Jump to main content
Jump to site search

Issue 1, 2017
Previous Article Next Article

Checkpoints for preliminary identification of small molecules found enriched in autophagosomes and activated mast cell secretions analyzed by comparative UPLC/MSe

Author affiliations

Abstract

We report the use of ultra high performance liquid chromatography (UPLC) coupled with acquisition of low- and high-collision energy mass spectra (MSe) to explore small molecule compositions that are unique to either enriched-autophagosomes or secretions of chemically activated murine mast cells. Starting with thousands of features, each defined by a chromatographic retention time, m/z value and ion intensity, manual examination of the extracted ion chromatograms (XIC) of chemometrically selected features was essential to eliminate false positives, occurring at rates of 33, 14 and 37% in samples of three biological systems. Forty-six percent of features that passed the XIC-based checkpoint, had IDs in compound databases used here. From these, 19% of IDs had experimental high-collision energy MSe spectra that were in agreement with in silico fragmentation. The importance of this second checkpoint was highlighted through validation with selected commercially available standards. This work illustrates that checkpoints in data processing are essential to ascertain reliability of unbiased metabolomic studies, thereby reducing the risk of generating ‘false identifications’ which is a major concern as ‘omics’ data continue to proliferate and be used as platforms to launch novel biological hypotheses.

Graphical abstract: Checkpoints for preliminary identification of small molecules found enriched in autophagosomes and activated mast cell secretions analyzed by comparative UPLC/MSe

Back to tab navigation

Supplementary files

Article information


Submitted
05 Sep 2016
Accepted
10 Oct 2016
First published
11 Oct 2016

Anal. Methods, 2017,9, 46-54
Article type
Paper

Checkpoints for preliminary identification of small molecules found enriched in autophagosomes and activated mast cell secretions analyzed by comparative UPLC/MSe

C. P. Satori, M. Ramezani, J. S. Koopmeiners, A. F. Meyer, J. A. Rodriguez-Navarro, M. M. Kuhns, T. H. Taylor, C. L. Haynes, J. J. Dalluge and E. A. Arriaga, Anal. Methods, 2017, 9, 46
DOI: 10.1039/C6AY02500E

Social activity

Search articles by author

Spotlight

Advertisements