Change search
CiteExportLink to record
Permanent link

Direct link
Cite
Citation style
  • apa
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf
Data analysis of non-targeted mass spectrometry experiments
Stockholm University, Faculty of Science, Department of Environmental Science and Analytical Chemistry. (Chemometrics)
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 [en]
Analytical chemistry, Chemometrics, mass spectrometry, HPLC, metabolomics
National Category
Analytical Chemistry
Research subject
Analytical Chemistry
Identifiers
URN: urn:nbn:se:su:diva-116820ISBN: 978-91-7649-175-1 (print)OAI: oai:DiVA.org:su-116820DiVA: diva2:808395
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At the time of the doctoral defense, the following paper was unpublished and had a status as follows: Paper 4: Submitted.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
List of papers
1. Discrimination between glycosylation patterns of therapeutic antibodies using a microfluidic platform, MALDI-MS and multivariate statistics
Open this publication in new window or tab >>Discrimination between glycosylation patterns of therapeutic antibodies using a microfluidic platform, MALDI-MS and multivariate statistics
2012 (English)In: Journal of Pharmaceutical and Biomedical Analysis, ISSN 0731-7085, E-ISSN 1873-264X, Vol. 70, 47-52 p.Article in journal (Refereed) Published
Abstract [en]

Optimal glycosylation with respect to the efficacy, serum half-life time, and immunogenic properties is essential in the generation of therapeutic antibodies. The glycosylation pattern can be affected by several different parameters during the manufacture of antibodies and may change significantly over cultivation time. Fast and robust methods for determination of the glycosylation patterns of therapeutic antibodies are therefore needed. We have recently presented an efficient method for the determination of glycans on therapeutic antibodies using a microfluidic CD platform for sample preparation prior to matrix-assisted laser-desorption mass spectrometry analysis. In the present work, this method is applied to analyse the glycosylation patterns of three commercially available therapeutic antibodies and one intended for therapeutic use. Two of the antibodies produced in mouse myeloma cell line (SP2/0) and one produced in Chinese hamster ovary (CHO) cells exhibited similar glycosylation patterns but could still be readily differentiated from each other using multivariate statistical methods. The two antibodies with most similar glycosylation patterns were also studied in an assessment of the method's applicability for quality control of therapeutic antibodies. The method presented in this paper is highly automated and rapid. It can therefore efficiently generate data that helps to keep a production process within the desired design space or assess that an identical product is being produced after changes to the process.

Keyword
Microfluidic CD, MALDI-TOF-MS, Recombinant antibodies, Glycosylation, Multivariate statistical analysis
National Category
Analytical Chemistry Pharmacology and Toxicology
Research subject
Analytical Chemistry
Identifiers
urn:nbn:se:su:diva-83031 (URN)10.1016/j.jpba.2012.05.020 (DOI)000309314600007 ()
Note

AuthorCount:4;

Available from: 2012-12-05 Created: 2012-12-03 Last updated: 2017-12-07Bibliographically approved
2. A concept study on non-targeted screening for chemical contaminants in food using liquid chromatography–mass spectrometry in combination with a metabolomics approach
Open this publication in new window or tab >>A concept study on non-targeted screening for chemical contaminants in food using liquid chromatography–mass spectrometry in combination with a metabolomics approach
2013 (English)In: Analytical and Bioanalytical Chemistry, ISSN 1618-2642, E-ISSN 1618-2650, Vol. 405, no 4, 1237-1243 p.Article in journal (Refereed) Published
Abstract [en]

A generic method to screen for new or unexpected contaminants at ppm levels in food has been developed. The method comprises an acidic acetonitrile extraction, detection with ultra-high-pressure liquid chromatography coupled to electrospray ionisation time-of-flight mass spectrometry and statistical evaluation using a metabolomics approach comparing suspected contaminated food with uncontaminated foods. The method was tested for 26 model contaminants from 100 μg/g down to 0.4 μg/g in three brands of fresh orange juice. Blinded statistical evaluation revealed signals from all added contaminants detectable by liquid chromatography –electrospray ionisation using positive ionisation mode, while only two false-positive signals were reported. The method is primarily intended to be used  for investigation of food samples suspected to be contaminated with unknown substances. Additionally it could be used to continuously monitor for appearance of new food contaminants as a complement to the specific targeted analysis that is today’s foundation of food safety analysis.

Keyword
Chemometrics/statistics, Foods/beverages, HPLC, Mass spectrometry/ICP-MS
National Category
Analytical Chemistry
Research subject
Analytical Chemistry
Identifiers
urn:nbn:se:su:diva-83995 (URN)10.1007/s00216-012-6506-5 (DOI)000313735000010 ()
Available from: 2012-12-17 Created: 2012-12-17 Last updated: 2017-12-06Bibliographically approved
3. TracMass 2-A Modular Suite of Tools for Processing Chromatography-Full Scan Mass Spectrometry Data
Open this publication in new window or tab >>TracMass 2-A Modular Suite of Tools for Processing Chromatography-Full Scan Mass Spectrometry Data
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.

National Category
Analytical Chemistry
Research subject
Analytical Chemistry
Identifiers
urn:nbn:se:su:diva-103973 (URN)10.1021/ac403905h (DOI)000333776600027 ()
Note

AuthorCount:3;

Available from: 2014-06-05 Created: 2014-05-27 Last updated: 2017-12-05Bibliographically approved
4. Exploiting the sample dimension to resolve ambiguities in chromatographic peak alignment
Open this publication in new window or tab >>Exploiting the sample dimension to resolve ambiguities in chromatographic peak alignment
(English)In: Journal of Chemometrics, ISSN 0886-9383, E-ISSN 1099-128XArticle in journal (Refereed) Submitted
National Category
Analytical Chemistry
Research subject
Analytical Chemistry
Identifiers
urn:nbn:se:su:diva-116818 (URN)
Available from: 2015-04-28 Created: 2015-04-28 Last updated: 2017-12-04Bibliographically approved

Open Access in DiVA

fulltext(1820 kB)117 downloads
File information
File name FULLTEXT01.pdfFile size 1820 kBChecksum SHA-512
f289e65cb99a8dbc90117b11fb710b83d827b624225602118dd099c2639df2a9facdd27152d365bdef2294e8a55823d0504aa19c8ba57ceb505090c369e8091d
Type fulltextMimetype application/pdf

Search in DiVA

By author/editor
Tengstrand, Erik
By organisation
Department of Environmental Science and Analytical Chemistry
Analytical Chemistry

Search outside of DiVA

GoogleGoogle Scholar
Total: 117 downloads
The number of downloads is the sum of all downloads of full texts. It may include eg previous versions that are now no longer available

isbn
urn-nbn

Altmetric score

isbn
urn-nbn
Total: 922 hits
CiteExportLink to record
Permanent link

Direct link
Cite
Citation style
  • apa
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf