(SW1) Data Independent Acquisition in Practice: Foundations and Resources for Implementing DIA

Abstracts

iPRG 2019 Metaproteomics Study

Speaker: Darryl Davis
Track:

Metaproteomics provides a range of technical challenges, from sampling to data analysis. In this study we will investigate where we are with respect to software and pipelines configurable or specially developed for metaproteomics data analysis.

The participants will receive label-free LC-MS/MS datasets of two mixed samples of known bacterial species composition, where the bacteria were grown under different conditions. The participants are free to use any software they like to answer one or more of the following questions: 1) What is the dominant organism in the sample? 2) Which other genera, species and strains can be identified in the sample, and what are their relative abundances? and 3) What could be inferred about differences in the environments from which the two samples were “collected”?

Specific Aims:

1.       Where are we as a field when it comes to analyzing data from multiple species?

2.       How are taxonomic compositions of samples determined and reported?

3.       What can be inferred about adaptation to the environment of the organisms in a sample?

In addition to discussing the 2019 Metaproteomics study, there will be time to have a mini workshop on data analysis workflows such as iPython and R markdown.

Authors:
  • Darryl L. Davis
    Author Email
    ddavis14@its.jnj.com
    Institution
    Janssen Research and Development LLC
  • Magnus Palmblad
    Author Email
    magnus.palmblad@gmail.com
    Institution
    Leiden University Medical Center
  • Susan T. Weintraub
    Author Email
    Weintraub@uthscsa.edu
    Institution
    Univ. of Texas Health Science Center at San Antonio

(SW1) Data Independent Acquisition in Practice: Foundations and Resources for Implementing DIA

Speaker:
Track:

Proteomics researchers are realizing the promise of Data-Independent Acquisition (DIA). In its 2017/2018 study, the ABRF Proteomics Research Group (PRG) have conducted a worldwide study to offer a go-to resource for sample processing, data acquisition and data analysis for new users interested in DIA studies. This workshop will facilitate an in-depth discussion of the PRG study results, and provide practical demonstrations utilizing those created during the PRG study.

Workshop Goals:

  • Educate and provide online educational resources for DIA that aid in the areas of sample preparation, data acquisition, data analysis and interpretation.
  • Enable academic and core facilities to use DIA technology by providing expert insights and possible improvements to existing workflows.
  • Share experience with attendees on some common lessons learnt during the PRG study.
  • Lay the foundation for attendees to implement DIA at their own institution.

Organizer:
Pratik Jagtap, University of Minnesota
Yan Wang, University of Maryland
Benjamin Neely, National institute of Standards and Technology
Joanna Kirkpatrick, Leibniz Institute on Aging  – Fritz Lipmann Institute (FLI)

Speakers:
Benjamin Neely, National institute of Standards and Technology
Mukul Midha, Institute of Systems Biology

Joanna Kirkpatrick, Leibniz Institute on Aging  – Fritz Lipmann Institute (FLI)
Pratik Jagtap, University of Minnesota

 

Authors:
  • Benjamin Neely
    Author Email
    benaneely@gmail.com
    Institution
    National institute of Standards and Technology
  • Joanna Kirkpatrick
    Author Email
    joanna.kirkpatrick@leibniz-fli.de
    Institution
    Leibniz Institute on Aging – Fritz Lipmann Institute (FLI)
  • Mukul Midha
    Author Email
    Mukul.Midha@systemsbiology.org
    Institution
    Institute of Systems Biology
  • Paul Stemmer
    Author Email
    pmstemmer@wayne.edu
    Institution
    Wayne State University
  • LeRoy Martin
    Author Email
    Roy_Martin@waters.com
    Institution
    Waters Corporation
  • Yan Wang
    Author Email
    yanwang@umd.edu
    Institution
    University of Maryland
  • Laura Herring
    Author Email
    laura_herring@med.unc.edu
    Institution
    University of North Carolina at Chapel Hill
  • Brett Phinney
    Author Email
    bsphinney@ucdavis.edu
    Institution
    University of California Davis
  • Baozhen Shan
    Author Email
    bshan@bioinfor.com
    Institution
    Bioinformatics Solutions Inc.
  • Allis Chien
    Author Email
    allis@stanford.edu
    Institution
    Stanford University
  • Pratik Jagtap
    Author Email
    pjagtap@umn.edu
    Institution
    University of Minnesota