Brazil: A place for Science and Friendship

Búzios

It'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, beaches, rum and "País do Carnaval". If you ask to someone in the streets of Germany or China about personalities from Brazil, they will mention Pelé. Breaking stereotypes is a task for years or centuries but we are going in the right direction.

Hotel Ferradura/ Ferradura Resort

Last December I attended to the 2nd Proteomics Meeting of the Brazilian Proteomics Society jointly with the 2nd Pan American HUPO Meeting in Hotel Ferradura/ Ferradura Resort, Búzios, Rio de Janeiro State, Brazil. The venue was gorgeous, mountains close to a small bay that offers calm, clear waters and the open sea. We arrived after 2 hours by car from Rio international airport. My plans, give a talk about PRIDE and ProteomeXchange but more than that, my talk was about "if we really need to share our proteomics data".  

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.

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 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.

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 http://www.sisweb.com/software/ms/nist.htm#whatsnew

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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 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.

SWATH-MS and next-generation targeted proteomics

For proteomics, two main LC-MS/MS strategies have been used thus far. They have in common that the sample proteins are converted by proteolysis into peptides, which are then separated by (capillary) liquid chromatography. They differ in the mass spectrometric method used.

The first and most widely used strategy is known as shotgun proteomics or discovery proteomics. For this method, the MS instrument is operated in data-dependent acquisition (DDA) mode, where fragment ion (MS2) spectra for selected precursor ions detectable in a survey (MS1) scan are generated (Figure 1 - Discovery workflow). The resulting fragment ion spectra are then assigned to their corresponding peptide sequences by sequence database searching (See Open source libraries and frameworks for mass spectrometry based proteomics: A developer's perspective).

The second main strategy is referred to as targeted proteomics. There, the MS instrument is operated in selected reaction monitoring (SRM) (also called multiple reaction monitoring) mode (Figure 1 - Targeted Workflow). With this method, a sample is queried for the presence and quantity of a limited set of peptides that have to be specified prior to data acquisition. SRM does not require the explicit detection of the targeted precursors but proceeds by the acquisition, sequentially across the LC retention time domain, of predefined pairs of precursor and product ion masses, called transitions, several of which constitute a definitive assay for the detection of a peptide in a complex sample (See Targeted proteomics) .

Figure 1 - Discovery and Targeted proteomics workflows