Assessment of the effects of repeated freeze thawing and extended bench top processing of plasma samples using untargeted metabolomics

Metabolomics ◽  
2021 ◽  
Vol 17 (3) ◽  
Author(s):  
Kelli Goodman ◽  
Matthew Mitchell ◽  
Anne M. Evans ◽  
Luke A. D. Miller ◽  
Lisa Ford ◽  
...  
Keyword(s):  
Untargeted Metabolomics ◽  
Plasma Samples

scholarly journals A Metabolomics Workflow for Analyzing Complex Biological Samples Using a Combined Method of Untargeted and Target-List Based Approaches

Metabolites ◽  
2020 ◽  
Vol 10 (9) ◽  
pp. 342 ◽  
Author(s):  
Thomas Züllig ◽  
Martina Zandl-Lang ◽  
Martin Trötzmüller ◽  
Jürgen Hartler ◽  
Barbara Plecko ◽  
...  
Keyword(s):  
Biological Samples ◽  
Chemical Properties ◽  
Software Tool ◽  
Untargeted Metabolomics ◽  
Plasma Samples ◽  
Target List ◽  
Manual Curation ◽  
Relative Standard ◽  
Wide Range ◽  
Targeted Approach

In the highly dynamic field of metabolomics, we have developed a method for the analysis of hydrophilic metabolites in various biological samples. Therefore, we used hydrophilic interaction chromatography (HILIC) for separation, combined with a high-resolution mass spectrometer (MS) with the aim of separating and analyzing a wide range of compounds. We used 41 reference standards with different chemical properties to develop an optimal chromatographic separation. MS analysis was performed with a set of pooled biological samples human cerebrospinal fluid (CSF), and human plasma. The raw data was processed in a first step with Compound Discoverer 3.1 (CD), a software tool for untargeted metabolomics with the aim to create a list of unknown compounds. In a second step, we combined the results obtained with our internally analyzed reference standard list to process the data along with the Lipid Data Analyzer 2.6 (LDA), a software tool for a targeted approach. In order to demonstrate the advantages of this combined target-list based and untargeted approach, we not only compared the relative standard deviation (%RSD) of the technical replicas of pooled plasma samples (n = 5) and pooled CSF samples (n = 3) with the results from CD, but also with XCMS Online, a well-known software tool for untargeted metabolomics studies. As a result of this study we could demonstrate with our HILIC-MS method that all standards could be either separated by chromatography, including isobaric leucine and isoleucine or with MS by different mass. We also showed that this combined approach benefits from improved precision compared to well-known metabolomics software tools such as CD and XCMS online. Within the pooled plasma samples processed by LDA 68% of the detected compounds had a %RSD of less than 25%, compared to CD and XCMS online (57% and 55%). The improvements of precision in the pooled CSF samples were even more pronounced, 83% had a %RSD of less than 25% compared to CD and XCMS online (28% and 8% compounds detected). Particularly for low concentration samples, this method showed a more precise peak area integration with its 3D algorithm and with the benefits of the LDAs graphical user interface for fast and easy manual curation of peak integration. The here-described method has the advantage that manual curation for larger batch measurements remains minimal due to the target list containing the information obtained by an untargeted approach.

scholarly journals Metabolomics Approach for Validation of Self-Reported Ibuprofen and Acetaminophen Use

Metabolites ◽  
2018 ◽  
Vol 8 (4) ◽  
pp. 55
Author(s):  
Kristine Dennis ◽  
Brian Carter ◽  
Susan Gapstur ◽  
Victoria Stevens
Keyword(s):  
Mass Spectrometry ◽  
Self Report ◽  
Untargeted Metabolomics ◽  
Plasma Samples ◽  
Serum Samples ◽  
Over The Counter ◽  
Blood Samples ◽  
Cutoff Value ◽  
Analgesic Use ◽  
Metabolomics Analysis

Over-the-counter analgesic use is common and is typically assessed through self-report; therefore, it is subject to misclassification. Detection of drug metabolites in biofluids offers a viable tool for validating self-reported analgesic use. Thus, the aim of this study was to determine the utility of a metabolomics approach for the validation of acetaminophen and ibuprofen use in blood samples. Untargeted mass spectrometry-based metabolomics analysis was conducted in serum samples from 1547 women and plasma samples from 556 men. The presence of two metabolites each for acetaminophen and ibuprofen at levels at or above a defined cutoff value was used to determine concordance with self-reported use. For acetaminophen use based on the presence of both acetaminophen and acetamidophenylglucuronide, concordance was 98.5–100% among individuals reporting use today, and 79.8–91.4% for those reporting never or rare use. Ibuprofen use based on the presence of both carboxyibuprofen and hydroxyibuprofen resulted in concordance of 51.3–52.5% for individuals reporting use today and 99.4–100% for those reporting never or rare use. Our findings suggest that an untargeted metabolomics approach in blood samples may be useful for validating self-reported acetaminophen use. However, this approach appears unlikely to be suitable for validating ibuprofen use.

scholarly journals Untargeted Metabolomics for Metabolic Diagnostic Screening with Automated Data Interpretation Using a Knowledge-Based Algorithm

2020 ◽  
Vol 21 (3) ◽  
pp. 979 ◽  
Author(s):  
Hanneke A. Haijes ◽  
Maria van der Ham ◽  
Hubertus C.M.T. Prinsen ◽  
Melissa H. Broeks ◽  
Peter M. van Hasselt ◽  
...  
Keyword(s):  
High Resolution Mass Spectrometry ◽  
Correct Diagnosis ◽  
Diagnostic Algorithm ◽  
Data Interpretation ◽  
Dried Blood Spots ◽  
Untargeted Metabolomics ◽  
Plasma Samples ◽  
Inborn Errors ◽  
Diagnostic Screening ◽  
Knowledge Based

Untargeted metabolomics may become a standard approach to address diagnostic requests, but, at present, data interpretation is very labor-intensive. To facilitate its implementation in metabolic diagnostic screening, we developed a method for automated data interpretation that preselects the most likely inborn errors of metabolism (IEM). The input parameters of the knowledge-based algorithm were (1) weight scores assigned to 268 unique metabolites for 119 different IEM based on literature and expert opinion, and (2) metabolite Z-scores and ranks based on direct-infusion high resolution mass spectrometry. The output was a ranked list of differential diagnoses (DD) per sample. The algorithm was first optimized using a training set of 110 dried blood spots (DBS) comprising 23 different IEM and 86 plasma samples comprising 21 different IEM. Further optimization was performed using a set of 96 DBS consisting of 53 different IEM. The diagnostic value was validated in a set of 115 plasma samples, which included 58 different IEM and resulted in the correct diagnosis being included in the DD of 72% of the samples, comprising 44 different IEM. The median length of the DD was 10 IEM, and the correct diagnosis ranked first in 37% of the samples. Here, we demonstrate the accuracy of the diagnostic algorithm in preselecting the most likely IEM, based on the untargeted metabolomics of a single sample. We show, as a proof of principle, that automated data interpretation has the potential to facilitate the implementation of untargeted metabolomics for metabolic diagnostic screening, and we provide suggestions for further optimization of the algorithm to improve diagnostic accuracy.

scholarly journals Untargeted metabolomics towards understanding molecular mechanisms of pulmonary arterial hypertension

2021 ◽  
Vol 42 (Supplement_1) ◽  
Author(s):  
R Wawrzyniak ◽  
A Dabrowska-Kugacka ◽  
S Macioszek ◽  
I Gockowska ◽  
M Biesemans ◽  
...  
Keyword(s):  
Lactic Acid ◽  
Pulmonary Arterial Hypertension ◽  
Arterial Hypertension ◽  
Molecular Mechanisms ◽  
Statistical Tests ◽  
Metabolic Changes ◽  
Untargeted Metabolomics ◽  
Control Group ◽  
Plasma Samples ◽  
Pulmonary Arterial

Abstract Background Pulmonary hypertension constitutes a rare disease characterized by a severe development and a high risk of premature death. One of its main clinical types is pulmonary arterial hypertension (PAH), in which the highest percentage of patients are affected by idiopathic PAH. The pathogenesis of this disease has not completely been discovered and elucidated so far, and non-specific clinical symptoms make the diagnosis of PAH a serious problem. Currently, PAH is confirmed with invasive examination based on right heart catheterization. Purpose The main aim of the study was to evaluate and compare both plasma and urine fingerprints of PAH patients and control group with the use of an untargeted metabolomics approach. The study also focused on correlation analysis between the observed metabolic changes and the clinical parameters to select specific indicators of PAH disease. Methods An untargeted metabolomics approach was applied to the plasma and urine samples with the use of gas chromatography coupled to triple quadrupole mass spectrometry (GC-QqQ/MS) and advanced statistical tests were applied to evaluate the potential metabolic indicators of PAH. The PAH patients (n=40) and healthy controls (n=39) were matched for age, sex, BMI and included in the study. The obtained raw datasets were properly processed (data deconvolution, signal correction using QCSVR method and PQN normalization) and subsequently subjected to uni- and multivariate statistical tests (Student's t-test, Welch's test, U Mann-Whitney test, PCA and OPLS-DA). The identification of the statistically significant metabolites was performed using universal libraries, such as: Fiehn's and NIST11. Results The statistically significant metabolites (n=10 and 11 for urine and plasma samples, respectively)originate from various biochemical pathways associated with the carbohydrate, amino acid, lipid, fatty acid and pyrimidine metabolism. The metabolic changes observed in the urine samples of PAH patients (compared to the control group) included different concentrations in: threonic acid, hippuric acid, acetic acid, sorbitol, butanoic acid and propionic acid. The metabolic alterations in the plasma samples covered changes in the levels of valine, leucine, lactic acid, hydroxybutanoic acid, nonanoic acid, cholesterol and octadecanoic acid. Metabolites representing the highest correlation with mean pulmonary arterial pressure include, for instance: propionic acid (r=0.85), valine (r=0.75) and lactic acid (r=0.63) Conclusions The observed metabolic changes are related to various biological processes that are disturbed in the course of PAH, namely: proliferation of pulmonary vascular cells or the functions of cardiomyocytes and the right ventricle of the heart. The obtained results confirmed the potential of a metabolomics approach to uncover and explain the underlying molecular mechanisms of PAH. FUNDunding Acknowledgement Type of funding sources: Public grant(s) – National budget only. Main funding source(s): Ministry of Science and High Education of Poland

Stability of antioxidant vitamins in whole human blood during overnight storage at 4°C and frozen storage up to 6 months

2018 ◽  
Vol 88 (3-4) ◽  
pp. 151-157 ◽  
Author(s):  
Scott W. Leonard ◽  
Gerd Bobe ◽  
Maret G. Traber
Keyword(s):  
Ascorbic Acid ◽  
Whole Blood ◽  
Healthy Subjects ◽  
Frozen Storage ◽  
Blood Collection ◽  
Plasma Samples ◽  
Optimal Conditions ◽  
Plasma Ascorbic Acid ◽  
Blood Samples ◽  
Sample Handling

Abstract. To determine optimal conditions for blood collection during clinical trials, where sample handling logistics might preclude prompt separation of erythrocytes from plasma, healthy subjects (n=8, 6 M/2F) were recruited and non-fasting blood samples were collected into tubes containing different anticoagulants (ethylenediaminetetra-acetic acid (EDTA), Li-heparin or Na-heparin). We hypothesized that heparin, but not EDTA, would effectively protect plasma tocopherols, ascorbic acid, and vitamin E catabolites (α- and γ-CEHC) from oxidative damage. To test this hypothesis, one set of tubes was processed immediately and plasma samples were stored at −80°C, while the other set was stored at 4°C and processed the following morning (~30 hours) and analyzed, or the samples were analyzed after 6 months of storage. Plasma ascorbic acid, as measured using HPLC with electrochemical detection (LC-ECD) decreased by 75% with overnight storage using EDTA as an anticoagulant, but was unchanged when heparin was used. Neither time prior to processing, nor anticoagulant, had any significant effects upon plasma α- or γ-tocopherols or α- or γ-CEHC concentrations. α- and γ-tocopherol concentrations remained unchanged after 6 months of storage at −80°C, when measured using either LC-ECD or LC/mass spectrometry. Thus, refrigeration of whole blood at 4°C overnight does not change plasma α- or γ-tocopherol concentrations or their catabolites. Ascorbic acid is unstable in whole blood when EDTA is used as an anticoagulant, but when whole blood is collected with heparin, it can be stored overnight and subsequently processed.

Factor XII Determinations in the Presence and Absence of Phospholipid Antibodies

1998 ◽  
Vol 79 (01) ◽  
pp. 87-90 ◽  
Author(s):  
D. W. Jones ◽  
M. Winter ◽  
M. J. Gallimore
Keyword(s):  
Lower Limit ◽  
Lupus Anticoagulant ◽  
Factor Xii ◽  
Chromogenic Substrate ◽  
Plasma Samples ◽  
Presence And Absence ◽  
Lower Limit Of Normal

SummaryFactor XII (FXII) levels were determined in plasma samples from 29 normal donors, 10 patients with inherited FXII deficiency (all lupus anticoagulant [LA] negative) and 67 LA positive patients, using clotting (FXIIct), chromogenic substrate (FXIIcs) and immunochemical (FXIIag) assays. Excellent correlations were obtained in the three FXII assays with the LA negative samples and between the FXIIcs and FXIIag assays in the LA positive samples. Correlations between both the FXIIcs and FXIIag with FXIIct in the LA positive patients were poor. Of 67 LA positive samples studied, 25 (37.3%) showed lower values in the FXIIct assay; 13 (19.4%) of these patients were pseudo FXII deficient with values of FXII below the lower limit of normal.These results indicate that a diagnosis of FXII deficiency can be made inappropriately in the presence of phospholipid antibodies and that such a diagnosis should not be made by FXIIct assay alone.

Fibrinogen-Fibrin-Related Antigen Pattern in Human Blood

1974 ◽  
Vol 32 (02/03) ◽  
pp. 266-276
Author(s):  
Carl D. Jacobsen ◽  
John C. Hoak ◽  
Kenneth K. WU ◽  
Glenna L. Fry
Keyword(s):  
Human Blood ◽  
Plasma Samples

SummaryIn serum from patients with DIC at least 3 different FR-antigenic components could be found. It was difficult to demonstrate these components in the corresponding plasma samples. It is possible that a portion of these antigens formed as a result of in vitro clotting despite the presence of proteolytic inhibitors. These results suggest that the interpretation of “increased split products in serum” may be more complex than current concepts indicate.

In Vitro Effects of Urokinase — Prevention by Different Inhibitors

1990 ◽  
Vol 64 (03) ◽  
pp. 402-406 ◽  
Author(s):  
M D Oethinger ◽  
E Seifried
Keyword(s):  
In Vitro Study ◽  
Thrombin Time ◽  
Plasma Samples ◽  
Temperature Dependent ◽  
Chloromethyl Ketone ◽  
Control Value ◽  
Dose Time ◽  
In Vitro Effects ◽  
Full Protection

SummaryThe present in vitro study investigated dose-, time- and temperature-dependent effects of two-chain urokinase plasminogen activato(u-PA, urokinase) on normal citrated plasma. When 10 μg/ml u-PA wereadded to pooled normal plasma and incubated for 30 min at an ambient temperature (25° C), α2-antiplas-min decreased to 8% of the control value. Incubation on ice yielded a decrease to 45% of control,whereas α2-antiplasmin was fully consumed at 37° C. Fibrinogen and plasminogen fell to 46% and 39%, respectively, after a 30 min incubation at 25° C. Thrombin time prolonged to 190% of control.Various inhibitors were studied with respect to their suitability and efficacy to prevent these in vitro effects. Aprotinin exhibited a good protective effect on fibrinogen at concentrations exceeding 500 KlU/ml plasma. Its use, however, was limited due to interferences with some haemostatic assays. We could demonstrate that L-Glutamyl-L-Glycyl-L-Arginyl chloromethyl ketone (GGACK) and a specific polyclonal anti-u-PA-antibody (anti-u-PA-IgG) effectively inhibited urokinase-induced plasmin generation without interfering with haemostatic assays. The anti-u-PA-antibody afforded full protection ofα2-antiplasmin at therapeutic levels of u-PA.It is concluded that u-PA in plasma samples from patients during thrombolytic therapy may induce in vitro effects which should be prevented by the use of a suitable inhibitor such as GGACK or specific anti-u-PA-antibody.

Immunoreactivity of Tissue Plasminogen Activator and of Its Inhibitor Complexes

1989 ◽  
Vol 61 (03) ◽  
pp. 409-414 ◽  
Author(s):  
M Rånby ◽  
G Nguyen ◽  
P Y Scarabin ◽  
M Samama
Keyword(s):  
Plasminogen Activator ◽  
Tissue Plasminogen Activator ◽  
Degradation Products ◽  
Gel Filtration ◽  
Free Form ◽  
Enzyme Linked Immunosorbent Assay ◽  
Plasma Samples ◽  
Significant Difference ◽  
Tissue Plasminogen ◽  
Pai 1

SummaryAn enzyme linked immunosorbent assay (ELISA) based on goat polyclonal antibodies against human tissue plasminogen activator (tPA) was evaluated. The relative immunoreactivity of tPA in free form and tPA in complex with inhibitors was estimated by ELISA and found to be 100, 74, 94, 92 and 8l% for free tPA and tPA in complex with PAI-1, PAI-2, α2-antiplasmin and C1-inhibitor, respectively. Addition of tPA to PAI-1 rich plasma resulted in rapid and total loss of tPA activity without detectable loss of ELISA response, indicating an immunoreactivity of tPA in tPA/PAI-1 complex of about l00%. Three different treatments of citrated plasma samples (acidification/reneutralization, addition of 5 mM EDTA or of 0.5 M lysine) prior to determination by ELISA all resulted in increased tPA levels. The fact that the increase was equally large in all three cases along with good analytical recovery of tPA added to plasffi, supported the notion that all tPA antigen present in plasma samples is measured by the ELISA. Analysis by ELISA of fractions obtained by gel filtration of plasma from a patient undergoing tPA treatment identified tPA/inhibitor complexes and free tPA but no low molecular weight degradation products of tPA. Determinations of tPA antigen were made at seven French clinical laboratories on coded and randomized plasma samples with known tPA antigen content. For undiluted samples there was no significant difference between the tPA levels found and those known to be present. The between-assay coefficient of variation was 7 to 10%. In conclusion, the ELISA appeared suited for determination of total tPA antigen in human plasma samples.

Effect of Aspirin on the Thrombelastogram of Human Blood

1973 ◽  
Vol 30 (03) ◽  
pp. 494-498 ◽  
Author(s):  
G de Gaetano ◽  
J Vermylen
Keyword(s):  
Oral Dose ◽  
Single Oral Dose ◽  
Platelet Function ◽  
Human Blood ◽  
Platelet Rich Plasma ◽  
Plasma Samples ◽  
Release Reaction ◽  
Platelet Release

SummaryThrombelastograms of both native blood and re-calcified platelet-rich plasma samples taken from subjects given a single oral dose of aspirin (1 gram) were not significantly different from the pretreatment recordings. Aspirin also did not modify the thrombelastogram when preincubated in vitro with platelet-rich plasma at concentrations inhibiting the platelet “release reaction” by collagen. Thrombelastography therefore cannot evaluate the effect of aspirin on platelet function.

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