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.

Some of the most cited manuscripts in Proteomics and Computational Proteomics (2013)

Some of the most cited manuscripts in 2013 in the field of Proteomics and Computational Proteomics (no order):

•  The Proteomics Identifications (PRIDE) database and associated tools: status in 2013: 

     The PRoteomics IDEntifications (PRIDE, http://www.ebi.ac.uk/pride) database 
     at the European Bioinformatics Institute is one of the most prominent data 
     repositories of mass spectrometry (MS)-based proteomics data. Here, we 
     summarize recent developments in the PRIDE database and related tools. 
     First, we provide up-to-date statistics in data content, splitting the figures by 
     groups of organisms and species, including peptide and protein 
     identifications, and post-translational modifications. We then describe the 
     tools that are part of the PRIDE submission pipeline, especially the recently 
     developed PRIDE Converter 2 (new submission tool) and PRIDE Inspector 
     (visualization and analysis tool). We also give an update about the integration 
     of PRIDE with other MS proteomics resources in the context of the 
     ProteomeXchange consortium. Finally, we briefly review the quality control 
     efforts that are ongoing at present and outline our future plans.

Creating an Open Source Revolution in Computational Proteomics

First of all, I don’t want to discuss in this post about Open-Source, its strengths & strengths. This post is about the most useful Open-Source packages, frameworks or libraries in the field of computational proteomics (a short version of our manuscript “Open source libraries and frameworks for Mass Spectrometry based Proteomics: A developer’s perspective”). 

Schema of the possible computational processing steps of a proteomics data set.

In proteomics like other Omics, the bioinformatics efforts can be divided in three major fields: data processing, storage and visualization. From MS/MS preprocessing to post-processing of the identifications results, even though the objectives of these libraries and packages can vary significantly, they usually share a number of features. Common use cases include the handling of protein and peptide sequences, the parsing of results from various proteomics search engines output files, and the visualization of MS-related information (including mass spectra and chromatograms).

Celebrating Ten Years of Mann and Aebersold’s “Mass spectrometry-based proteomics” review.

In 2003 Mann & Aebersold reviewed on the pages of Nature the challenges and perspectives of the then-nascent field of MS-based proteomics. Mass spectrometry (MS) has since entrenched itself as the method of choice for analyzing complex protein samples, and MS-based proteomics has become an indispensable technology for interpreting genomic data and performing protein analyses (primary sequence, post-translational modifications (PTMs) or protein–protein interactions).

" The ability of mass spectrometry to identify and, increasingly, to precisely quantify thousands of proteins from complex samples can be expected to impact broadly on biology and medicine."

The manuscript by Mann & Aebersold is one of the most cited manuscripts in the field of MS proteomics, For this reason is one of the “core papers” in the field of proteomics and computational proteomics, outlining most of the basic concepts required to understand the fundamentals of this discipline.

Ten years after its publication the main workflow described in the manuscript do not change dramatically. In this period major advances are related to the development of the Thermo’s Orbitrap Mass Spectrometer (Velos, LTQ, Exactive, etc) and new fragmentations types (ETD, HCD). Separation techniques (electrophoretic and chromatographic) were explored extensively in these ten years. Aebersold pioneered in 2005 the use of OFFGEL electrophoresis and electrophoresis fragmentation at peptide level (Heller 2005) and Mann’s group developed the FASP method for sample preparation before protein digestion (Wiśniewski JR et al 2009),both of which have contributed significantly to the dramatic increase in the number of identified proteins characterizing today’s proteomic projects. Surprisingly, the development of electrophoretic methods in the last 3 years looks like a “passed-on topic”. In ten years we moved from identifying at most 500 species in complex samples to identifying 60% of the human proteome.