Saturday, 4 October 2014

Analysis of histone modifications with PEAKS 7: A respond to Search Engines comparison from PEAKs Team

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 the  PEAKS Team just published a blog post with the reanalysis of the dataset. Here the results:

Originally Posted in Peaks Blog:
The complex nature of histone modification patterns has posed as a challenge for bioinformatics analysis over the years. Yuan et al. [1] conducted a study using two datasets from human HeLa histone samples, to benchmark the performance of current proteomic search engines. This article was published in J Proteome Res. 2014 Aug 28 (PubMed), and the data from the two datasets, HCD_Histone and CID_Histone (PXD001118), was made publically available through ProteomeXchange. With this data, the article uses eight different proteomic search engines to compare and evaluate the performance and capability of each. The evaluated search engines in this study are: pFind, Mascot, SEQUEST, ProteinPilot, PEAKS 6, OMSSA, TPP and MaxQuant. 
In this study, PEAKS 6 was used to compare the performance capabilities between search engines. However, PEAKS 7, which was released November 2013, is the latest version available of the PEAKS Studio software. PEAKS 7 not only includes better performance than PEAKS 6, but a lot of additional and improved features. Our team has reanalyzed the two datasets HCD_Histone and CID_Histone with PEAKS 7 to update the ID results presented in the publication by Yuan et al.  These updated results showed that instead, it is PEAKS, pFind and Mascot that identify the most confident results.

Wednesday, 17 September 2014

Who is a senior developer anyway?

Who is a senior developer anyway?

What makes you a “senior developer”? Everyone and their dog calls themselves a senior developer these days. From fresh graduates to the CTO, everyone is a senior developer. But what the hell does it even mean?


Some developers are avid technologists. They got into programming really because they like tinkering. If it hadn’t been 7 languages in 7 weeks, it would have been a box of meccano or they’d be in their shed busy inventing the battery operated self-tieing tie. These people are great to have on your team, they’ll be the ones continually bombarding you with the latest and greatest shiny. If you ever want to know if there’s an off the shelf solution to your problem, they’ll know the options, have tried two of them, and currently have a modified version of a third running on their raspberry pi.

The trouble with technologists is more technology is always the answer. Why have a HTTP listener when you can have a full stack application server? Why use plain old TCP when you can introduce an asynchronous messaging backbone? Why bother trying to deliver software when there’s all these toys to play with!

Tuesday, 16 September 2014

Installing 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
    make -f Makefile_STANDALONE_LINUX

Sunday, 14 September 2014

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 analysisproteomics repositories and databases or identification algorithms I'm sure that the most painful and no grateful job is work with file formats: writing, reading, and dealing with end-users. 

File formats (the way that we use to represent, storage and exchange our data) are fundamentals piece in bioinformatics, more than that, are one of the milestone of the Information Era. In some fields the topic is more stable than others, but the topic is still in the table for most of us. To have a quick idea see the evolution of general standards in recent years like XML, JSON and recently YAML.

Wednesday, 10 September 2014

New 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) – Biognosys AG, a Swiss Proteomics Company,  announced today the next release of its Spectronaut™ software for analysis of Hyper Reaction Monitoring (HRM) data that will now also be available for industry partners upon request. HRM-MSTM is a targeted proteomics technology developed by Biognosys that enables reproducible and accurate quantification of 1000s of proteins in a single instrument run. HRM is based on data-independent acquisition (DIA or SWATH), which can be performed on most state of the art high-resolution mass spectrometric systems. Founded in 2008 as spin-off from the lab of proteomics pioneer Ruedi Aebersold at ETH Zurich, Biognosys is dedicated to transform life science with superior technology and software.


Proteomics & personalized medicine Issue in Proteomics

A new issue in Proteomics was recently edited and published by RenĂ© P. Zahedi et al. regarding proteomics and personalized medicine. This Focus Issue comprises a total of eight valuable contributions from various experts in the field of proteomics research, ranging from methodical development and optimisation to applications dealing with complex samples in biomedical research. Urbani et al. report direct analytical assessment of sample quality for biomarker investigation. They pinpoint the impact of pre-analytical variables that cause major errors in clinical testing. Marko-Varga et al. describe the usage of MALDI imaging as novel tool for personalised diagnostics, as they follow drug action upon treatment of malignant melanoma. Selheim et al. established a novel super-SILAC mix for acute myeloid leukemia (AML) and demonstrate its usage as internal standard for personalized proteomics of AML patients. Jiang et al. demonstrate how SILAC can be utilized to investigate the secretome of activated hepatic stellate cells, the main fibroblast cell type in liver fibrosis. This is an important step for a better understanding of cellular mechanisms during the recovery of liver fibrosis. Borchers et al. introduce novel software for a fast analysis of large datasets derived from crosslinking experiments in order to study protein-protein interactions from large-scale experiments. Gevaert et al. present a technology that allows studying the specificity of methionine sulfoxide reductases and apply it to human samples. The oxidation of free and protein-bound methionine into methionine sulfoxide is a frequently occurring modification caused by reactive oxygen species. This modification may interfere with the identification of posttranslational modification such as protein phosphorylation as well as the peptide identification itself. Mechtler et al. push technology development forward to ultra-low flow nanoHPLC separations. This technology allows obtaining comprehensive proteomic data from less than 100 ng of protein starting material. Finally, Shen et al. demonstrate a rapid and reproducible one-dimensional fast and quantitative LC-MS/MS technology avoiding time- and sample-consuming prefractionation strategies.