uu.seUppsala University Publications
Change search
Link to record
Permanent link

Direct link
BETA
Alternative names
Publications (10 of 392) Show all publications
Ubhayasekera, K., Acharya, S. R. & Bergquist, J. (2018). A novel, fast and sensitive supercritical fluid chromatography-tandem mass spectrometry (SFC-MS/MS) method for analysis of arachidonic acid metabolites. The Analyst, 143(15), 3661-3669
Open this publication in new window or tab >>A novel, fast and sensitive supercritical fluid chromatography-tandem mass spectrometry (SFC-MS/MS) method for analysis of arachidonic acid metabolites
2018 (English)In: The Analyst, ISSN 0003-2654, E-ISSN 1364-5528, Vol. 143, no 15, p. 3661-3669Article in journal (Refereed) Published
Abstract [en]

The development of a rapid, sensitive and reliable method for the quantification of bioactive arachidonic acid metabolites (AA-metabolites) in biological samples is quite challenging due to the minute concentration, short half-life and their structural complexity arising from different isomers. In this study, a simple, fast and environmentally friendly supercritical fluid chromatography-tandem mass spectrometry (SFC-MS/MS) method was developed and validated for simultaneous measurement of five (PGD(2), PGE(2), PGF(2), 6KetoPGF(1) and LTB4) AA-metabolites in biological samples. These analytes were extracted by protein precipitation followed by separation and quantification. The analysis was completed within 3 minutes. The matrix matched linear calibration ranged from 0.5-100 ng mL(-1) (r(2) 0.995), whilst, the limit of quantification of PGD(2), PGE(2), PGF(2), and LTB4 was 0.5 ng mL(-1) and was 2.5 ng mL(-1) for 6KetoPGF(1). The interday and intraday precisions of the method were less than 15% while the accuracy of most of the analytes varied between 83 and 109%. Finally, as a proof of concept, the method was successfully applied for the determination of eicosanoids in human samples, which expands the possibility to explore physiological states, disease phenotypes, and novel biomarkers.

Place, publisher, year, edition, pages
ROYAL SOC CHEMISTRY, 2018
National Category
Analytical Chemistry
Identifiers
urn:nbn:se:uu:diva-361490 (URN)10.1039/c8an00788h (DOI)000439586400019 ()29971278 (PubMedID)
Funder
Swedish Research Council, 2015-4870
Available from: 2018-09-27 Created: 2018-09-27 Last updated: 2018-09-27Bibliographically approved
Bergquist, J. & Turner, C. (2018). Analytical chemistry for a sustainable society - trends and implications. Analytical and Bioanalytical Chemistry, 410(14), 3235-3237
Open this publication in new window or tab >>Analytical chemistry for a sustainable society - trends and implications
2018 (English)In: Analytical and Bioanalytical Chemistry, ISSN 1618-2642, E-ISSN 1618-2650, Vol. 410, no 14, p. 3235-3237Article in journal, Editorial material (Other academic) Published
National Category
Analytical Chemistry
Identifiers
urn:nbn:se:uu:diva-357652 (URN)10.1007/s00216-018-1036-4 (DOI)000431401000004 ()29663055 (PubMedID)
Available from: 2018-08-28 Created: 2018-08-28 Last updated: 2018-08-28Bibliographically approved
Neupane, R., Källsten, M., Lehmann, F. & Bergquist, J. (2018). Effect of mobile phase composition on the analysis of aggregates of antibody drug conjugates (ADCs) using size exclusion chromatography. Analytical Methods, 10(9), 938-941
Open this publication in new window or tab >>Effect of mobile phase composition on the analysis of aggregates of antibody drug conjugates (ADCs) using size exclusion chromatography
2018 (English)In: Analytical Methods, ISSN 1759-9660, E-ISSN 1759-9679, Vol. 10, no 9, p. 938-941Article in journal (Refereed) Published
Abstract [en]

In this study, the effect of mobile phase composition for size exclusion chromatography (SEC) on antibody drug conjugate (ADC) aggregate analysis was investigated. The use of organic components as well as high ionic strength during aggregate analysis was demonstrated to be advantageous.

Place, publisher, year, edition, pages
ROYAL SOC CHEMISTRY, 2018
National Category
Analytical Chemistry
Identifiers
urn:nbn:se:uu:diva-350281 (URN)10.1039/c7ay02696j (DOI)000426696100001 ()
Funder
Swedish Research Council, SRC 2015-4870Swedish Foundation for Strategic Research , ID14-0081
Available from: 2018-05-09 Created: 2018-05-09 Last updated: 2018-05-09Bibliographically approved
Undin, T., Dahlin, A. P., Bergquist, J. & Bergström Lind, S. (2018). Mass Spectrometric Determination of the Effect of Surface Deactivation on Membranes Used for In-Situ Sampling of Cerebrospinal Fluid (CSF). Separations, 5(2), Article ID 27.
Open this publication in new window or tab >>Mass Spectrometric Determination of the Effect of Surface Deactivation on Membranes Used for In-Situ Sampling of Cerebrospinal Fluid (CSF)
2018 (English)In: Separations, ISSN 2297-8739, Vol. 5, no 2, article id 27Article in journal (Refereed) Published
Abstract [en]

In this paper, a strategy for structured monitoring of surface modifications to control protein adsorption to membrane structures is presented. The already established on-surface enzymatic digestion (oSED) method combined with nano-liquid chromatography and tandem mass spectrometry (LC-MS/MS) analysis was employed for the analysis of proteins in ventricular cerebrospinal fluid (vCSF) from neurointensive care patients. Protein adsorption was studied by in-situ sampling in a temporally resolved manner on both immobilized native and Pluronic-deactivated membranes. Deactivation was significantly reducing the protein adsorption but it also induced novel selective properties of the surface. The proposed versatile strategy will facilitate protein-biomaterial, protein-polymer, protein-protein interaction studies in the future.

Keywords
Protein Adsorption, Mass Spectrometry, oSED, Surface modification, Coating, Poloxamer 407, Pluronic F127, Trypsin, Digestion, Shotgun, Bottom-up, peptides
National Category
Analytical Chemistry Engineering and Technology
Research subject
Chemistry with specialization in Analytical Chemistry; Chemistry with specialization in Surface Biotechnology
Identifiers
urn:nbn:se:uu:diva-248631 (URN)10.3390/separations5020027 (DOI)000436515600007 ()
Funder
Magnus Bergvall Foundation, 2015-01200Åke Wiberg Foundation, M14-0127Swedish Research Council, 2015-4870Magnus Bergvall Foundation, 2016-01675Carl Tryggers foundation , CST 15:57Berzelii Centre EXSELENT
Available from: 2015-04-05 Created: 2015-04-05 Last updated: 2018-10-12Bibliographically approved
Patriarca, C., Bergquist, J., Sjöberg, P. J., Tranvik, L. & Hawkes, J. A. (2018). Online HPLC-ESI-HRMS Method for the Analysis and Comparison of Different Dissolved Organic Matter Samples. Environmental Science and Technology, 52(4), 2091-2099
Open this publication in new window or tab >>Online HPLC-ESI-HRMS Method for the Analysis and Comparison of Different Dissolved Organic Matter Samples
Show others...
2018 (English)In: Environmental Science and Technology, ISSN 0013-936X, E-ISSN 1520-5851, Vol. 52, no 4, p. 2091-2099Article in journal (Refereed) Published
Abstract [en]

Natural dissolved organic matter (DOM) is an ultracomplex mixture that is essential to global carbon cycling but is poorly understood because of its complexity. The most powerful tool for the DOM characterization is high-resolution mass spectrometry (HRMS) generally combined to direct infusion (DI) as sample introduction. Liquid chromatography (LC) represents a compelling alternative to DI; however, state-of-the-art techniques involve only offline LC-HRMS approaches, which have important logistical drawbacks that make DOM analysis more challenging. This study introduces a new method based on online coupling of liquid chromatography to high resolution mass spectrometry, able to overcome the disadvantages of usual approaches. It is characterized by high reproducibility (% Bray–Curtis dissimilarity among replicates ≈ 2.5%), and it reduces transient complexity and contaminant interferences, thus increasing the signal-to-noise ratio (S/N), leading to the identification of an overall larger number of formulas in the mixture. Moreover, the application of an in silico fractionation prior to the statistical analysis allows an easy, flexible, fast, and detailed comparison of DOM samples from a variety of sources with a single chromatographic run.

National Category
Analytical Chemistry
Research subject
Chemistry with specialization in Analytical Chemistry
Identifiers
urn:nbn:se:uu:diva-341015 (URN)10.1021/acs.est.7b04508 (DOI)000426143300045 ()
Funder
Knut and Alice Wallenberg Foundation, 2013.0091Swedish Research Council, SRC 2015-4870Swedish Research Council, SRC 2014-04264
Available from: 2018-02-06 Created: 2018-02-06 Last updated: 2018-04-19Bibliographically approved
Attermeyer, K., Catalan, N., Einarsdóttir, K., Freixa, A., Groeneveld, M. M., Hawkes, J. A., . . . Tranvik, L. (2018). Organic Carbon Processing During Transport Through Boreal Inland Waters: Particles as Important Sites. Journal of Geophysical Research - Biogeosciences, 123(8), 2412-2428
Open this publication in new window or tab >>Organic Carbon Processing During Transport Through Boreal Inland Waters: Particles as Important Sites
Show others...
2018 (English)In: Journal of Geophysical Research - Biogeosciences, ISSN 2169-8953, E-ISSN 2169-8961, Vol. 123, no 8, p. 2412-2428Article in journal (Refereed) Published
Abstract [en]

The degradation and transformation of organic carbon (C) in inland waters result in significant CO2 emissions from inland waters. Even though most of the C in inland waters occurs as dissolved organic carbon (DOC), studies on particulate organic carbon (POC) and how it influences the overall reactivity of organic C in transport are still scarce. We sampled 30 aquatic ecosystems following an aquatic continuum including peat surface waters, streams, rivers, and lakes. We report DOC and POC degradation rates, relate degradation patterns to environmental data across these systems, and present qualitative changes in dissolved organic matter and particulate organic matter during degradation. Microbial degradation rates of POC were approximately 15 times higher compared to degradation of DOC, with POC half-lives of only 17 +/- 3 (mean +/- SE) days across all sampled aquatic ecosystems. Rapid POC decay was accompanied by a shift in particulate C: N ratios, whereas dissolved organic matter composition did not change at the time scale of incubations. The faster degradation of the POC implies a constant replenishment to sustain natural POC concentrations. We suggest that degradation of organic matter transported through the inland water continuum might occur to a large extent via transition of DOC into more rapidly cycling POC in nature, for example, triggered by light. In this way, particles would be a dominant pool of organic C processing across the boreal aquatic continuum, partially sustained by replenishment via flocculation of DOC.

Place, publisher, year, edition, pages
AMER GEOPHYSICAL UNION, 2018
National Category
Environmental Sciences
Identifiers
urn:nbn:se:uu:diva-363637 (URN)10.1029/2018JG004500 (DOI)000445731100009 ()
Funder
Knut and Alice Wallenberg Foundation, KAW 2013.0091Swedish Research Council, 2014-04264Swedish Research Council, 2015-4870
Available from: 2018-10-18 Created: 2018-10-18 Last updated: 2018-10-18Bibliographically approved
Wei, X., Zhang, Y., Yu, S., Li, S., Jiang, W., Zhu, Y., . . . Song, F. (2018). PDLIM5 identified by label-free quantitative proteomics as a potential novel biomarker of papillary thyroid carcinoma. Biochemical and Biophysical Research Communications - BBRC, 499(2), 338-344
Open this publication in new window or tab >>PDLIM5 identified by label-free quantitative proteomics as a potential novel biomarker of papillary thyroid carcinoma
Show others...
2018 (English)In: Biochemical and Biophysical Research Communications - BBRC, ISSN 0006-291X, E-ISSN 1090-2104, Vol. 499, no 2, p. 338-344Article in journal (Refereed) Published
Abstract [en]

In order to better understand the mechanisms underlying the development of papillary thyroid carcinoma (PTC), and to identify new potential biomarkers, high-resolution label-free mass spectrometry was performed on PTC tissues and adjacent normal thyroid tissues from six patients. In this process, 2788 proteins were identified, out of which 49 proteins presented significant differences between PTC tissues and adjacent normal thyroid tissues. Gene ontology revealed that the majority of these proteins are involved in the catalytic activity and binding. We selected three proteins with differential expressions: PDZ and LIM domain 5 (PDLIM5), PDLIM1 and ALDH1A1; Protein expressions were further verified by RT-PCR and western blot. Among these, expression of PDLIM5 and PDLIM1 was up-regulated, while that of ALDH1A1 was down-regulated in PTC tissues. Next, we confirmed their expression through quantitative dot blot (QDB) technique. We found that knockdown of PDLIM5 expression in the B-CPAP cell line could inhibit the migration, invasion and proliferation of PTC cells. In addition, PDLIM5 knockdown reduced Ras and Phospho-ERK1/2 expression. Thus, we suggested that PDLIM5 promotes PTC via activation of the Ras-ERK pathway. Our research provides new molecular insight into the function of PDLIM5, which may assist in studying the mechanism of PTC. In addition, PDLIM5 could be further explored as a potential candidate for PTC treatment.

Keywords
Papillary thyroid cancer, PDZ and UM domain 5, Proteomics
National Category
Biochemistry and Molecular Biology
Identifiers
urn:nbn:se:uu:diva-353360 (URN)10.1016/j.bbrc.2018.03.159 (DOI)000430159400036 ()29574154 (PubMedID)
Available from: 2018-06-12 Created: 2018-06-12 Last updated: 2018-06-12Bibliographically approved
Abu Hamdeh, S., Shevchenko, G., Mi, J., Musunuri, S., Bergquist, J. & Marklund, N. (2018). Proteomic differences between focal and diffuse traumatic brain injury in human brain tissue. Scientific Reports, 8, Article ID 6807.
Open this publication in new window or tab >>Proteomic differences between focal and diffuse traumatic brain injury in human brain tissue
Show others...
2018 (English)In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 8, article id 6807Article in journal (Refereed) Published
Abstract [en]

The early molecular response to severe traumatic brain injury (TBI) was evaluated using biopsies of structurally normal-appearing cortex, obtained at location for intracranial pressure (ICP) monitoring, from 16 severe TBI patients. Mass spectrometry (MS; label free and stable isotope dimethyl labeling) quantitation proteomics showed a strikingly different molecular pattern in TBI in comparison to cortical biopsies from 11 idiopathic normal pressure hydrocephalus patients. Diffuse TBI showed increased expression of peptides related to neurodegeneration (Tau and Fascin, p < 0.05), reduced expression related to antioxidant defense (Glutathione S-transferase Mu 3, Peroxiredoxin-6, Thioredoxin-dependent peroxide reductase; p < 0.05) and increased expression of potential biomarkers (e.g. Neurogranin, Fatty acid-binding protein, heart p < 0.05) compared to focal TBI. Proteomics of human brain biopsies displayed considerable molecular heterogeneity among the different TBI subtypes with consequences for the pathophysiology and development of targeted treatments for TBI.

National Category
Neurosciences Neurology
Identifiers
urn:nbn:se:uu:diva-341912 (URN)10.1038/s41598-018-25060-0 (DOI)000431113100005 ()29717219 (PubMedID)
Funder
The Swedish Brain FoundationVINNOVASwedish Research CouncilLars Hierta Memorial FoundationStiftelsen Gamla Tjänarinnor
Available from: 2018-02-15 Created: 2018-02-15 Last updated: 2018-07-13Bibliographically approved
Kask, L., Hörnaeus, K., Åberg, M., Jorsback, A., Bergquist, J. & Siegbahn, A. (2018). Proteomic, functional and receptor studies of growth differentiation factor 15, GDF-15. Paper presented at 5th Congress of the ESC-Council-on-Basic-Cardiovascular-Science on Frontiers in Cardio Vascular Biology, APR 20-22, 2018, Vienna, AUSTRIA. Cardiovascular Research, 114, S76-S76
Open this publication in new window or tab >>Proteomic, functional and receptor studies of growth differentiation factor 15, GDF-15
Show others...
2018 (English)In: Cardiovascular Research, ISSN 0008-6363, E-ISSN 1755-3245, Vol. 114, p. S76-S76Article in journal, Meeting abstract (Other academic) Published
Place, publisher, year, edition, pages
OXFORD UNIV PRESS, 2018
National Category
Cardiac and Cardiovascular Systems
Identifiers
urn:nbn:se:uu:diva-357492 (URN)000430678500211 ()
Conference
5th Congress of the ESC-Council-on-Basic-Cardiovascular-Science on Frontiers in Cardio Vascular Biology, APR 20-22, 2018, Vienna, AUSTRIA
Available from: 2018-08-17 Created: 2018-08-17 Last updated: 2018-08-17Bibliographically approved
Edvardsson Rasmussen, J., Laurell, G., Rask-Andersen, H., Bergquist, J. & Eriksson, P. O. (2018). The proteome of perilymph in patients with vestibular schwannoma: A possibility to identify biomarkers for tumor associated hearing loss?. PLoS ONE, 13(6), Article ID e0198442.
Open this publication in new window or tab >>The proteome of perilymph in patients with vestibular schwannoma: A possibility to identify biomarkers for tumor associated hearing loss?
Show others...
2018 (English)In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 13, no 6, article id e0198442Article in journal (Refereed) Published
Abstract [en]

Background Due to the surrounding bone, the human inner ear is relatively inaccessible and difficult to reach for cellular and molecular analyses. However, these types of investigations are needed to better understand the etiology, pathophysiology and progression of several inner ear disorders. Moreover, the fluid from the inner ear cannot be sampled for micro-chemical analyses from healthy individuals in vivo. Therefore, in the present paper, we studied patients with vestibular schwannoma (VS) undergoing trans-labyrinthine surgery (TLS). Our primary aim was to identify perilymph proteins in patients with VS on an individual level. Our second aim was to investigate the proteins identified at a functional level and our final aim was to search for biological markers for tumor-associated hearing loss and tumor diameter. Methods and findings Sixteen patients underwent TLS for sporadic VS. Perilymph was aspirated through the round window before opening the labyrinth. One sample was contaminated and excluded resulting in 15 usable samples. Perilymph samples were analyzed with an online tandem LTQ-Orbitrap mass spectrometer. Data were analyzed with MaxQuant software to identify the total number of proteins and to quantify proteins in individual samples. Protein function was analyzed using the PANTHER Overrepresentation tool. Associations between perilymph protein content, clinical parameters, tumor-associated hearing loss and tumor diameter were assessed using Random Forest and Boruta. In total, 314 proteins were identified; 60 in all 15 patients and 130 proteins only once in 15 patients. Ninety-one proteins were detected in at least 12 out of 15 patients. Random Forest followed by Boruta analysis confirmed that alpha-2-HS-glycoprotein (P02765) was an independent variable for tumor-associated hearing loss. In addition, functional analysis showed that numerous processes were significantly increased in the perilymph. The top three enriched biological processes were: 1) secondary metabolic processes; 2) complement activation and 3) cell recognition. Conclusions The proteome of perilymph in patients with vestibular schwannoma has an inter-individual stable section. However, even in a cohort with homogenous disease, the variation between individuals represented the majority of the detected proteins. Alpha-2-HS-glycoprotein, P02765, was shown to be an independent variable for tumor-associated hearing loss, a finding that needs to be verified in other studies. In pathway analysis perilymph had highly enriched functions, particularly in terms of increased immune and metabolic processes.

Place, publisher, year, edition, pages
PUBLIC LIBRARY SCIENCE, 2018
National Category
Otorhinolaryngology
Identifiers
urn:nbn:se:uu:diva-358705 (URN)10.1371/journal.pone.0198442 (DOI)000433900800126 ()29856847 (PubMedID)
Funder
Swedish Research Council, 2015-4870
Available from: 2018-08-31 Created: 2018-08-31 Last updated: 2018-08-31Bibliographically approved
Organisations
Identifiers
ORCID iD: ORCID iD iconorcid.org/0000-0002-4597-041x

Search in DiVA

Show all publications