‘Omics Experimental Design / iPRG, sPRG, PRG

iPRG
Magnus Palmblad
The iPRG will present information about the 2020 study on metaproteomics, describing the experimental design, how the data were acquired and what questions will be asked of participants. This study is a bit different than most in the past in that participants will not need to quantify specific peptides or proteins, but rather, to deduce the organisms in the metaproteomics sample (“who is there?”) and what biological phenomena have taken place (“what did they do?”).

The 2020 study is the first in which hints to answering the study questions will be made available in stages. This will not only assist participants who have hit any roadblocks, but it will also enhance the interactive nature of the study by making it possible for participants to update their submission after receiving the additional information.

In this presentation, there will also be a demonstration of some of the new and freely-available metaproteomics analysis tools that not only can be used in answering some of the study questions, but also are of general utility in proteomics and metaproteomics.

PRG
The Proteomics Research Group initiated a study in 2018 to facilitate the adoption of data-independent acquisition (DIA) by providing participants with generic methods and test samples containing a HeLa digest spiked with different levels of four non-endogenous proteins. This resulted in the generation of 49 participant datasets submitted by laboratories across the world (20 countries and 16 states in the U.S.). The files from two laboratories were selected for further analysis using varied library approaches. The data (which will be made available via MassIVE) can be used by software developers or experts evaluating performance with different acquisition settings in addition to DIA newcomers to help them implement the technique in their laboratory.

sPRG
The focus of the Proteomics Standards Research Group (sPRG) over the last three years has been development of a standard containing a pool of stable isotope-labeled phosphopeptides in order to help core facilities establish/implement sample preparation, analysis and data processing workflows. The standard contains 144 tandem-MS verified phosphopeptides that were specifically chosen to cover as many known biologically interesting phosphosites as possible from seven different signaling networks. In this presentation, the sPRG will discuss data-independent acquisition experiments to characterize this standard in a HeLa background.