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Danielsson, Rolf
Alternative names
Publications (10 of 15) Show all publications
Fuevesi, J., Danielsson, R., Bencsik, K., Hanrieder, J., Zsiros, V., Rajda, C., . . . Bergquist, J. (2014). Cerebrospinal fluid proteome analysis reveals differentially abundant proteins in multiple sclerosis. Paper presented at Joint ACTRIMS-ECTRIMS Meeting, SEP 10-13, 2014, Boston, MA. Multiple Sclerosis, 20, 180-181
Open this publication in new window or tab >>Cerebrospinal fluid proteome analysis reveals differentially abundant proteins in multiple sclerosis
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2014 (English)In: Multiple Sclerosis, ISSN 1352-4585, E-ISSN 1477-0970, Vol. 20, p. 180-181Article in journal (Refereed) Published
National Category
Neurology
Identifiers
urn:nbn:se:uu:diva-257372 (URN)000354441300418 ()
Conference
Joint ACTRIMS-ECTRIMS Meeting, SEP 10-13, 2014, Boston, MA
Available from: 2015-07-01 Created: 2015-07-01 Last updated: 2017-12-04Bibliographically approved
Danielsson, R., Allard, E., Sjöberg, P. & Bergquist, J. (2011). Exploring liquid chromatography-mass spectrometry fingerprints of urine samples from patients with prostate or urinary bladder cancer. Chemometrics and Intelligent Laboratory Systems, 108(1), 33-48
Open this publication in new window or tab >>Exploring liquid chromatography-mass spectrometry fingerprints of urine samples from patients with prostate or urinary bladder cancer
2011 (English)In: Chemometrics and Intelligent Laboratory Systems, ISSN 0169-7439, E-ISSN 1873-3239, Vol. 108, no 1, p. 33-48Article in journal (Refereed) Published
Abstract [en]

Data processing and analysis have become true rate and success limiting factors for molecular research where a large number of samples of high complexity are included in the data set. In general rather complicated methodologies are needed for the combination and comparison of information as obtained from selected analytical platforms. Although commercial as well as freely accessible software for high-throughput data processing are available for most platforms, tailored in-house solutions for data management and analysis can provide the versatility and transparency eligible for e.g. method development and pilot studies. This paper describes a procedure for exploring metabolic fingerprints in urine samples from prostate and bladder cancer patients with a set of in-house developed Matlab tools. In spite of the immense amount of data produced by the LC-MS platform, in this study more than 1010 data points, it is shown that the data processing tasks can be handled with reasonable computer resources. The preprocessing steps include baseline subtraction and noise reduction, followed by an initial time alignment. In the data analysis the fingerprints are treated as 2-D images, i.e. pixel by pixel, in contrast to the more common list-based approach after peak or feature detection. Although the latter approach greatly reduces the data complexity, it also involves a critical step that may obscure essential information due to undetected or misaligned peaks. The effects of remaining time shifts after the initial alignment are reduced by a binning and [‘]blurring’ procedure prior to the comparative multivariate and univariate data analyses. Other factors than cancer assignment were taken into account by ANOVA applied to the PCA scores as well as to the individual variables (pixels). It was found that the analytical day-to-day variations in our study had a large confounding effect on the cancer related differences, which emphasizes the role of proper normalization and/or experimental design. While PCA could not establish significant cancer related patterns, the pixel-wise univariate analysis could provide a list of about a hundred [‘]hotspots’ indicating possible biomarkers. This was also the limited goal for this study, with focus on the exploration of a really huge and complex data set. True biomarker identification, however, needs thorough validation and verification in separate patient sets.

Keywords
Urine profile, LC MS, Metabolic fingerprinting
National Category
Analytical Chemistry
Research subject
Analytical Chemistry
Identifiers
urn:nbn:se:uu:diva-110321 (URN)10.1016/j.chemolab.2011.03.008 (DOI)000293430300005 ()
Available from: 2009-11-10 Created: 2009-11-10 Last updated: 2017-12-12Bibliographically approved
Daszykowski, M., Danielsson, R. & Walczak, B. (2008). No-alignment-strategies for exploring a set of two-way data tables obtained from capillary electrophoresis-mass spectrometry. Journal of Chromatography A, 1192(1), 157-165
Open this publication in new window or tab >>No-alignment-strategies for exploring a set of two-way data tables obtained from capillary electrophoresis-mass spectrometry
2008 (English)In: Journal of Chromatography A, ISSN 0021-9673, E-ISSN 1873-3778, Vol. 1192, no 1, p. 157-165Article in journal (Refereed) Published
Abstract [en]

Hyphenated techniques such as capillary electrophoresis-mass spectrometry (CE-MS) or high-performance liquid chromatography with diode array detection (HPLC-DAD), etc., are known to produce a huge amount of data since each sample is characterized by a two-way data table. In this paper different ways of obtaining sample-related information from a set of such tables are discussed. Working with original data requires alignment techniques due to time shifts caused by unavoidable variations in separation conditions. Other pre-processing techniques have been suggested to facilitate comparison among samples without prior peak alignment, for example, 'binning' and/or 'blurring' the data along the time dimension. All these techniques, however, require optimization of some parameters, and in this paper an alternative parameter-free method is proposed. The individual data tables (X) are represented as Gram matrices (XXT), where the summation is taken over the time dimension. Hence the possible variations in time scale are eliminated, while the time information is at least partly preserved by the correlation structure between the detection channels. For comparison among samples, a similarity matrix is constructed and explored by principal component analysis and hierarchical clustering. The Gram matrix approach was tested and compared to some other methods using 'binned' and 'blurred' data for a data set with CE-MS runs on urine samples. In addition to data exploration by principal component analysis and hierarchical clustering, a discriminant partial least squares model was constructed to discriminate between the samples that were taken with and without the prior intake of a drug. The result showed that the proposed method is at least as good as the others with respect to cluster identification and class prediction. A distinct advantage is that there is no need for parameter optimization, while a potential drawback is the large size of the Gram matrices for data with high mass resolution.

National Category
Chemical Sciences
Identifiers
urn:nbn:se:uu:diva-16215 (URN)10.1016/j.chroma.2008.03.027 (DOI)000256200700020 ()
Available from: 2008-05-13 Created: 2008-05-13 Last updated: 2017-12-08Bibliographically approved
Vallin, Ö., Lindberg, U., Danielsson, R. & Thornell, G. (2007). Polishing of quartz by rapid etching in ammonium bifluoride. IEEE Transactions on Ultrasonics, Ferroelectrics and Frequency Control, 54(7), 1454-1462
Open this publication in new window or tab >>Polishing of quartz by rapid etching in ammonium bifluoride
2007 (English)In: IEEE Transactions on Ultrasonics, Ferroelectrics and Frequency Control, ISSN 0885-3010, E-ISSN 1525-8955, Vol. 54, no 7, p. 1454-1462Article in journal (Refereed) Published
Abstract [en]

The etch rate and surface roughness of polished and lapped AT-cut quartz subjected to hot (90, 110, and 130 degrees C), concentrated (50, 65, 80 wt %) ammonium bi-fluoride have been investigated. Having used principal component analysis to verify experimental solidity and analyze data, we claim with confidence that this parameter space does not, as elsewhere stated, allow for a polishing effect or even a preserving setting. Etch rates were found to correlate well, and possibly logarithmically, with temperature except for the hottest etching applied to lapped material. Roughness as a function of temperature and concentration behaved well for the lapped material, but lacked systematic variation in the case of the polished material. At the lowest temperature, concentration had no effect on etch rate or roughness. Future efforts are targeted at temperatures and concentrations closer to the solubility limit.

National Category
Engineering and Technology
Identifiers
urn:nbn:se:uu:diva-93222 (URN)10.1109/TUFFC.2007.406 (DOI)000247578700020 ()
Available from: 2005-05-17 Created: 2005-05-17 Last updated: 2017-12-14Bibliographically approved
Johannesson, N., Olsson, L., Bäckström, D., Wetterhall, M., Danielsson, R. & Bergquist, J. (2007). Screening for biomarkers in plasma from patients with gangrenous phlegmonous appendicitis using CE and CEC in combination with MS. Electrophoresis, 28(9), 1435-1443
Open this publication in new window or tab >>Screening for biomarkers in plasma from patients with gangrenous phlegmonous appendicitis using CE and CEC in combination with MS
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2007 (English)In: Electrophoresis, ISSN 0173-0835, E-ISSN 1522-2683, Vol. 28, no 9, p. 1435-1443Article in journal (Refereed) Published
Abstract [en]

Today a high degree of "false" appendicitis diagnoses are occurring. In this study, a screening experiment of biomarkers of two different kinds of appendicitis, gangrenous and phlegmonous, were conducted with CE and CEC coupled to MS. Plasma samples were obtained from patients pre- and post-surgery. A large amount of data was generated to be able to compare them, and chemometrics tools were utilized to visualize the differences. Indicative patterns were found for both pre- and post-surgery of the two types of inflammation as well as between them. The divergences were traced back to the MS peaks obtained in the CE- and CEC-MS setups as possible biomarkers for the two forms of appendicitis.

Keywords
Appendicitis, Biomarker, Fourier transform ion cyclotron resonance-MS, Open tubular CEC, TOF-MS
National Category
Medical and Health Sciences
Identifiers
urn:nbn:se:uu:diva-96249 (URN)10.1002/elps.200600606 (DOI)000246557400018 ()17372941 (PubMedID)
Available from: 2007-09-21 Created: 2007-09-21 Last updated: 2017-12-14Bibliographically approved
Ahlgren, J., Reitzel, K., Danielsson, R., Gogoll, A. & Rydin, E. (2006). Biogenic phosphorus in oligotropic mountain lake sediments: Differences in composition measured with NMR spectroscopy. Water Research (40), 3705-3712
Open this publication in new window or tab >>Biogenic phosphorus in oligotropic mountain lake sediments: Differences in composition measured with NMR spectroscopy
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2006 (English)In: Water Research, no 40, p. 3705-3712Article in journal (Refereed) Published
Keywords
Phosphorus species, 31P-NMR spectroscopy, Reservoirs, Oligotrophication, Method validation, 31P-NMR accuracy
National Category
Analytical Chemistry Organic Chemistry Other Earth and Related Environmental Sciences
Identifiers
urn:nbn:se:uu:diva-18049 (URN)doi:10.1016/j.watres.2006.09.006 (DOI)
Available from: 2006-11-20 Created: 2006-11-20 Last updated: 2011-01-11
Isaac, G., Fredriksson, A., Danielsson, R., Eriksson, P. & Bergquist, J. (2006). Brain lipid composition in postnatal iron-induced motor behavior alterations following chronic neuroleptic administration in mice. FEBS Journal (273), 2232-2243
Open this publication in new window or tab >>Brain lipid composition in postnatal iron-induced motor behavior alterations following chronic neuroleptic administration in mice
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2006 (English)In: FEBS Journal, no 273, p. 2232-2243Article in journal (Refereed) Published
Keywords
neuroleptics, neurodegenerative and psychiatric disorders, phosphatidylcholine, postnatal iron treatment, sphingomyelin
Identifiers
urn:nbn:se:uu:diva-80644 (URN)doi:10.1111/j.1742-4658.2006.05236.x (DOI)
Available from: 2007-01-24 Created: 2007-01-24 Last updated: 2011-01-11
Petersson, E., Rosén, J., Turner, C., Danielsson, R. & Hellenäs, K.-E. (2006). Critical factors and pitfalls affecting the extraction of acrylamide from foods: An optimisation study. Analytica Chimica Acta (557), 287-295
Open this publication in new window or tab >>Critical factors and pitfalls affecting the extraction of acrylamide from foods: An optimisation study
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2006 (English)In: Analytica Chimica Acta, no 557, p. 287-295Article in journal (Refereed) Published
Keywords
Acrylamide, Foods, Analysis, LC-MS/MS, Extraction, Optimisation, Method optimisation
Identifiers
urn:nbn:se:uu:diva-77761 (URN)doi:10.1016/j.aca.2005.10.014 (DOI)
Available from: 2006-03-15 Created: 2006-03-15 Last updated: 2011-01-11
Danielsson, R., Bäckström, D. & Ullsten, S. (2006). Rapid multivariate analysis of LC/GC/CE data (single or multiple channel detection) without prior peak alignment. Chemometrics and Intelligent Laboratory Systems, 84(1-2), 33-39
Open this publication in new window or tab >>Rapid multivariate analysis of LC/GC/CE data (single or multiple channel detection) without prior peak alignment
2006 (English)In: Chemometrics and Intelligent Laboratory Systems, ISSN 0169-7439, E-ISSN 1873-3239, Vol. 84, no 1-2, p. 33-39Article in journal (Refereed) Published
Abstract [en]

One- or two-dimensional data obtained with LC/GC/CE and single or multiple channel detection (MS, UV/VIS) are often used as 'fingerprints' in order to characterize complex samples. The relation between samples is then explored by multivariate data analysis (PCA, hierarchical clustering), but inevitable more or less random variation in separation conditions obstructs the analysis. Several methods for peak alignment have been developed, with more or less increase of time and efforts for computations. In this work another approach is presented, based on a correlation measure less sensitive for variations in retention/migration time. The merits of the method as a fast initial data exploration tool are demonstrated for a case study of urine profiling with CE/MS.

National Category
Chemical Sciences
Identifiers
urn:nbn:se:uu:diva-96250 (URN)10.1016/j.chemolab.2006.04.009 (DOI)000242768200006 ()
Available from: 2007-09-21 Created: 2007-09-21 Last updated: 2017-12-14Bibliographically approved
Bergström, S. K., Goiny, M., Danielsson, R., Ungerstedt, U., Andersson, M. & Markides, K. E. (2006). Screening of microdialysates taken before and after induced liver damage; on-line solid phase extraction-electrospray ionization-mass spectrometry. Journal of Chromatography A, 1120(1-2), 21-26
Open this publication in new window or tab >>Screening of microdialysates taken before and after induced liver damage; on-line solid phase extraction-electrospray ionization-mass spectrometry
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2006 (English)In: Journal of Chromatography A, ISSN 0021-9673, E-ISSN 1873-3778, Vol. 1120, no 1-2, p. 21-26Article in journal (Refereed) Published
Abstract [en]

A novel method is described to follow known and unknown compounds in biological processes using microdialysis sampling and mass spectrometric detection. By implementation of internal standard, desalting/enrichment for the sample work-up, and multivariate data analysis, this methodology is a basis for future applications in early diagnosis of diseases and organ damage, as a complement to the routinely used clinical methods for biological samples. The present study includes screening without specific target analytes, of samples collected by microdialysis from liver of anaesthetized rats before and after local damage to this organ. Sample series were classified by principal component analysis, and the stimulation was identified in the chemical patterns produced by the presented analytical tool.

Keywords
In vivo microdialysis, Screening, Biomarkers, On-line desalting, Mass Spectrometry, Chemometrics
National Category
Analytical Chemistry
Identifiers
urn:nbn:se:uu:diva-81344 (URN)10.1016/j.chroma.2006.01.110 (DOI)
Available from: 2006-08-17 Created: 2006-08-17 Last updated: 2017-12-14Bibliographically approved
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