mIMT-visHTS: A novel method for multiplexing isobaric mass tagged datasets with an accompanying visualization high throughput screening tool for protein profiling

Piero Ricchiuto; Hiroshi Iwata; Katsumi Yabusaki; Iwao Yamada; Brett Pieper; Amitabh Sharma; Masanori Aikawa; Sasha A Singh

doi:10.1016/j.jprot.2015.07.024

mIMT-visHTS: A novel method for multiplexing isobaric mass tagged datasets with an accompanying visualization high throughput screening tool for protein profiling

J Proteomics. 2015 Oct 14:128:132-40. doi: 10.1016/j.jprot.2015.07.024. Epub 2015 Jul 29.

Authors

Piero Ricchiuto¹, Hiroshi Iwata¹, Katsumi Yabusaki¹, Iwao Yamada¹, Brett Pieper¹, Amitabh Sharma², Masanori Aikawa³, Sasha A Singh⁴

Affiliations

¹ Center for Interdisciplinary Cardiovascular Sciences, Division of Cardiovascular Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA.
² Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA.
³ Center for Interdisciplinary Cardiovascular Sciences, Division of Cardiovascular Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA; Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA.
⁴ Center for Interdisciplinary Cardiovascular Sciences, Division of Cardiovascular Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA. Electronic address: sasingh@partners.org.

PMID: 26232111
DOI: 10.1016/j.jprot.2015.07.024

Abstract

Isobaric mass tagging (IMT) methods enable the analysis of thousands of proteins simultaneously. We used tandem mass tagging reagents (TMT™) to monitor the relative changes in the proteome of the mouse macrophage cell line RAW264.7 at the same six time points after no stimulation (baseline phenotype), stimulation with interferon gamma (pro-inflammatory phenotype) or stimulation with interleukin-4 (anti-inflammatory phenotype). The combined TMT datasets yielded nearly 12,000 protein profiles for comparison. To facilitate this large analysis, we developed a novel method that combines or multiplexes the separate IMT (mIMT) datasets into a single super dataset for subsequent model-based clustering and co-regulation analysis. Specially designed visual High Throughput Screening (visHTS) software screened co-regulated proteins. visHTS generates an interactive and visually intuitive color-coded bullseye plot that enables users to browse the cluster outputs and identify co-regulated proteins.

Keywords: Bioinformatics; Macrophage differentiation; Model-based clustering; Proteomics.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Animals
Gene Expression Profiling / methods*
High-Throughput Screening Assays / methods
Mice
Proteome / chemistry*
Proteome / metabolism*
RAW 264.7 Cells
Reproducibility of Results
Sensitivity and Specificity
Software*
Tandem Mass Spectrometry / methods*
User-Computer Interface*

Substances

Proteome