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Wetterhall, Magnus
Publications (10 of 38) Show all publications
Sjödin, M. O. .., Wetterhall, M., Kultima, K. & Artemenko, K. (2013). Comparative study of label and label-free techniques using shotgun proteomics for relative protein quantification. Journal of chromatography. B, 928, 83-92.
Open this publication in new window or tab >>Comparative study of label and label-free techniques using shotgun proteomics for relative protein quantification
2013 (English)In: Journal of chromatography. B, ISSN 1570-0232, E-ISSN 1873-376X, Vol. 928, 83-92 p.Article in journal (Refereed) Published
Abstract [en]

The analytical performance of three different strategies, iTRAQ (isobaric tag for relative and absolute quantitation), dimethyl labeling (DML) and label free (LF) for relative protein quantification using shotgun proteomics have been evaluated. The methods have been explored using samples containing (i) Bovine proteins in known ratios and (ii) Bovine proteins in known ratios spiked into E.Coli. The latter case mimics the actual conditions in a typical biological sample with a few differentially expressed proteins and a bulk of proteins with unchanged ratios. Additionally, the evaluation was performed on both Q-TOF and LTQ-FTICR mass spectrometers. LF LTQ-FTICR was found to have the highest proteome coverage (94 %) while the highest accuracy based on the artificially regulated proteins was found for DML LTQ-FTICR (54%). A good linearity (r2: 0.61-0.96) was shown for all methods within selected dynamic ranges. All methods were found to consistently underestimate bovine protein ratios when matrix proteins were added. However LF LTQ-FTICR was more tolerant towards a compression effect.  A single peptide was demonstrated to be sufficient for a reliable quantification using iTRAQ. A ranking system utilizing several parameters important for quantitative proteomics demonstrated that the overall performance of the five different methods were; DML LTQ-FTICR > iTRAQ QTOF > LF LTQ-FTICR > DML Q-TOF > LF Q-TOF.

Keyword
Relative quantification, Proteomics, Mass spectrometry, Stable isotope labeling, Label free
National Category
Analytical Chemistry
Research subject
Analytical Chemistry
Identifiers
urn:nbn:se:uu:diva-180105 (URN)10.1016/j.jchromb.2013.03.027 (DOI)000319236700011 ()
Note

De två (2) sista författarna delar sistaförfattarskapet.

Available from: 2012-08-29 Created: 2012-08-29 Last updated: 2017-12-07Bibliographically approved
Loov, C., Shevchenko, G., Nadadhur, A. G., Clausen, F., Hillered, L., Wetterhall, M. & Erlandsson, A. (2013). Identification of Injury Specific Proteins in a Cell Culture Model of Traumatic Brain Injury. PLoS ONE, 8(2), e55983.
Open this publication in new window or tab >>Identification of Injury Specific Proteins in a Cell Culture Model of Traumatic Brain Injury
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2013 (English)In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 8, no 2, e55983- p.Article in journal (Refereed) Published
Abstract [en]

The complicated secondary molecular and cellular mechanisms following traumatic brain injury (TBI) are still not fully understood. In the present study, we have used mass spectrometry to identify injury specific proteins in an in vitro model of TBI. A standardized injury was induced by scalpel cuts through a mixed cell culture of astrocytes, oligodendrocytes and neurons. Twenty-four hours after the injury, cell culture medium and whole-cell fractions were collected for analysis. We found 53 medium proteins and 46 cell fraction proteins that were specifically expressed after injury and the known function of these proteins was elucidated by an extensive literature survey. By using time-lapse microscopy and immunostainings we could link a large proportion of the proteins to specific cellular processes that occur in response to trauma; including cell death, proliferation, lamellipodia formation, axonal regeneration, actin remodeling, migration and inflammation. A high percentage of the proteins uniquely expressed in the medium after injury were actin-related proteins, which normally are situated intracellularly. We show that two of these, ezrin and moesin, are expressed by astrocytes both in the cell culture model and in mouse brain subjected to experimental TBI. Interestingly, we found many inflammation-related proteins, despite the fact that cells were present in the culture. This study contributes with important knowledge about the cellular responses after trauma and identifies several potential cell-specific biomarkers.

National Category
Medical and Health Sciences
Identifiers
urn:nbn:se:uu:diva-197400 (URN)10.1371/journal.pone.0055983 (DOI)000315157200097 ()
Available from: 2013-04-01 Created: 2013-03-25 Last updated: 2017-12-06Bibliographically approved
Shevchenko, G., Musunuri, S., Wetterhall, M. & Bergquist, J. (2012). Comparison of Extraction Methods for the Comprehensive Analysis of Mouse Brain Proteome using Shotgun-based Mass Spectrometry. Journal of Proteome Research, 11(4), 2441-2451.
Open this publication in new window or tab >>Comparison of Extraction Methods for the Comprehensive Analysis of Mouse Brain Proteome using Shotgun-based Mass Spectrometry
2012 (English)In: Journal of Proteome Research, ISSN 1535-3893, E-ISSN 1535-3907, Vol. 11, no 4, 2441-2451 p.Article in journal (Refereed) Published
Abstract [en]

This study compares 16 different extraction methods for the comprehensive extraction of mouse brain proteome in combination with "shotgun"-based mass spectrometry (MS). Membrane proteins (MPs) are responsible for a large part of the regulatory functions of the cell and are therefore of great interest to extract and analyze. Sixteen protein extraction protocols were evaluated in regards to protein yield and number of identified proteins with emphasis on MPs. The extracted proteins were delipidated, on-filter digested, and analyzed by reversed phase nanoliquid chromatography (RP-nanoLC) in combination with electrospray ionization (ESI) tandem mass spectrometry (MS/MS) using a 7 T hybrid LTQ: FT mass spectrometer. Detergent-based lysis buffers showed higher efficiencies and yields in the extraction of proteins from the brain tissue compared to solubilization with organic solvents or organic acids. The detergent octyl-beta-D-glucopyranoside gave the highest number of identified proteins (541) as well as numbers and percentages of identified MPs (29%). Detergent-based protocols are the best sample preparation tools for central nervous system (CNS) tissue and can readily be applied to screen for candidate biomarkers of neurological diseases.

Keyword
brain, proteomics, membrane proteins (MPs), transmembrane proteins (TMPs), mass spectrometry (MS), sample preparation, extraction
National Category
Analytical Chemistry
Identifiers
urn:nbn:se:uu:diva-173655 (URN)10.1021/pr201169q (DOI)000302388100034 ()
Available from: 2012-05-02 Created: 2012-05-02 Last updated: 2017-12-07Bibliographically approved
Undin, T., Bergquist, J., Dahlin, A. P. & Wetterhall, M. (2012). Competitive Protein Adsorption as Observed and Quantified by - Surface Enzymatic Digestion (oSED) and Mass Spectrometry. In: 60th ASMS Conference on Mass Spectrometry and Allied Topics, May 20 - 24, Vancouver, Canada. Paper presented at 60th ASMS Conference on Mass Spectrometry and Allied Topics, May 20 - 24, Vancouver, Canada. .
Open this publication in new window or tab >>Competitive Protein Adsorption as Observed and Quantified by - Surface Enzymatic Digestion (oSED) and Mass Spectrometry
2012 (English)In: 60th ASMS Conference on Mass Spectrometry and Allied Topics, May 20 - 24, Vancouver, Canada, 2012Conference paper, Published paper (Refereed)
National Category
Analytical Chemistry Engineering and Technology
Research subject
Engineering Science with specialization in Microsystems Technology
Identifiers
urn:nbn:se:uu:diva-188861 (URN)
Conference
60th ASMS Conference on Mass Spectrometry and Allied Topics, May 20 - 24, Vancouver, Canada
Available from: 2012-12-20 Created: 2012-12-20 Last updated: 2013-03-04Bibliographically approved
Lööv, C., Shevchenko, G., Hillered, L., Wetterhall, M. & Erlandsson, A. (2012). Identification of unique proteins after injury in a cell culture model of TBI. Paper presented at The International Brain Injury Association's Ninth World Congress on Brain Injury. March 21-25 in Edinburgh, Scotland.. Brain Injury, 26(4-5), 487-488.
Open this publication in new window or tab >>Identification of unique proteins after injury in a cell culture model of TBI
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2012 (English)In: Brain Injury, ISSN 0269-9052, E-ISSN 1362-301X, Vol. 26, no 4-5, 487-488 p.Article in journal, Meeting abstract (Other academic) Published
National Category
Medical and Health Sciences
Identifiers
urn:nbn:se:uu:diva-175974 (URN)10.3109/02699052.2012.660091 (DOI)000304104600325 ()
Conference
The International Brain Injury Association's Ninth World Congress on Brain Injury. March 21-25 in Edinburgh, Scotland.
Available from: 2012-06-15 Created: 2012-06-14 Last updated: 2017-12-07Bibliographically approved
Shevchenko, G., Wetterhall, M., Bergquist, J., Höglund, K., Andersson, L. I. & Kultima, K. (2012). Longitudinal characterization of the brain proteomes for the tg2576 amyloid mouse model using shotgun based mass spectrometry. Journal of Proteome Research, 11(12), 6159-74.
Open this publication in new window or tab >>Longitudinal characterization of the brain proteomes for the tg2576 amyloid mouse model using shotgun based mass spectrometry
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2012 (English)In: Journal of Proteome Research, ISSN 1535-3893, E-ISSN 1535-3907, Vol. 11, no 12, 6159-74 p.Article in journal (Refereed) Published
Abstract [en]

Neurodegenerative disorders are often defined pathologically by the presence of protein aggregates, such as amyloid plaques composed of β-amyloid (Aβ) peptide in Alzheimer's disease. Such aggregates are the result of abnormal protein accumulation and may lead to neuronal dysfunction and cell death. In this study, APPSWE transgenic mice (Tg2576), which overexpress the Swedish mutated form of human amyloid precursor protein (APP), were used to study the brain proteome associated with amyloid plaque deposition. The major aim of the study was to map and compare the Tg2576 model brain proteome profiles during pathology progression using a shotgun approach based on label free quantification with mass spectrometry. Overall, 1085 proteins were identified and longitudinally quantified. Principal component analysis (PCA) showed the appearance of the pathology onset between twelve and fifteen months, correlating with sharp amyloid plaque accumulation within the same ages. Cluster analysis followed by protein-protein interaction analysis revealed an age-dependent decrease in mitochondrial protein expression. We identified 57 significantly affected mitochondrial proteins, several of which have been reported to alter expression in neurological diseases. We also found ten proteins that are upregulated early in the amyloid driven pathology progression with high confidence, some of which are directly involved in the onset of mitochondrial apoptosis and may represent potential markers for use in human neurological diseases prognosis. Our results further contribute to identifying common pathological pathways involved in both aging and progressive neurodegenerative disorders enhancing the understanding of disease pathogenesis.

National Category
Neurosciences
Identifiers
urn:nbn:se:uu:diva-190916 (URN)10.1021/pr300808h (DOI)000311925900051 ()23050487 (PubMedID)
Available from: 2013-01-09 Created: 2013-01-09 Last updated: 2018-01-11Bibliographically approved
Wetterhall, M., Sjödin, M. O., Bergquist, J., Hillered, L., Hjort, K. & Dahlin, A. P. (2012). Mapping the protein distribution within a microdialysis sampling system by on-surface enzymatic digestion in combination with mass spectrometry. In: Monitoring Molecules in Neuroscience: 14th International Conference, September 16 – 20, London, U.K.. Paper presented at Monitoring Molecules in Neuroscience: 14th International Conference, September 16 – 20, London, U.K.. .
Open this publication in new window or tab >>Mapping the protein distribution within a microdialysis sampling system by on-surface enzymatic digestion in combination with mass spectrometry
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2012 (English)In: Monitoring Molecules in Neuroscience: 14th International Conference, September 16 – 20, London, U.K., 2012Conference paper, Published paper (Refereed)
National Category
Analytical Chemistry Engineering and Technology
Research subject
Engineering Science with specialization in Microsystems Technology
Identifiers
urn:nbn:se:uu:diva-188862 (URN)
Conference
Monitoring Molecules in Neuroscience: 14th International Conference, September 16 – 20, London, U.K.
Available from: 2012-12-20 Created: 2012-12-20 Last updated: 2013-02-08Bibliographically approved
Dahlin, A. P., Hjort, K., Hillered, L., Sjödin, M. O. .., Bergquist, J. & Wetterhall, M. (2012). Multiplexed quantification of proteins adsorbed to surface-modified and non-modified microdialysis membranes. Analytical and Bioanalytical Chemistry, 402(6), 2057-2067.
Open this publication in new window or tab >>Multiplexed quantification of proteins adsorbed to surface-modified and non-modified microdialysis membranes
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2012 (English)In: Analytical and Bioanalytical Chemistry, ISSN 1618-2642, E-ISSN 1618-2650, Vol. 402, no 6, 2057-2067 p.Article in journal (Refereed) Published
Abstract [en]

A simple and straightforward method for discovery and quantification of proteins adsorbed onto delicate and sensitive membrane surfaces is presented. The adsorbed proteins were enzymatically cleaved while still adsorbed onto the membranes using an on-surface enzymatic digestion (oSED). This was followed by isobaric tagging, nanoliquid chromatography, and tandem mass spectrometry. Protein adsorption on tri-block copolymer Poloxamer 407 surface-modified microdialysis (MD) membranes were compared with protein adsorption on unmodified MD membranes. Ventricular cerebrospinal fluid (vCSF) kept at 37 °C was used as sample matrix. In total, 19 proteins were quantified in two biological replicates. The surface-modified membranes adsorbed 33% less proteins than control membranes and the most abundant proteins were subunits of hemoglobin and clusterin. The adsorption of clusterin on the modified membranes was on average 36% compared to control membranes. The most common protein in vCSF, Albumin, was not identified adsorbed to the surface at all. It was also experimentally verified that oSED, in conjunction with tandem mass spectrometry can be used to quantify femtomole amounts of proteins adsorbed on limited and delicate surfaces, such as MD membranes. The method has great potential and can be used to study much more complex protein adsorption systems than previously reported.

National Category
Chemical Sciences Medical and Health Sciences Engineering and Technology
Research subject
Engineering Science with specialization in Microsystems Technology
Identifiers
urn:nbn:se:uu:diva-166977 (URN)10.1007/s00216-011-5614-y (DOI)000300308400008 ()
Available from: 2012-01-18 Created: 2012-01-18 Last updated: 2017-12-08Bibliographically approved
Taube, A. B., Hardenborg, E., Wetterhall, M., Artemenko, K., Hanrieder, J., Andersson, M., . . . Bergquist, J. (2012). Proteins in aqueous humor from cataract patients with and without pseudoexfoliation syndrome. European journal of mass spectrometry, 18(6), 531-541.
Open this publication in new window or tab >>Proteins in aqueous humor from cataract patients with and without pseudoexfoliation syndrome
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2012 (English)In: European journal of mass spectrometry, ISSN 1469-0667, E-ISSN 1751-6838, Vol. 18, no 6, 531-541 p.Article in journal (Refereed) Published
Abstract [en]

The aim of this study was to investigate the protein content in aqueous humor in eyes with and without pseudoexfoliations (PEX) and to evaluate the quantitative proteomics method, isobaric tagging for relative and absolute protein quantification (iTRAQ), in combination with two separation methods followed by matrix-assisted Laser desorption/ionization (MALDI) mass spectrometry and tandem mass spectrometry (MS/MS). During cataract surgery, samples of aqueous humor were collected from 20 eyes with PEX and from 18 control eyes. The relative concentrations of proteins in the pooled samples of ten PEX eyes and eight controls were evaluated after trypsin digestion and labeling of the peptides with (iTRAQ) reagent. Two separation methods, Liquid chromatography (LC) and capillary electrophoresis (CE) were used, followed by MALDI mass spectrometry and MS/MS. Furthermore, 1D gel electrophoresis was performed on the remaining ten pooled PEX samples and ten control samples. The gel material was separated by nano-liquid chromatography (nano-LC) followed by Linear-ion-trap quadrupole Fourier transformation ion cyclotron resonance (FT-ICR). Fifty four proteins were identified in the LC runs and 24 with CE. The relative concentrations of beta-crystallines B2 and S were raised and those of angiotensinogen and osteopontin lowered in the PEX sample compared to the control. The trends regarding beta-crystallines B2, angiotensinogen and osteopontin were confirmed by the 1D gel electrophoresis.

Keyword
pseudoexfoliations (PEX), isobaric tagging, protein quantification, proteomics, aqueous humour, osteopontin, angiotensinogen
National Category
Medical and Health Sciences
Identifiers
urn:nbn:se:uu:diva-197670 (URN)10.1255/ejms.1208 (DOI)000315745600007 ()
Available from: 2013-04-02 Created: 2013-04-02 Last updated: 2017-12-06Bibliographically approved
Dahlin, A. P., Hjort, K., Hillered, L., Sjödin, M. O., Bergquist, J. & Wetterhall, M. (2012). Quantification of Proteins Adsorbed to Surface Modified and Non-Modified Microdialysis Membranes using on-Surface Enzymatic Digestion (oSED) iTRAQ-MALDI-TOF/TOF MS. In: 60th ASMS Conference on Mass Spectrometry and Allied Topics, May 20 - 24, Vancouver, Canada: . Paper presented at 60th ASMS Conference on Mass Spectrometry and Allied Topics, May 20 - 24, Vancouver, Canada. .
Open this publication in new window or tab >>Quantification of Proteins Adsorbed to Surface Modified and Non-Modified Microdialysis Membranes using on-Surface Enzymatic Digestion (oSED) iTRAQ-MALDI-TOF/TOF MS
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2012 (English)In: 60th ASMS Conference on Mass Spectrometry and Allied Topics, May 20 - 24, Vancouver, Canada, 2012Conference paper, Published paper (Refereed)
National Category
Analytical Chemistry Engineering and Technology
Research subject
Engineering Science with specialization in Microsystems Technology
Identifiers
urn:nbn:se:uu:diva-188854 (URN)
Conference
60th ASMS Conference on Mass Spectrometry and Allied Topics, May 20 - 24, Vancouver, Canada
Available from: 2012-12-20 Created: 2012-12-20 Last updated: 2014-01-09
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