Aleš Kvasnička | Palacky University, Olomouc (original) (raw)

Papers by Aleš Kvasnička

Research paper thumbnail of MS-DIAL 5 multimodal mass spectrometry data mining unveils lipidome complexities

bioRxiv (Cold Spring Harbor Laboratory), Feb 8, 2024

Lipidomics and metabolomics communities comprise various informatics tools; however, software pro... more Lipidomics and metabolomics communities comprise various informatics tools; however, software programs that can handle multimodal mass spectrometry (MS) data with structural annotations guided by the Lipidomics Standards Initiative are limited. Here, we provide MS-DIAL 5 to facilitate the in-depth structural elucidation of lipids through electron-activated dissociation (EAD)-based tandem MS, as well as determine their molecular localization through MS imaging (MSI) data using a species/tissue-specific lipidome database containing the predicted collision-cross section (CCS) values. With the optimized EAD settings using 14 eV kinetic energy conditions, the program correctly delineated the lipid structures based on EAD-MS/MS data from 96.4% of authentic standards. Our workflow was showcased by annotating the sn-and double-bond positions of eye-specific phosphatidylcholine molecules containing very-longchain polyunsaturated fatty acids (VLC-PUFAs), characterized as PC n-3-VLC-PUFA/FA. Using MSI data from the eye and HeLa cells supplemented with n-3-VLC-PUFA, we identified glycerol 3-phosphate (G3P) acyltransferase (GPAT) as an enzyme candidate responsible for incorporating n-3 VLC-PUFAs into the sn-1 position of phospholipids in mammalian cells, which was confirmed using recombinant proteins in a cell-free system. Therefore, the MS-DIAL 5 environment, combined with optimized MS data acquisition methods, facilitates a better understanding of lipid structures and their localization, offering novel insights into lipid biology. .

Research paper thumbnail of MS-DIAL 5 multimodal mass spectrometry data mining unveils lipidome complexities

bioRxiv (Cold Spring Harbor Laboratory), Feb 8, 2024

Lipidomics and metabolomics communities comprise various informatics tools; however, software pro... more Lipidomics and metabolomics communities comprise various informatics tools; however, software programs that can handle multimodal mass spectrometry (MS) data with structural annotations guided by the Lipidomics Standards Initiative are limited. Here, we provide MS-DIAL 5 to facilitate the in-depth structural elucidation of lipids through electron-activated dissociation (EAD)-based tandem MS, as well as determine their molecular localization through MS imaging (MSI) data using a species/tissue-specific lipidome database containing the predicted collision-cross section (CCS) values. With the optimized EAD settings using 14 eV kinetic energy conditions, the program correctly delineated the lipid structures based on EAD-MS/MS data from 96.4% of authentic standards. Our workflow was showcased by annotating the sn-and double-bond positions of eye-specific phosphatidylcholine molecules containing very-longchain polyunsaturated fatty acids (VLC-PUFAs), characterized as PC n-3-VLC-PUFA/FA. Using MSI data from the eye and HeLa cells supplemented with n-3-VLC-PUFA, we identified glycerol 3-phosphate (G3P) acyltransferase (GPAT) as an enzyme candidate responsible for incorporating n-3 VLC-PUFAs into the sn-1 position of phospholipids in mammalian cells, which was confirmed using recombinant proteins in a cell-free system. Therefore, the MS-DIAL 5 environment, combined with optimized MS data acquisition methods, facilitates a better understanding of lipid structures and their localization, offering novel insights into lipid biology. .

Research paper thumbnail of Parallel Metabolomics and Lipidomics of a PSMA/GCPII Deficient Mouse Model Reveal Alteration of NAAG Levels and Brain Lipid Composition

ACS chemical neuroscience, Feb 20, 2024

Research paper thumbnail of Wide metabolite coverage LC-MS/MS assay for the diagnosis of inherited metabolic disorders in urine

Research paper thumbnail of Patients with Neurodegenerative Proteinopathies Exhibit Altered Tryptophan Metabolism in the Serum and Cerebrospinal Fluid

ACS Chemical Neuroscience, Jan 8, 2024

Research paper thumbnail of Alterations in lipidome profiles distinguish early-onset hyperuricemia, gout, and the effect of urate-lowering treatment

Research paper thumbnail of Systematic Comparison of Advanced Network Analysis and Visualization of Lipidomics Data

Lecture Notes in Computer Science, 2023

Research paper thumbnail of Changes in lipid metabolism track with the progression of neurofibrillary pathology in tauopathies

BackgroundAbnormal aggregation of tau protein that leads to brain inclusions is a common feature ... more BackgroundAbnormal aggregation of tau protein that leads to brain inclusions is a common feature of neurodegenerative disorders called tauopathies. Recent evidence suggests the involvement of lipid metabolic deregulations in the pathogenesis of tauopathies. However, the role of tau protein in the regulation of lipid metabolism is much less characterized and not well understood.MethodsWe used a transgenic rat model for tauopathy to reveal metabolic alterations induced by neurofibrillary pathology. Transgenic rats express a tau fragment truncated at the N-and C-terminals. For phenotypic profiling, we performed targeted metabolomic and lipidomic analysis of brain tissue, CSF, and plasma, based on the LC-MS platform. To monitor disease progression, we employed samples from transgenic and control rats aged 4, 6, 8, 10, 12, and 14 months. To study neuron-glia interplay in lipidome changes induced by pathological tau we used well well-established multicomponent cell model system. Univariat...

Research paper thumbnail of Selective pivot logratio coordinates for partial least squares discriminant analysis modelling with applications in metabolomics

Research paper thumbnail of Rapid and efficient LC-MS/MS diagnosis of inherited metabolic disorders: a semi-automated workflow for analysis of organic acids, acylglycines, and acylcarnitines in urine

Clinical Chemistry and Laboratory Medicine (CCLM)

Objectives The analysis of organic acids in urine is an important part of the diagnosis of inheri... more Objectives The analysis of organic acids in urine is an important part of the diagnosis of inherited metabolic disorders (IMDs), for which gas chromatography coupled with mass spectrometry is still predominantly used. Methods Ultra-performance liquid chromatography-tandem mass spectrometry (LC-MS/MS) assay for urinary organic acids, acylcarnitines and acylglycines was developed and validated. Sample preparation consists only of dilution and the addition of internal standards. Raw data processing is quick and easy using selective scheduled multiple reaction monitoring mode. A robust standardised value calculation as a data transformation together with advanced automatic visualisation tools are applied for easy evaluation of complex data. Results The developed method covers 146 biomarkers consisting of organic acids (n=99), acylglycines (n=15) and acylcarnitines (n=32) including all clinically important isomeric compounds present. Linearity with r2>0.98 for 118 analytes, inter-day ...

Research paper thumbnail of Clinical lipidomics in the era of the big data

Clinical Chemistry and Laboratory Medicine (CCLM)

Lipidomics as a branch of metabolomics provides unique information on the complex lipid profile i... more Lipidomics as a branch of metabolomics provides unique information on the complex lipid profile in biological materials. In clinically focused studies, hundreds of lipids together with available clinical information proved to be an effective tool in the discovery of biomarkers and understanding of pathobiochemistry. However, despite the introduction of lipidomics nearly twenty years ago, only dozens of big data studies using clinical lipidomics have been published to date. In this review, we discuss the lipidomics workflow, statistical tools, and the challenges of standartisation. The consequent summary divided into major clinical areas of cardiovascular disease, cancer, diabetes mellitus, neurodegenerative and liver diseases is demonstrating the importance of clinical lipidomics. In these publications, the potential of lipidomics for prediction, diagnosis or finding new targets for the treatment of selected diseases can be seen. The first of these results have already been implemen...

Research paper thumbnail of Altered plasma, urine, and tissue profiles of sulfatides and sphingomyelins in patients with renal cell carcinoma

Renal cell carcinoma (RCC) represents the most common type of kidney cancer and, despite the prog... more Renal cell carcinoma (RCC) represents the most common type of kidney cancer and, despite the progress of surgical and medical management, is associated with high mortality. In this study, we demonstrate that RCC-related processes change body fluids sphingolipid concentrations, which may be used to monitor tumor presence using non-invasive lipid-based blood and urine tests. We investigate 674 plasma, urine, and tissue samples from 369 RCC patients and controls. For the first time, we show the significant concentration changes of low abundant sulfatides in plasma and urine of RCC patients. Elevated concentrations of lactosylsulfatides, decreased concentrations of sphingomyelins with long saturated N-fatty acyls and sulfatides with hydroxylated fatty acyls are the crucial alternations in RCC. These changes are stage-dependent and are more emphasized in late-stage RCC. Similar trends in body fluids and tissues indicate that RCC widely influences lipid metabolism and highlights the poten...

Research paper thumbnail of SLIDE—Novel Approach to Apocrine Sweat Sampling for Lipid Profiling in Healthy Individuals

International Journal of Molecular Sciences, 2021

We designed a concept of 3D-printed attachment with porous glass filter disks—SLIDE (Sweat sampLI... more We designed a concept of 3D-printed attachment with porous glass filter disks—SLIDE (Sweat sampLIng DevicE) for easy sampling of apocrine sweat. By applying advanced mass spectrometry coupled with the liquid chromatography technique, the complex lipid profiles were measured to evaluate the reproducibility and robustness of this novel approach. Moreover, our in-depth statistical evaluation of the data provided an insight into the potential use of apocrine sweat as a novel and diagnostically relevant biofluid for clinical analyses. Data transformation using probabilistic quotient normalization (PQN) significantly improved the analytical characteristics and overcame the ‘sample dilution issue’ of the sampling. The lipidomic content of apocrine sweat from healthy subjects was described in terms of identification and quantitation. A total of 240 lipids across 15 classes were identified. The lipid concentrations varied from 10−10 to 10−4 mol/L. The most numerous class of lipids were ceram...

Research paper thumbnail of Lipidomic and metabolomic analysis reveals changes in biochemical pathways for non-small cell lung cancer tissues

Biochimica et Biophysica Acta (BBA) - Molecular and Cell Biology of Lipids

Research paper thumbnail of Evaluation of the Determination of Dabigatran, Rivaroxaban, and Apixaban in Lupus Anticoagulant-Positive Patients

Diagnostics

Background: The effect of direct oral anticoagulants (DOAC) on laboratory tests dependent on the ... more Background: The effect of direct oral anticoagulants (DOAC) on laboratory tests dependent on the production of their targets, factor IIa and factor Xa, is a well-known problem and can cause both false positive and negative results. In particular, the situation in patients who develop lupus anticoagulant (LA) antibodies is highly complex. To evaluate the effectiveness of DOAC therapy in lupus-positive patients, 31 samples were enrolled in this retrospective study. All patient samples were spiked with three types of DOAC (dabigatran, DABI; rivaroxaban, RIVA; and apixaban, API) in a concentration that significantly influenced the screening test for LA and thus can mask the presence of LA. Subsequently, the DOAC was always unbound by the DOAC-Stop procedure. DOAC levels before and after binding were determined by functional assays, followed by liquid chromatography coupled with mass spectrometry (LC-MS) analysis. Methods: The determination of DOAC levels was performed by direct thrombin...

Research paper thumbnail of Novel LC-MS tools for diagnosing inborn errors of metabolism

Research paper thumbnail of MS-DIAL 5 multimodal mass spectrometry data mining unveils lipidome complexities

bioRxiv (Cold Spring Harbor Laboratory), Feb 8, 2024

Lipidomics and metabolomics communities comprise various informatics tools; however, software pro... more Lipidomics and metabolomics communities comprise various informatics tools; however, software programs that can handle multimodal mass spectrometry (MS) data with structural annotations guided by the Lipidomics Standards Initiative are limited. Here, we provide MS-DIAL 5 to facilitate the in-depth structural elucidation of lipids through electron-activated dissociation (EAD)-based tandem MS, as well as determine their molecular localization through MS imaging (MSI) data using a species/tissue-specific lipidome database containing the predicted collision-cross section (CCS) values. With the optimized EAD settings using 14 eV kinetic energy conditions, the program correctly delineated the lipid structures based on EAD-MS/MS data from 96.4% of authentic standards. Our workflow was showcased by annotating the sn-and double-bond positions of eye-specific phosphatidylcholine molecules containing very-longchain polyunsaturated fatty acids (VLC-PUFAs), characterized as PC n-3-VLC-PUFA/FA. Using MSI data from the eye and HeLa cells supplemented with n-3-VLC-PUFA, we identified glycerol 3-phosphate (G3P) acyltransferase (GPAT) as an enzyme candidate responsible for incorporating n-3 VLC-PUFAs into the sn-1 position of phospholipids in mammalian cells, which was confirmed using recombinant proteins in a cell-free system. Therefore, the MS-DIAL 5 environment, combined with optimized MS data acquisition methods, facilitates a better understanding of lipid structures and their localization, offering novel insights into lipid biology. .

Research paper thumbnail of MS-DIAL 5 multimodal mass spectrometry data mining unveils lipidome complexities

bioRxiv (Cold Spring Harbor Laboratory), Feb 8, 2024

Lipidomics and metabolomics communities comprise various informatics tools; however, software pro... more Lipidomics and metabolomics communities comprise various informatics tools; however, software programs that can handle multimodal mass spectrometry (MS) data with structural annotations guided by the Lipidomics Standards Initiative are limited. Here, we provide MS-DIAL 5 to facilitate the in-depth structural elucidation of lipids through electron-activated dissociation (EAD)-based tandem MS, as well as determine their molecular localization through MS imaging (MSI) data using a species/tissue-specific lipidome database containing the predicted collision-cross section (CCS) values. With the optimized EAD settings using 14 eV kinetic energy conditions, the program correctly delineated the lipid structures based on EAD-MS/MS data from 96.4% of authentic standards. Our workflow was showcased by annotating the sn-and double-bond positions of eye-specific phosphatidylcholine molecules containing very-longchain polyunsaturated fatty acids (VLC-PUFAs), characterized as PC n-3-VLC-PUFA/FA. Using MSI data from the eye and HeLa cells supplemented with n-3-VLC-PUFA, we identified glycerol 3-phosphate (G3P) acyltransferase (GPAT) as an enzyme candidate responsible for incorporating n-3 VLC-PUFAs into the sn-1 position of phospholipids in mammalian cells, which was confirmed using recombinant proteins in a cell-free system. Therefore, the MS-DIAL 5 environment, combined with optimized MS data acquisition methods, facilitates a better understanding of lipid structures and their localization, offering novel insights into lipid biology. .

Research paper thumbnail of Parallel Metabolomics and Lipidomics of a PSMA/GCPII Deficient Mouse Model Reveal Alteration of NAAG Levels and Brain Lipid Composition

ACS chemical neuroscience, Feb 20, 2024

Research paper thumbnail of Wide metabolite coverage LC-MS/MS assay for the diagnosis of inherited metabolic disorders in urine

Research paper thumbnail of Patients with Neurodegenerative Proteinopathies Exhibit Altered Tryptophan Metabolism in the Serum and Cerebrospinal Fluid

ACS Chemical Neuroscience, Jan 8, 2024

Research paper thumbnail of Alterations in lipidome profiles distinguish early-onset hyperuricemia, gout, and the effect of urate-lowering treatment

Research paper thumbnail of Systematic Comparison of Advanced Network Analysis and Visualization of Lipidomics Data

Lecture Notes in Computer Science, 2023

Research paper thumbnail of Changes in lipid metabolism track with the progression of neurofibrillary pathology in tauopathies

BackgroundAbnormal aggregation of tau protein that leads to brain inclusions is a common feature ... more BackgroundAbnormal aggregation of tau protein that leads to brain inclusions is a common feature of neurodegenerative disorders called tauopathies. Recent evidence suggests the involvement of lipid metabolic deregulations in the pathogenesis of tauopathies. However, the role of tau protein in the regulation of lipid metabolism is much less characterized and not well understood.MethodsWe used a transgenic rat model for tauopathy to reveal metabolic alterations induced by neurofibrillary pathology. Transgenic rats express a tau fragment truncated at the N-and C-terminals. For phenotypic profiling, we performed targeted metabolomic and lipidomic analysis of brain tissue, CSF, and plasma, based on the LC-MS platform. To monitor disease progression, we employed samples from transgenic and control rats aged 4, 6, 8, 10, 12, and 14 months. To study neuron-glia interplay in lipidome changes induced by pathological tau we used well well-established multicomponent cell model system. Univariat...

Research paper thumbnail of Selective pivot logratio coordinates for partial least squares discriminant analysis modelling with applications in metabolomics

Research paper thumbnail of Rapid and efficient LC-MS/MS diagnosis of inherited metabolic disorders: a semi-automated workflow for analysis of organic acids, acylglycines, and acylcarnitines in urine

Clinical Chemistry and Laboratory Medicine (CCLM)

Objectives The analysis of organic acids in urine is an important part of the diagnosis of inheri... more Objectives The analysis of organic acids in urine is an important part of the diagnosis of inherited metabolic disorders (IMDs), for which gas chromatography coupled with mass spectrometry is still predominantly used. Methods Ultra-performance liquid chromatography-tandem mass spectrometry (LC-MS/MS) assay for urinary organic acids, acylcarnitines and acylglycines was developed and validated. Sample preparation consists only of dilution and the addition of internal standards. Raw data processing is quick and easy using selective scheduled multiple reaction monitoring mode. A robust standardised value calculation as a data transformation together with advanced automatic visualisation tools are applied for easy evaluation of complex data. Results The developed method covers 146 biomarkers consisting of organic acids (n=99), acylglycines (n=15) and acylcarnitines (n=32) including all clinically important isomeric compounds present. Linearity with r2>0.98 for 118 analytes, inter-day ...

Research paper thumbnail of Clinical lipidomics in the era of the big data

Clinical Chemistry and Laboratory Medicine (CCLM)

Lipidomics as a branch of metabolomics provides unique information on the complex lipid profile i... more Lipidomics as a branch of metabolomics provides unique information on the complex lipid profile in biological materials. In clinically focused studies, hundreds of lipids together with available clinical information proved to be an effective tool in the discovery of biomarkers and understanding of pathobiochemistry. However, despite the introduction of lipidomics nearly twenty years ago, only dozens of big data studies using clinical lipidomics have been published to date. In this review, we discuss the lipidomics workflow, statistical tools, and the challenges of standartisation. The consequent summary divided into major clinical areas of cardiovascular disease, cancer, diabetes mellitus, neurodegenerative and liver diseases is demonstrating the importance of clinical lipidomics. In these publications, the potential of lipidomics for prediction, diagnosis or finding new targets for the treatment of selected diseases can be seen. The first of these results have already been implemen...

Research paper thumbnail of Altered plasma, urine, and tissue profiles of sulfatides and sphingomyelins in patients with renal cell carcinoma

Renal cell carcinoma (RCC) represents the most common type of kidney cancer and, despite the prog... more Renal cell carcinoma (RCC) represents the most common type of kidney cancer and, despite the progress of surgical and medical management, is associated with high mortality. In this study, we demonstrate that RCC-related processes change body fluids sphingolipid concentrations, which may be used to monitor tumor presence using non-invasive lipid-based blood and urine tests. We investigate 674 plasma, urine, and tissue samples from 369 RCC patients and controls. For the first time, we show the significant concentration changes of low abundant sulfatides in plasma and urine of RCC patients. Elevated concentrations of lactosylsulfatides, decreased concentrations of sphingomyelins with long saturated N-fatty acyls and sulfatides with hydroxylated fatty acyls are the crucial alternations in RCC. These changes are stage-dependent and are more emphasized in late-stage RCC. Similar trends in body fluids and tissues indicate that RCC widely influences lipid metabolism and highlights the poten...

Research paper thumbnail of SLIDE—Novel Approach to Apocrine Sweat Sampling for Lipid Profiling in Healthy Individuals

International Journal of Molecular Sciences, 2021

We designed a concept of 3D-printed attachment with porous glass filter disks—SLIDE (Sweat sampLI... more We designed a concept of 3D-printed attachment with porous glass filter disks—SLIDE (Sweat sampLIng DevicE) for easy sampling of apocrine sweat. By applying advanced mass spectrometry coupled with the liquid chromatography technique, the complex lipid profiles were measured to evaluate the reproducibility and robustness of this novel approach. Moreover, our in-depth statistical evaluation of the data provided an insight into the potential use of apocrine sweat as a novel and diagnostically relevant biofluid for clinical analyses. Data transformation using probabilistic quotient normalization (PQN) significantly improved the analytical characteristics and overcame the ‘sample dilution issue’ of the sampling. The lipidomic content of apocrine sweat from healthy subjects was described in terms of identification and quantitation. A total of 240 lipids across 15 classes were identified. The lipid concentrations varied from 10−10 to 10−4 mol/L. The most numerous class of lipids were ceram...

Research paper thumbnail of Lipidomic and metabolomic analysis reveals changes in biochemical pathways for non-small cell lung cancer tissues

Biochimica et Biophysica Acta (BBA) - Molecular and Cell Biology of Lipids

Research paper thumbnail of Evaluation of the Determination of Dabigatran, Rivaroxaban, and Apixaban in Lupus Anticoagulant-Positive Patients

Diagnostics

Background: The effect of direct oral anticoagulants (DOAC) on laboratory tests dependent on the ... more Background: The effect of direct oral anticoagulants (DOAC) on laboratory tests dependent on the production of their targets, factor IIa and factor Xa, is a well-known problem and can cause both false positive and negative results. In particular, the situation in patients who develop lupus anticoagulant (LA) antibodies is highly complex. To evaluate the effectiveness of DOAC therapy in lupus-positive patients, 31 samples were enrolled in this retrospective study. All patient samples were spiked with three types of DOAC (dabigatran, DABI; rivaroxaban, RIVA; and apixaban, API) in a concentration that significantly influenced the screening test for LA and thus can mask the presence of LA. Subsequently, the DOAC was always unbound by the DOAC-Stop procedure. DOAC levels before and after binding were determined by functional assays, followed by liquid chromatography coupled with mass spectrometry (LC-MS) analysis. Methods: The determination of DOAC levels was performed by direct thrombin...

Research paper thumbnail of Novel LC-MS tools for diagnosing inborn errors of metabolism