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  • 1.
    Aeppli, Christoph
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för tillämpad miljövetenskap (ITM).
    Holmstrand, Henry
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för tillämpad miljövetenskap (ITM).
    Andersson, Per
    Gustafsson, Örjan
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för tillämpad miljövetenskap (ITM).
    Direct compound-specific stable chlorine isotope analysis of organic compounds with quadrupole GC/MS using standard isotope bracketing2010Inngår i: Analytical Chemistry, ISSN 0003-2700, E-ISSN 1520-6882, Vol. 82, nr 1, s. 420-426Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    A method has been developed for the direct determination of the stable chlorine isotope composition (delta(37)Cl) of organochlorines that eliminates sample preparation, achieves precision comparable to earlier techniques while improving the sensitivity, and makes use of benchtop gas chromatography-quadrupole mass spectrometry instruments (GCqMS). The method is based on the use of multiple injections (n = 8-10) of the sample, bracketed by a molecularly identical isotopic standard with known delta(37)Cl, determined using off-line thermal ionization mass spectrometry (TIMS). Mass traces of two isotopologues differing by one chlorine isotope were used to calculate delta(37)Cl values. Optimization of mass spectrometry and peak integration parameters as well as method validation was achieved using tetrachloroethene (PCE), p,p'-dichlorodiphenyltrichloroethane (DDT), and pentachlorophenol (PCP), spanning a delta(37)Cl range of -5.5 to +3.2 per thousand vs SMOC. Injecting 1.6-1100 pmol resulted in standard deviations (1sigma) of 0.6-1.3 per thousand, and the delta(37)Cl results agreed with values independently measured with TIMS. The method was tested by determining the Rayleigh fractionation during evaporation of pure liquid PCE, resulting in a chlorine isotopic enrichment factor of epsilon(Cl) = -1.1 +/- 0.4 per thousand. Furthermore, position-specific delta(37)Cl analysis based on analysis of DDT mass fragments was evaluated. The GCqMS-delta(37)Cl method offers a simplified yet sensitive approach for compound-specific chlorine isotope analysis.

  • 2.
    Amini, Nahid
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för analytisk kemi.
    Shariatgorji, Mohammadreza
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för analytisk kemi.
    Crescenzi, Carlo
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för analytisk kemi.
    Thorsen, Gunnar
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för analytisk kemi.
    Screening and Quantification of Pesticides in Water Using a Dual-Function Graphitized Carbon Black Disk (Addition/Correction)2011Inngår i: Analytical Chemistry, ISSN 0003-2700, E-ISSN 1520-6882, Vol. 83, s. 631-631Artikkel i tidsskrift (Fagfellevurdert)
  • 3.
    Amini, Nahid
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för analytisk kemi.
    Shariatgorji, Mohammadreza
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för analytisk kemi.
    Crescenzi, Carlo
    Thorsén, Gunnar
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för analytisk kemi.
    Screening and Quantification of Pesticides in Water Using a Dual-Function Graphitized Carbon Black Disk2010Inngår i: Analytical Chemistry, ISSN 0003-2700, E-ISSN 1520-6882, Vol. 82, nr 1, s. 290-296Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    A simple platform for combining solid phase extraction (SPE) and surface-assisted laser desorption ionization mass spectrometry (SALDI-MS) of extracted analytes, using disks prepared by embedding graphitized carbon black (GCB-4) particles in a network of polytetrafluoroethylene (PTFE), is presented. The system provides a convenient approach for rapid SALDI-MS screening of substances in aqueous samples, which can be followed by robust quantitative and/or structural analyses by liquid chromatography (LC)/MS/MS of positive samples. The extraction discs are easily transferred between gaskets where the sample extraction and desorption of selected samples is performed and the mass spectrometer. The SPE and SALDI properties of the new GCB-4 disc have been characterized for 15 pesticides with varying chemical properties, and the screening strategy has been applied to the analysis of pesticides in agricultural drainage water. Atrazine and atrazine-desethyl-2-hydroxy were detected in the sampled water by SALDI-MS screening and subsequently confirmed and quantified using LC/MS/MS.

  • 4. Bogdal, Christian
    et al.
    Alsberg, Tomas
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för miljövetenskap och analytisk kemi.
    Diefenbacher, Pascal S.
    MacLeod, Matthew
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för miljövetenskap och analytisk kemi.
    Berger, Urs
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för miljövetenskap och analytisk kemi.
    Fast Quantification of Chlorinated Paraffins in Environmental Samples by Direct Injection High-Resolution Mass Spectrometry with Pattern Deconvolution2015Inngår i: Analytical Chemistry, ISSN 0003-2700, E-ISSN 1520-6882, Vol. 87, nr 5, s. 2852-2860Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Chlorinated paraffins (CPs) are high production volume chemicals, but data about their environmental fate are scarce. CP mixtures composed of thousands of isomers represent a major challenge for quantification at low levels in environmental samples. Here, we present a novel analytical method for analysis of short-chain, medium-chain, and long-chain CPs in a single injection, that also yields information about congener group pattern. Our detection method is based on direct injection into an atmospheric pressure chemical ionization source operated in negative ion mode under chlorine-enhanced conditions, followed by quadrupole time-of-flight high-resolution mass spectrometry (APCI-qTOF-HRMS) operated in full-scan mode. A mathematical algorithm is applied to deconvolute the CP patterns in the analyzed samples into a linear combination of patterns of technical CP mixtures and to quantify CPs using technical mixtures as external calibration standards. For CP mixtures with known composition, the new method provided concentrations that were within a factor of 1.2 of the target value. Accuracies for CPs spiked to sediment and fish extracts were between 91% and 123%. Concentrations determined in unspiked field samples were within a factor of 5 for short-chain CPs and a factor of 16 for medium-chain CPs of results obtained with an independent method based on gas chromatography/electron capture negative ionization high-resolution mass spectrometry (GC/ECNI-HRMS). The presented APCI-qTOF-HRMS pattern deconvolution method is an interesting alternative for CP analysis in environmental samples. It is particularly sensitive for medium- and long-chain CPs and has the advantage of being extremely fast (instrumental analysis time, less than 1 min).

  • 5. Donolato, Marco
    et al.
    Antunes, Paula
    Bejhed, Rebecca S.
    Gómez de la Torre, Teresa Zardán
    Österberg, Frederik W.
    Strömberg, Mattias
    Nilsson, Mats
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för biokemi och biofysik. Stockholms universitet, Science for Life Laboratory (SciLifeLab).
    Strømme, Maria
    Svedlindh, Peter
    Hansen, Mikkel F.
    Vavassori, Paolo
    Novel Readout Method for Molecular Diagnostic Assays Based on Optical Measurements of Magnetic Nanobead Dynamics2015Inngår i: Analytical Chemistry, ISSN 0003-2700, E-ISSN 1520-6882, Vol. 87, nr 3, s. 1622-1629Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    We demonstrate detection of DNA coils formed from a Vibrio cholerae DNA target at picomolar concentrations using a novel optomagnetic approach exploiting the dynamic behavior and optical anisotropy of magnetic nanobead (MNB) assemblies. We establish that the complex second harmonic optical transmission spectra of MNB suspensions measured upon application of a weak uniaxial AC magnetic field correlate well with the rotation dynamics of the individual MNBs. Adding a target analyte to the solution leads to the formation of permanent MNB clusters, namely, to the suppression of the dynamic MNB behavior. We prove that the optical transmission spectra are highly sensitive to the formation of permanent MNB clusters and, thereby to the target analyte concentration. As a specific clinically relevant diagnostic case, we detect DNA coils formed via padlock probe recognition and isothermal rolling circle amplification and benchmark against a commercial equipment. The results demonstrate the fast optomagnetic readout of rolling circle products from bacterial DNA utilizing the dynamic properties of MNBs in a miniaturized and low-cost platform requiring only a transparent window in the chip.

  • 6. Ibáñez, Clara
    et al.
    Simó, Carolina
    Martín-Álvarez, Pedro J.
    Kivipelto, Miia
    Stockholms universitet, Samhällsvetenskapliga fakulteten, Centrum för forskning om äldre och åldrande (ARC), (tills m KI).
    Winblad, Bengt
    Stockholms universitet, Samhällsvetenskapliga fakulteten, Centrum för forskning om äldre och åldrande (ARC), (tills m KI).
    Cedazo-Mínguez, Angel
    Stockholms universitet, Samhällsvetenskapliga fakulteten, Centrum för forskning om äldre och åldrande (ARC), (tills m KI).
    Cifuentes, Alejandro
    Toward a predictive model of Alzheimer's disease progression using capillary electrophoresis-mass spectrometry metabolomics2012Inngår i: Analytical Chemistry, ISSN 0003-2700, E-ISSN 1520-6882, Vol. 84, nr 20, s. 8532-8540Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Alzheimer’s disease (AD) is the most prevalent form of dementia with an estimated worldwide prevalence of over 30 million people, and its incidence is expected to increase dramatically with an increasing elderly population. Up until now, cerebrospinal fluid (CSF) has been the preferred sample to investigate central nervous system (CNS) disorders since its composition is directly related to metabolite production in the brain. In this work, a nontargeted metabolomic approach based on capillary electrophoresis–mass spectrometry (CE–MS) is developed to examine metabolic differences in CSF samples from subjects with different cognitive status related to AD progression. To do this, CSF samples from 85 subjects were obtained from patients with (i) subjective cognitive impairment (SCI, i.e. control group), (ii) mild cognitive impairment (MCI) which remained stable after a follow-up period of 2 years, (iii) MCI which progressed to AD within a 2-year time after the initial MCI diagnostic and, (iv) diagnosed AD. A prediction model for AD progression using multivariate statistical analysis based on CE–MS metabolomics of CSF samples was obtained using 73 CSF samples. Using our model, we were able to correctly classify 97–100% of the samples in the diagnostic groups. The prediction power was confirmed in a blind small test set of 12 CSF samples, reaching a 83% of diagnostic accuracy. The obtained predictive values were higher than those reported with classical CSF AD biomarkers (Aβ42 and tau) but need to be confirmed in larger samples cohorts. Choline, dimethylarginine, arginine, valine, proline, serine, histidine, creatine, carnitine, and suberylglycine were identified as possible disease progression biomarkers. Our results suggest that CE–MS metabolomics of CSF samples can be a useful tool to predict AD progression.

  • 7.
    Kirillova, Elena N.
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för tillämpad miljövetenskap (ITM).
    Sheesley, Rebecca J.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för tillämpad miljövetenskap (ITM).
    Andersson, August
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för tillämpad miljövetenskap (ITM).
    Gustafsson, Örjan
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för tillämpad miljövetenskap (ITM).
    Natural Abundance C-13 and C-14 Analysis of Water-Soluble Organic Carbon in Atmospheric Aerosols2010Inngår i: Analytical Chemistry, ISSN 0003-2700, E-ISSN 1520-6882, Vol. 82, nr 19, s. 7973-7978Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Water-soluble organic carbon (WSOC) constitutes a large fraction of climate-forcing organic aerosols in the atmosphere, yet the sources of WSOC are poorly constrained. A method was developed to measure the stable carbon isotope (delta C-13) and radiocarbon (delta C-14) composition of WSOC for apportionment between fossil fuel and different biogenic sources. Synthetic WSOC test substances and ambient aerosols were employed to investigate the effect of both modern and fossil carbon contamination and any method-induced isotope fractionation. The method includes extraction of aerosols collected on quartz filters followed by purification and preparation for off-line delta C-13 and Delta C-14 determination. The preparative freeze-drying step for isotope analysis yielded recoveries of only similar to 70% for ambient aerosols and WSOC probes. However, the delta C-13 of the WSOC isolates were in agreement with the delta C-13 of the unprocessed starting material, even for the volatile oxalic acid probe (6.59 +/- 0.37 parts per thousand vs 6.33 +/- 0.31 parts per thousand; 2 sd). A C-14-fossil phthalic acid WSOC probe returned a fraction modern biomass of <0.008 whereas a C-14-modern sucrose sucrose standard yielded a fraction modern of >0.999, indicating the Delta C-14-WSOC method to be free of both fossil and contemporary carbon contamination. Application of the (delta C-13/Delta C-14-WSOC method to source apportion climate-affecting aerosols was illustrated be constraining that WSOC in ambient Stockholm aerosols were 88% of contemporary biogenic C3 plant origin.

  • 8.
    Lundborg, Magnus
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Widmalm, Göran
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Structural analysis of glycans by NMR chemical shift prediction2011Inngår i: Analytical Chemistry, ISSN 0003-2700, E-ISSN 1520-6882, Vol. 83, nr 5, s. 1514-1517Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Structural determination of N- and O-linked glycans as well as polysaccharides is hampered by the limited spectral dispersion. The computerized approach CASPER, an acronym for computer assisted spectrum evaluation of regular polysaccharides, uses liquid state NMR data to elucidate carbohydrate structure based on agreement with predicted 1H and 13C chemical shifts. We here demonstrate developments based on multiple through-bond J-based correlations that significantly enhance the credence to the sequence connectivities proposed in the analysis exemplified by an oligosaccharide and a bacterial polysaccharide. The approach is also suitable for predicting 1H and 13C NMR chemical shifts of synthesized oligosaccharides and glycoconjugates, thereby corroborating a proposed structure.

  • 9. Mori, R.A.
    et al.
    Paris, E.
    Giuli, G.
    Eeckhout, S.
    Kavcic, M.
    Zitnic, M.
    Bucar, K.
    Pettersson, Lars G.M.
    Stockholms universitet, Naturvetenskapliga fakulteten, Fysikum.
    Glatzel, Pieter
    The electronic structure of Sulfur studied by X-ray absorption and emission spectroscopy2009Inngår i: Analytical Chemistry, ISSN 0003-2700, E-ISSN 1520-6882, Vol. 81, s. 6516-6525Artikkel i tidsskrift (Fagfellevurdert)
  • 10.
    Moruz, Luminita
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för biokemi och biofysik. Stockholms universitet, Science for Life Laboratory (SciLifeLab).
    Pichler, Peter
    Stranzl, Thomas
    Mechtler, Karl
    Kall, Lukas
    Optimized Nonlinear Gradients for Reversed-Phase Liquid Chromatography in Shotgun Proteomics2013Inngår i: Analytical Chemistry, ISSN 0003-2700, E-ISSN 1520-6882, Vol. 85, nr 16, s. 7777-7785Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Reversed-phase liquid chromatography has become the preferred method for separating peptides in most of the mass spectrometry-based proteomics workflows of today. In the way the technique is typically applied, the peptides are released from the chromatography column by the gradual addition of an organic buffer according to a linear function. However, when applied to complex peptide mixtures, this approach leads to unequal spreads of the peptides over the chromatography time. To address this, we investigated the use of nonlinear gradients, customized for each setup at hand. We developed an algorithm to generate optimized gradient functions for shotgun proteomics experiments and evaluated it for two data sets consisting each of four replicate runs of a human complex sample. Our results show that the optimized gradients produce a more even spread of the peptides over the chromatography run, while leading to increased numbers of confident peptide identifications. In addition, the list of peptides identified using nonlinear gradients differed considerably from those found with the linear ones, suggesting that such gradients can be a valuable tool for increasing the proteome coverage of mass spectrometry-based experiments.

  • 11. Nugroho, Ferry A. A.
    et al.
    Xu, Chao
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK).
    Hedin, Niklas
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK).
    Langhammer, Christoph
    UV-Visible and Plasmonic Nanospectroscopy of the CO2 Adsorption Energetics in a Microporous Polymer2015Inngår i: Analytical Chemistry, ISSN 0003-2700, E-ISSN 1520-6882, Vol. 87, nr 20, s. 10161-10165Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    In the context of carbon capture and storage (CCS), micro- and mesoporous polymers have received significant attention due to their ability to selectively adsorb and separate CO2, from gas streams. The performance of such materials is critically dependent on the isosteric heat of adsorption (Q(st)) of CO2, directly related to the interaction strength between CO2, and the adsorbent. Here, we show using the microporous polymer PIM-1 as a model system that its Q(st) can be conveniently determined by in situ UV-vis optical transmission spectroscopy directly applied on the adsorbent or, with higher resolution, by indirect nanoplasmonic sensing based on localized surface plasmon resonance in metal nanoparticles. Taken all together, this study provides a general blueprint for efficient optical screening of micro- and mesoporous polymeric materials for CCS in terms of their CO2, adsorption energetics and kinetics.

  • 12.
    Pavankumar, Asalapuram R.
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för biokemi och biofysik. Stockholms universitet, Science for Life Laboratory (SciLifeLab).
    Engström, Anna
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för biokemi och biofysik. Stockholms universitet, Science for Life Laboratory (SciLifeLab).
    Liu, Jie
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för biokemi och biofysik. Stockholms universitet, Science for Life Laboratory (SciLifeLab).
    Herthnek, David
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för biokemi och biofysik. Stockholms universitet, Science for Life Laboratory (SciLifeLab).
    Nilsson, Mats
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för biokemi och biofysik. Stockholms universitet, Science for Life Laboratory (SciLifeLab).
    Proficient Detection of Multi-Drug-Resistant Mycobacterium tuberculosis by Padlock Probes and Lateral Flow Nucleic Acid Biosensors2016Inngår i: Analytical Chemistry, ISSN 0003-2700, E-ISSN 1520-6882, Vol. 88, nr 8, s. 4277-4284Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Tuberculosis is a major communicable disease. Its causative agent, Mycobacterium tuberculosis, becomes resistant to antibiotics by acquisition of point mutations in the chromosome. Multi-drug-resistant tuberculosis (MDR-TB) is an increasing public health threat, and prompt detection of such strains is of critical importance. As rolling circle amplification of padlock probes can be used to robustly distinguish single-nucleotide variants, we combined this technique with a sensitive lateral flow nucleic acid biosensor to develop a rapid molecular diagnostic test for MDR-TB, A proof-of-concept test was established for detection of the most common mutations [rpoB 531 (TCG/TTG) and katG 315 (AGC/ACC)] causing MDR-TB and verification of loss of the respective wild type. The molecular diagnostic test produces visual signals corresponding to the respective genotypes on lateral flow strips in approximately 75 min. By detecting only two mutations, the test can detect about 60% of all MDR-TB cases. The padlock probe-lateral flow (PLP-LF) test is the first of its kind and can ideally be performed at resource-limited clinical laboratories. Rapid information about the drug-susceptibility pattern can assist clinicians to choose suitable treatment regimens and take appropriate infection control actions rather than prescribing empirical treatment, thereby helping to control the spread of MDR-TB in the community.

  • 13.
    Persson, Per-Olov
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för tillämpad miljövetenskap (ITM).
    Andersson, Per S.
    Zhang, Jing
    Porcelli, Don
    Determination of Nd Isotopes in Water: A Chemical Separation Technique for Extracting Nd from Seawater Using a Chelating Resin2011Inngår i: Analytical Chemistry, ISSN 0003-2700, E-ISSN 1520-6882, Vol. 83, nr 4, s. 1336-1341Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    A new preconcentration technique for the determination of the concentration and isotopic composition of neodymium in aqueous samples is presented. The method uses a resin, Nobias PA1 from Hitachi High-Technologies, which has a hydrophilic methacrylate polymer backbone where the functional groups ethylenediaminetriacetic and iminodiacetic acids are immobilized. The function of the resin has been tested by preconcentrating 110-350 pmol of Nd from test solutions as well as from natural brackish water and seawater samples with different salinities and Nd concentrations. Samples were loaded onto the resin after the pH was adjusted, and the Nd fraction was eluted using 3 M HNO(3). The method shows yields of about 90% or higher at pH 6 when the samples were buffered using ammonium acetate. Without the addition of buffer the yield decreased to below 80%. The isotopic composition of Nd in samples preconcentrated using Nobias PA1 agree within error with published data or data obtained by other methods. The total blank, including contributions from preconcentration, separation, and mass spectrometry, is estimated to be 0.2-0.4 pmol (30-60 pg) of Nd. The described preconcentration method, which can be used in the field, is easy, fast (about 8 h for a 3.6 kg sample), and reliable for preconcentration of Nd from a seawater matrix.

  • 14.
    Plassmann, Merle M.
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för tillämpad miljövetenskap (ITM).
    Berger, Urs
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för tillämpad miljövetenskap (ITM).
    Trace Analytical Methods for Semifluorinated n-Alkanes in Snow, Soil, and Air2010Inngår i: Analytical Chemistry, ISSN 0003-2700, E-ISSN 1520-6882, Vol. 82, nr 11, s. 4551-4557Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Semifluorinated n-alkanes (SFAs) are anthropogenic chemicals that are used in ski waxes and, thus, are released directly into the environment, but their subsequent fate and distribution are as yet unknown. Therefore, simple, selective, and sensitive methods were developed for analyzing trace amounts of SFAs in snow/water, soil, and air samples by gas chromatography coupled to electron capture negative ionization mass spectrometry (GC/ECNI-MS). Recoveries were generally in the range of 70-120%, depending on the compound and matrix. The analytical sensitivity was higher for SFAs with longer fluorinated chains, and the instrumental limits of detection ranged from 0.3 to 260 pg injected, providing method detection limits of 0.54-311 ng L-1, 0.004-9.86 ng g(-1), and 0.4-531 ng m(-3) for snow (analyzed as its meltwater), soil, and air samples, respectively. Using the developed procedures, SFAs were found in snow (meltwater) and soil samples from a small cross-country ski area in Sweden at concentrations up to 1.3 mu g L-1 and 47 pg g(-1), respectively.

  • 15. Russell, Camilla
    et al.
    Roy, Subhadeep
    Ganguly, Saheli
    Qian, Xiaoyan
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för biokemi och biofysik. Stockholms universitet, Science for Life Laboratory (SciLifeLab).
    Caruthers, Marvin H.
    Nilsson, Mats
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för biokemi och biofysik. Stockholms universitet, Science for Life Laboratory (SciLifeLab). Uppsala University, Sweden.
    Formation of Silver Nanostructures by Rolling Circle Amplification Using Boranephosphonate-Modified Nucleotides2015Inngår i: Analytical Chemistry, ISSN 0003-2700, E-ISSN 1520-6882, Vol. 87, nr 13, s. 6660-6666Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    We investigate the efficiency of incorporation of boranephosphonate-modified nucleotides by phi29 DNA poly, merase and present a simple method for forming large defined silver nanostructures by rolling circle amplification (RCA) using boranephosphonate internudeotide linkages. RCA is a linear DNA amplification technique that can use specifically circularized DNA probes for detection of target nucleic acids and proteins. The resulting product is a collapsed single-stranded DNA molecule with tandem repeats of the DNA probe. By substituting each of the natural nucleotides with the corresponding 5'-(alpha-P-borano)-deoxynudeosidetriphosphate, only a small reduction in amplification rate is observed. Also, by substituting all four natural nucleotides, it is possible to enzymatically synthesize a micrometensized, single-stranded DNA molecule with only boranephosphonate internucleotide linkages. Well-defined silver particles are then readily formed along the rolling circle product.

  • 16.
    Shariatgorji, Mohammadreza
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för analytisk kemi.
    Amini, Nahid
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för analytisk kemi.
    Thorsen, Gunnar
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för analytisk kemi.
    Crescenzi, Carlo
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för analytisk kemi.
    Ilag, Leopold
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för analytisk kemi.
    µ-trap for the SALDI-MS screening of organic compounds prior to LC/MS analysis2008Inngår i: Analytical Chemistry, ISSN 0003-2700, E-ISSN 1520-6882, Vol. 80, nr 14, s. 5515-5523Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    A procedure for rapidly screening and quantitatively analyzing organic molecules is presented, in which a miniaturized solid-phase extraction (SPE) cartridge containing 0.6 mg of graphitized carbon black (the GCB-mu-trap) is used for sample pretreatment. Then surface-assisted laser desorption ionization dine-of-flight mass spectrometry (SALDI-TOF-MS) screening is followed by liquid chromatography/mass spectrometry (LC/MS) for robust quantitative analysis of samples containing analytes of interest. Liquid samples with volumes up to 100 mL were extracted using the GCB-mu-trap, and SALDI screening was performed by transferring a few particles of the GCB 4 sorbent from the mu-trap onto a stainless steel plate. Analytes were then simply ionized and desorbed by irradiating the GCB 4 particles without any further pretreatment. GCB 4 was found to be an excellent surface for the SALDI analysis of small molecules, providing spectra with very clean backgrounds. The small size of the cartridge (micropipet filter tip) results in enrichment of the analytes on a small surface area, affording low SALDI-TOF-MS detection limits. Furthermore, the removal of just a few particles from the p-trap does not significantly affect the subsequent quantitative determination. This approach offers considerable reductions in analytical costs by eliminating unnecessary SPE-LC/MS analyses.

  • 17.
    Shariatgorji, Mohammadreza
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för analytisk kemi.
    Astorga-Wells, J
    Jornvall, H
    Ilag, Leopold
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för analytisk kemi.
    Microfluidic electrocapture-assisted mass spectrometry of membrane-associated polypeptides2008Inngår i: Analytical Chemistry, ISSN 0003-2700, E-ISSN 1520-6882, Vol. 80, s. 7116-7120Artikkel i tidsskrift (Fagfellevurdert)
  • 18.
    Tengstrand, Erik
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för analytisk kemi.
    Lindberg, Johan
    Åberg, K. Magnus
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för analytisk kemi.
    TracMass 2-A Modular Suite of Tools for Processing Chromatography-Full Scan Mass Spectrometry Data2014Inngår i: Analytical Chemistry, ISSN 0003-2700, E-ISSN 1520-6882, Vol. 86, nr 7, s. 3435-3442Artikkel i tidsskrift (Fagfellevurdert)
    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.

  • 19.
    Yuan, Bo
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för miljövetenskap och analytisk kemi.
    Alsberg, Tomas
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för miljövetenskap och analytisk kemi.
    Bogdal, Christian
    MacLeod, Matthew
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för miljövetenskap och analytisk kemi.
    Berger, Urs
    Gao, Wei
    Wang, Yawei
    de Wit, Cynthia A.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för miljövetenskap och analytisk kemi.
    Deconvolution of Soft Ionization Mass Spectra of Chlorinated Paraffins To Resolve Congener Groups2016Inngår i: Analytical Chemistry, ISSN 0003-2700, E-ISSN 1520-6882, Vol. 88, nr 18, s. 8980-8988Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    We describe and illustrate a three-step data-processing approach that enables individual congener groups of chlorinated-paraffins (CPs) to be resolved in mass spectra obtained from either-of two soft ionization methods: electron capture negative-ionization mass spectrometry (ECNI-MS) or atmospheric pressure chemical ionization mass spectrometry (APCI-MS). In the first step, general fragmentation pathways of CPs are deduced from analysis of mass spectra of individual CP congeners. In the-Second step, all possible fragment ions in the general fragmentation pathways of CPs with 10 to 20 carbon atoms are enumerated and compared to mass spectra of CP mixture standards, and a deconvolution algorithm is applied to identify fragment ions that are actually observed. In the third step, isotope permutations of the observed fragment ions are calculated and used to identify isobaric overlaps, so that mass intensities of indivichial CP congener groups can be deconvolved from the unresolved isobaric ion signal intensities in mass spectra. For a specific instrument; the three steps only need to be done once to enable deconvolution of CPs in unknown samples. This approach enables congener group-level resolution of CP mixtures in environmental samples, and: it opens up the possibility, for quantification of congener group.

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