass spec instruments using the public data in PRIDE Archive. It can help to...
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Brazil: A place for Science and Friendship
BúziosIt's really difficult to break stereotypes, especially for developing countries, like Brazil. If you mention its name around the world they are immediately associated with: sports, music,...
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It's impossible to conduct research without software, say 7 out of 10 UK...
By Simon Hettrick, Deputy Director. Originally posted in SSINo one knows how much software is used in research. Look around any lab and you’ll see software – both standard and bespoke – being used by...
View ArticleBioinformatics for Proteomics Course, Bergen, April 21-24th 2015
The course will include lectures and practicals on open access software for the analysis of mass spectrometry generated proteomics data. Among the tools covering both protein identification and...
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Quick Guide to the New Uniprot Web
Probably Uniprot is one of the most used and well-established services in bioinformatics worldwide. With more than 12 years, is one of the major resources of biological information and the reference...
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GPMDB identifications by Original source
Source:@GPMDB BTW do you have an idea how many datasets in GPMDB comes from MassIVE, PRIDE, Tranche and how many were deposited direct in GPMDB.— Yasset Perez-Riverol (@ypriverol) March 8,...
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Quick Guide to the New Uniprot Web
Probably Uniprot is one of the most used and well-established services in bioinformatics worldwide. With more than 12 years, is one of the major resources of biological information and the reference...
View ArticleA Trans-Proteomic Pipeline (TPP) Docker container
By +Felipe Leprevost & +Yasset Perez-RiverolIn my initial post in this blog, I will teach you how to use a Docker container with the Trans-Proteomic Pipeline software installation.Docker is a great...
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