DIA-Umpire Pipeline Using BioDocker containers.

By  +Felipe Leprevost and +Yasset Perez-Riverol

The complexity of some bioinformatic softwares is well-known and it has been commented in different papers and blog posts, etc. Especially, those softwares that depend of many software components and tools making impossible for a testing/new-user try for the first time the software. @BioDocker aim to simplify the process of testing/compiling/deploying bioinfo softwares. Our previously post shows how to use the TPP software from System Biology team. 

Recently, the Data Independent Acquisition Methods has been receiving a lot of attention by the proteomics community, specially SWATH. In this example We are going to demonstrate the importance of Docker through the use of a complex and powerful pipeline called DIA-Umpire. In this example I will demonstrate how to download, run and obtain the results from the DIA-Umpire pipeline.

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. First, I will try to describe with a couple of sentences (for sure I will fai) the incredible venue, the Schloss Reinhartshausen Kempinski. When I saw for the first time the hotel, first thing came to my mind was those films from the 50s. Everything was elegant, classic, sophisticated - from the decoration to a small latch. The food was incredible and the service is first class from the moment you set foot on the front step and throughout the whole stay. 

  

Standardization is the process of developing and implementing technical standards. Standardization can help to maximize compatibility, interoperability, safety, repeatability, or quality. It can also facilitate commoditization of formerly custom processes. In bioinformatics, the standardization of file formats, vocabulary, and resources is a job that all of us appreciate but for several reasons nobody wants to do. First of all, standardization in bioinformatics means that you need to organize and merge different experimental and in-silico pipelines to have a common way to represent the information. In proteomics for example, you can use different sample preparation, combined with different fractionation techniques and different mass spectrometers; and finally using different search engines and post-processing tools. The diversity and possible combinations is needed because allow to explore different solutions for complex problems. (Standarization in Proteomics: From raw data to metadata files).

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