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.

Monday, 8 September 2014

Evaluation of Proteomic Search Engines for PTMs Identification

The peptide-centric MS strategy is called bottom-up, in which proteins are extracted from cells, digested into peptides with proteases, and analyzed by liquid chromatography tandem mass spectrometry (LC−MS/MS). More specifically, peptides are resolved by chromatography, ionized in mass spectrometers, and scanned to obtain full MS spectra. Next, some high-abundance peptides (precursor ions) are selected and fragmented to obtain MS/MS spectra by high- energy C-trap dissociation (HCD) or collision-induced dissociation (CID). 

Then, peptides are commonly identified by searching the MS/MS spectra against a database and finally assembled into identified proteins. Database searching plays an important role in proteomics analysis because it can be used to translate thousands of MS/MS spectra into protein identifications (IDs). 

Many database search engines have been developed to quickly and accurately analyze large volumes of proteomics data. Some of the more well-known search engines are MascotSEQUEST, PEAKS DB, ProteinPilot, Andromeda, and X!Tandem. Here a list of commonly use search engines in proteomics and mass spectrometry.

Sunday, 7 September 2014

Start a startup or Work for someone else?

Originally posted on P4P:

When you look online for advice about entrepreneurship, you will see a lot of "just do it": 
The best way to get experience... is to start a startup. So, paradoxically, if you're too inexperienced to start a startup, what you should do is start one. That's a way more efficient cure for inexperience than a normal job. - Paul Graham, Why to Not Not Start a Startup
There is very little you will learn in your current job as a {consultant, lawyer, business person, economist, programmer} that will make you better at starting your own startup. Even if you work at someone else’s startup right now, the rate at which you are learning useful things is way lower than if you were just starting your own. -  David Albert, When should you start a startup?
This advice almost never comes with citations to research or quantitative data, from which I have concluded:
The sort of person who jumps in and gives advice to the masses without doing a lot of research first generally believes that you should jump in and do things without doing a lot of research first. 

Friday, 5 September 2014

NEW NIST 2014 mass spectral library

Originally posted in NIST 2014.

Identify your mass spectra with the new NIST 14 Mass Spectral Library and Search Software.

NIST 14 - The successor to NIST 11 (2011) - Is a collection of:

  • Electron ionization (EI) mass spectra
  • Tandem MS/MS spectra (ion trap and collision cell)
  • GC method and retention data
  • Chemical structures and names
  • Software for searching and identifying your mass spectra
  • NIST 14 is integrated with most mass spectral data systems, including Agilent ChemStation/MassHunter, Thermo Xcalibur, and others. The NIST Library is known for its high quality, broad coverage, and accessibility. It is a product of a three decade, comprehensive evaluation and expansion of the world's most widely used and trusted mass spectral reference library compiled by a team of experienced mass spectrometrists in which each spectrum was examined for correctness.

Improvements from 2011 version:

  • Increased coverage in all libraries: 32,355 more EI spectra; 138,875 more MS/MS spectra; 37,706 more GC data sets
  • Retention index usable in spectral match scoring
  • Improved derivative naming, user library features, links to InChIKey, and other metadata.
  • Upgrade discount for any previous version
  • Lowest Agilent format price available

MS/MS and GC libraries may now be optionally purchased separately at very low cost
Learn what`s new

 Pick related PDFs

Thursday, 4 September 2014

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 catalog of protein sequence in the World. The aim of Uniprot is provide the scientific community with a single, centralized, authoritative resource for protein sequences and functional information. It started in 2002 when the Swiss‐Prot, TrEMBL and PIR protein database activities have united to form the Universal Protein Knowledgebase (UniProt) consortium.

Wednesday, 3 September 2014

What is Markdown?

Markdown is a plain text format for writing structured documents, based on conventions used for indicating formatting in email and usenet posts. It was developed in 2004 by John Gruber, who wrote the first markdown-to-html converter in Perl, and it soon became widely used in websites. by 2014 there were dozens of implementations in many languages.