Article
Reference
Dedicated Software Enhancing Data-independent Acquisition Methods in Mass Spectrometry
BILBAO PENA, Aivett, LISACEK, Frédérique, HOPFGARTNER, Gerard
BILBAO PENA, Aivett, LISACEK, Frédérique, HOPFGARTNER, Gerard. Dedicated Software Enhancing Data-independent Acquisition Methods in Mass Spectrometry. Chimia , 2016, vol. 70, no. 4, p. 293-293
DOI : 10.2533/chimia.2016.293
Available at:
http://archive-ouverte.unige.ch/unige:143297
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Columns CHIMIA2016,70, No. 4 293
doi:10.2533/chimia.2016.293
Highlights of Analytical Sciences in Switzerland
Division of Analytical Sciences
A Division of the Swiss Chemical Society Dedicated Software Enhancing Data-independent Acquisition Methods in Mass Spectrometry Aivett Bilbaoab, Frédérique Lisacek*bc,
and Gérard Hopfgartner*a
*Correspondence:Prof. Dr. G. Hopfgartnera, E-mail: Gerard.Hopfgartner@unige.
ch; Dr. F. Lisacekb, E-mail: Frederique.Lisacek@isb-sib.ch;aLife Sciences Mass Spectrometry, Department of Inorganic and Analytical Chemistry, University of Geneva, 30, quai Ernest-Ansermet, CH-1211 Geneva 4;bProteome Informatics Group, SIB Swiss Institute of Bioinformatics, CMU, rue Michel Servet, CH-1211 Geneva;cComputer Science Department, University of Geneva, Geneva
Keywords:Data-independent acquisition · Interference removal
· Metabolomics · Proteomics · SWATH · Variable-precursor- isolation-window widths
Mass spectrometry combined with liquid chromatography has become the main analytical platform to characterize proteins and low-molecular-weight compounds in complex samples. In proteomics and metabolomics, samples are commonly analyzed by data-dependent acquisition (DDA) methods. However, the intensity-based semi-stochastic selection of precursor ions favors highly abundant analytes while under-sampling the low- abundance ones. In contrast to this sequential detection, selection, and analysis of individual ions, alternative data-independent acquisition (DIA) methods systematically parallelize the fragmentation of all detectable ions within a wide mass range regardless of their intensity. The mass spectra recorded by DIA are a continuous map of multiplexed fragment chromatographic profiles of all detectable analytes. Therefore, DIA integrates qualitative and quantitative information, providing broader dynamic range of detected signals, improved reproducibility for identification, and better sensitivity and accuracy for quantification.
Despite these advantages, the concurrent fragmentation of analytes has the drawback of increasing the likelihood of interference due to the overlap of fragment ions from different
precursors. We
developed two solutions to tackle this issue and further expand the benefits of DIA.
The first solution comprises a program called SwathTUNER, implemented to design and optimize different DIA methods using stepwise isolation windows (e.g. SWATH).
The benefits of utilizing acquisition methods with variable-precursor-
isolation-window widths were demonstrated for the profiling of proteomic and metabolic samples.
The second solution is the ‘non-outlier fragment ion’ (NOFI) ranking algorithm. NOFI assigns low priority to fragment ions affected by interference during DIA acquisition. The optimal subset of high-priority fragment ions defined by NOFI effectively excludes interfered fragment ions from quantification.
Improvement for label-free quantification was illustrated on a well-defined quantitative dataset and on a biologically relevant cell digest.
DIA methods coupled with adequate software solutions deliver comprehensive information in a single-shot analysis to study the full range of small to large molecules and unravel biological processes.
References
A. Bilbao, E. Varesio, J. Luban, C. Strambio-De-Castillia, G. Hopfgartner, M. Müller, F. Lisacek, Proteomics 2015, 15, 964.
Y. Zhang, A. Bilbao, T. Bruderer, J. Luban, C. Strambio-De-Castillia, F. Lisacek, G. Hopfgartner, E. Varesio, J. Proteome Res. 2015, 14, 4359.
A. Bilbao, Y. Zhang, E. Varesio, J. Luban, C. Strambio-De-Castillia, F. Lisacek, G. Hopfgartner, J. Proteome Res. 2015, 14, 4581.
Can you show us your analytical highlight?
Please contact: Dr. Veronika R. Meyer, Unterstrasse 58, CH-9000 St.Gallen Tel.: +41 71 222 16 81, E-mail: VRMeyer@bluewin.ch
Analogy for cross fragment ion interference. Several waves causing interference to each other. Photo:
quapan (https://www.flickr.com/photos/
hinkelstone/7001475448), sepia recolor.
Intensity
Time Precursor
m/zrange
3) Precursor ion isolation (windows per cycle)
4) Fragmentation
5) Fragment ion detection (MS2)
2) Precursor ion detection (MS1) MS1 scan optional for some methods
Stepwise windows (fixed or variable widths) XDIA, PaCIFIC, FT-ARM,SWATH
Pr
1 Pr
Pris (windo
2 Pr
Fragm
3 Fr
detect5) FrFr
4dete
0 300 600 900
500 750 1000 1250
Numberofprecursorions m/z
0 100 200 300 400
500 750 1000 1250
350 1250
Numberofprecursorions m/z
Total ion current chromatogram
MULTIPLEXED FRAGMENT-ION SPECTRA
MULTIPLEXED FRAGMENT-ION MAP (first window) MUFRAG (firs
Intensity
Time Total ion current
chromatogram (MS2)
Data-independent acquisition using stepwise isolation windows. Green boxes show examples of the frequency distribution of all detected precursor ions in a run for methods using fixed or variable widths optimized with SwathTUNER.
