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TracMass 2-A Modular Suite of Tools for Processing Chromatography-Full Scan Mass Spectrometry Data
Stockholm University, Faculty of Science, Department of Analytical Chemistry.
Stockholm University, Faculty of Science, Department of Analytical Chemistry.
2014 (English)In: Analytical Chemistry, ISSN 0003-2700, E-ISSN 1520-6882, Vol. 86, no 7, 3435-3442 p.Article in journal (Refereed) Published
Abstract [en]

In untargeted proteomics and metabolomics, raw data obtained with an LC/MS instrument are processed into a format that can be used for statistical analysis. Full scan MS data from chromatographic separation of biological samples are complex and analyte concentrations need to be extracted and aligned so that they can be compared across the samples. Several computer programs and methods have been developed for this purpose. There is still a need to improve the ease of use and feedback to the user because of the advanced multi-parametric algorithms used. Here, we present and make publicly available, TracMass 2, a suite of computer programs that gives immediate graphical feedback to the data analyst on parameter settings and processing results, as well as producing state-of-the-art results. The main advantage of TracMass 2 is that the feedback and transparency of the processing steps generate confidence in the end result, which is a table of peak intensities. The data analyst can easily validate every step of the processing pipeline. Because the user receives feedback on how all parameter values affect the result before starting a lengthy computation, the user's learning curve is enhanced and the total time used for data processing can be reduced. TracMass 2 has been released as open source and is included in the Supporting Information. We anticipate that TracMass 2 will set a new standard for how chemometrical algorithms are implemented in computer programs.

Place, publisher, year, edition, pages
2014. Vol. 86, no 7, 3435-3442 p.
National Category
Analytical Chemistry
Research subject
Analytical Chemistry
Identifiers
URN: urn:nbn:se:su:diva-103973DOI: 10.1021/ac403905hISI: 000333776600027OAI: oai:DiVA.org:su-103973DiVA: diva2:721818
Note

AuthorCount:3;

Available from: 2014-06-05 Created: 2014-05-27 Last updated: 2017-12-05Bibliographically approved
In thesis
1. Data analysis of non-targeted mass spectrometry experiments
Open this publication in new window or tab >>Data analysis of non-targeted mass spectrometry experiments
2015 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Data processing tools are valuable to the analytical chemist as they can speed up the analysis, and sometimes solve problems that are not feasible to solve in a traditional manner. However, the complexity of many data processing tools can make their use daunting for the inexperienced user.

This thesis includes two applications and two tools for data processing. The first application focuses on minimizing the manual input, reducing the time required for a simple task. The second application required more manual input, in the form of parameter selection, but process far more data.  The data processing tools both include features that simplify the manual work required. The first by including visual diagnostics tools that helps in setting the parameters. The second via internal validation that makes the tool’s process more robust and reliable, and thereby less sensitive to small changes in the parameters.

No matter how good or precise a data processing tool is, if it is so cumbersome that it is not used by the analytical chemists that need it, it is useless. Therefore, the main focus of this thesis is to make data processing easier.

Place, publisher, year, edition, pages
Stockholm: Department of Environmental Science and Analytical Chemistry, Stockholm University, 2015
Keyword
Analytical chemistry, Chemometrics, mass spectrometry, HPLC, metabolomics
National Category
Analytical Chemistry
Research subject
Analytical Chemistry
Identifiers
urn:nbn:se:su:diva-116820 (URN)978-91-7649-175-1 (ISBN)
Public defence
2015-06-08, Magnelisalen, Kemiska övningslaboratoriet, Svante Arrhenius väg 16 B, Stockholm, 10:00 (English)
Opponent
Supervisors
Note

At the time of the doctoral defense, the following paper was unpublished and had a status as follows: Paper 4: Submitted.

Available from: 2015-05-15 Created: 2015-04-28 Last updated: 2015-05-25Bibliographically approved

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