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Title: Qualitative and quantitative characterization of plasma proteins when incorporating traveling wave ion mobility into a liquid chromatography−mass spectrometry workflow for biomarker discovery : use of product ion quantitation as an alternative data analysis tool for label free quantitation
Authors: Daly, Charlotte E.
Ng, Leong L.
Hakimi, Amirmansoor
Willingale, Richard
Jones, Donald J. L.
First Published: 7-Jan-2014
Publisher: American Chemical Society
Citation: Analytical Chemistry, 2014, 86 (4), pp. 1972-1979
Abstract: Discovery of protein biomarkers in clinical samples necessitates significant prefractionation prior to liquid chromatography−mass spectrometry (LC−MS) analysis. Integrating traveling wave ion mobility spectrometry (TWIMS) enables in-line gas phase separation which when coupled with nanoflow liquid chromatography and data independent acquisition tandem mass spectrometry, confers significant advantages to the discovery of protein biomarkers by improving separation and inherent sensitivity. Incorporation of TWIMS leads to a packet of concentrated ions which ultimately provides a significant improvement in sensitivity. As a consequence of ion packeting, when present at high concentrations, accurate quantitation of proteins can be affected due to detector saturation effects. Human plasma was analyzed in triplicate using liquid-chromatography data independent acquisition mass spectrometry (LC-DIA-MS) and using liquid-chromatography ion-mobility data independent acquisition mass spectrometry (LC-IM-DIA-MS). The inclusion of TWIMS was assessed for the effect on sample throughput, data integrity, confidence of protein and peptide identification, and dynamic range. The number of identified proteins is significantly increased by an average of 84% while both the precursor and product mass accuracies are maintained between the modalities. Sample dynamic range is also maintained while quantitation is achieved for all but the most abundant proteins by incorporating a novel data interpretation method that allows accurate quantitation to occur. This additional separation is all achieved within a workflow with no discernible deleterious effect on throughput. Consequently, TWIMS greatly enhances proteome coverage and can be reliably used for quantification when using an alternative product ion quantification strategy. Using TWIMS in biomarker discovery in human plasma is thus recommended.
DOI Link: 10.1021/ac403901t
ISSN: 0003-2700
eISSN: 1520-6882
Version: Publisher Version
Status: Peer-reviewed
Type: Journal Article
Rights: Copyright © the authors, 2014. This is an open-access article distributed under the terms of the Creative Commons Attribution License ( ), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Appears in Collections:Published Articles, Dept. of Cancer Studies and Molecular Medicine

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