Custom analyses and case studies
APAF bioinformatics has been involved in projects across all areas of proteomics, with particular recent emphasis on Bioplex data analysis, and bioinformatics supporting novel MS techniques such as SWATH. We have also had long standing collaborations and expertise in the area of plant proteomics. Custom analyses are available upon consultation.
The brief case studies included below describe some of our more recent projects.
Agricultural Plant Proteomics
Cytokine analysis in the study of disease
Proteomics bioinformatics and statistical methodology
Software tools for SWATH analysis
APAF bioinformatics contributed an open source software package to enable and evaluate integration of SWATH libraries across various instruments. The SwathXtend package is currently available from Bioconductor, and will soon be available from BaseSpace.
Detailed information is included in the publication below
Software tools for labelled and label-free proteomics analysis
APAF bioinformatics contributed a number of open source R packages implementing various data analysis approaches for developing proteomics techniques. The methods were developed in consultation with Macquarie university researchers or APAF mass spectrometry specialists.
- Label free analysis, found in the book Proteomics for Biomarker Discovery Methods in Molecular Biology Pages 205-222 http://link.springer.com/protocol/10.1007/978-1-62703-360-2_17#page-1
- iTRAQ analysis Combining Protein Ratio p-Values as a Pragmatic Approach to the Analysis of Multirun iTRAQ Experiments J. Proteome Res., 2015, 14 (2), pp 738–746 DOI: 10.1021/pr501091e Publication Date (Web): December 12, 2014
- TMT analysis – book chapter to appear
Statistical methodology for cytokine analysis
APAF bioinformatics using advanced data normalization and multivariate statistical analysis aim to obtain the best estimation of patient/sample immune system responses possible:
 Breen EJ, Polaskova V, Khan A. Bead-based multiplex immuno-assays for cytokines, chemokines, growth factors and other analytes: median fluorescence intensities versus their derived absolute concentration values for statistical analysis. Cytokine. 2015;71:188-98.
 Breen EJ, Tan W, Khan A. The Statistical Value of Raw Fluorescence Signal in Luminex xMAP Based Multiplex Immunoassays. Sci Rep. 2016;6:26996.
R recipes for Cytokine Analysis
APAF bioinformatics are contributing to plasma and serum proteomics by proving bioinformatics R recipes for multiplexed immunoassays analysis to appear in:
Methods in Molecular Biology Series: An Updated Serum / Plasma Proteomics (2017) Edited by Dr Greening and Prof Simpson