Publications by authors named "Frank Vitzthum"

17 Publications

  • Page 1 of 1

Factor VII-activating protease: sex-related association with coronary artery calcification.

Blood Coagul Fibrinolysis 2017 Oct;28(7):558-563

aDepartment of Cardiology, Hospital of South West Denmark, Esbjerg and Institute of Regional Health Research, University of Southern Denmark bDepartment of Clinical Biochemistry, Hospital of South West Denmark, Esbjerg and Unit for Thrombosis Research, Department of Public Health, University of Southern Denmark cDepartment of Cardiology, Skejby University Hospital, Aarhus, Denmark dDepartment of Cardiology, Odense University Hospital, Odense, Denmark eSiemens Healthcare Diagnostics Inc., Tarry town, NY, USA fSiemens Healthcare Diagnostics Products GmbH., Marburg, Germany.

: Factor VII-activating protease (FSAP) may regulate development of cardiovascular disease (CVD). We evaluated sex differences in FSAP measures and examined the association between FSAP and coronary artery calcification (CAC) in a middle-aged population. Participants were randomly selected citizens aged 50 or 60 without CVD, diabetes mellitus, Marburg I polymorphism, or hormone replacement therapy (HRT). FSAP protein concentration (total FSAP), FSAP urokinase-activating capacity (FSAP GP), and FSAP GP/total FSAP (specific FSAP activity) were measured. Cardiac computed tomography (CT) determined the Agatston score, dividing the study population in three groups: (1) Agatston score = 0 U, (2) Agatston score = 1-99 U, or (3) Agatston score more than 99 U. A total of 134 women and 116 men were included. Total FSAP, FSAP GP, and specific FSAP activity were independently higher in women (97.4%, 81.1%, 0.84, respectively) compared with men (87.5%, 68.7%, 0.79, respectively) (P < 0.001). In women, total FSAP was significantly different between (3) Agatston score (111.5%) and (1) Agatston score (95.4%), respectively, (2) Agatston score (96.8%), (P < 0.05). Also, the specific activity of FSAP was significantly different between (3) Agatston score (0.77) and (1) Agatston score (0.85), respectively, (2) Agatston score (0.86) (P < 0.05). No difference in FSAP measures was observed in men. FSAP measures are higher in women compared with age-matched men. The extent of CAC in women is positively associated with total FSAP, but negatively associated with the specific activity of FSAP suggesting that FSAP may play a role in the evolution of CVD in women.
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http://dx.doi.org/10.1097/MBC.0000000000000640DOI Listing
October 2017

Plasma factor VII-activating protease is increased by oral contraceptives and induces factor VII activation in-vivo.

Thromb Res 2011 Nov 6;128(5):e67-72. Epub 2011 Jul 6.

Unit for Thrombosis Research, Institute of Public Health, University of Southern Denmark, Esbjerg, Denmark.

Unlabelled: Oral contraceptive (OC) use influences the hemostatic system significantly and is a risk factor for development of cardiovascular disease. Factor VII-activating protease (FSAP) has potential effects on hemostasis. The 1601GA genotype of the 1601G/A polymorphism in the FSAP gene expresses a FSAP alloenzyme with reduced pro-fibrinolytic activity. Presently, we address whether OC use and OC formulation affect FSAP measures in human blood. Healthy women (n=588) were allocated to six cycles of OCs with estrogen contents of 20 μg (n=158), 30 μg (n=284), 35 μg (n=79) or 50 μg (n=67) combined with various progestins. FSAP genotypes, FSAP and factor VII (FVII) plasma measures were assessed at baseline and after 6 cycles of OC. The 1601GA genotype was present in 49 (8.3%) of the women and was associated with significantly reduced levels of FSAP (P≤0.001). OC use increased FSAP antigen by 25% and FSAP activity by 59% (P<0.001). The FSAP increase was comparable in the seven different OC treatment groups (P>0.05). The relative increase in FSAP activity was significantly higher in women carrying the 1601GG genotype (63%) than in women carrying 1601GA genotype (50%) (P=0.01) and was associated with an increased activation of FVII.

In Conclusion: OC use increases the plasma measures of FSAP. The increase in FSAP is comparable in the seven OC-groups studied but is more significant in women carrying the 1601GG genotype than in women with the 1601GA genotype and results in increased activation of FVII suggesting that FSAP-induced activation of FVII takes place in-vivo and not only in-vitro as hitherto described.
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http://dx.doi.org/10.1016/j.thromres.2011.06.013DOI Listing
November 2011

Direct chromogenic substrate immuno-capture activity assay for testing of factor VII-activating protease.

Clin Chem Lab Med 2011 Jul 13;49(7):1199-204. Epub 2011 Jun 13.

Siemens Healthcare Diagnostics Products GmbH, Marburg, Germany.

Background: The Marburg I (MRI) single nucleotide polymorphism (SNP) of the factor VII-activating protease (FSAP) gene has been associated with thrombophilia and atherosclerotic disease. PCR is used to detect the SNP. Also, the specific FSAP activity to cleave single-chain urokinase-type plasminogen activator (scu-PA) serves as a surrogate for PCR testing. Development of further assays is indicated in order to increase testing opportunities for future studies.

Methods: A direct chromogenic substrate immuno-capture activity assay for FSAP (FSAP dcs activity assay) was established. Performance characteristics of the FSAP dcs activity assay were compared to the FSAP scu-PA activity assay.

Results: The FSAP dcs activity assay detects FSAP activity from 25% to 150% of the norm. Total CVs ranged from 6% to 10% for FSAP wild type samples and 9%-18% for MRI samples. Correlation between the FSAP dcs and scu-PA activity assays was low (R=0.7). The FSAP dcs activity determined the presence of the MRI FSAP alloenzyme with a diagnostic sensitivity and specificity of 100% [95% confidence interval (CI): 89.6%-100%] and 96.2% (95% CI: 93.2%-97.4%), respectively, whereas the specific FSAP dcs activity increased specificity to 99.0% (95% CI: 97.2%-99.6%).

Conclusions: The specific FSAP dcs activity represents a reliable method for the detection of the FSAP MRI alloenzyme. Due to the limited correlation between the FSAP dcs and scu-PA activity assays, these different measurands may exhibit different utility in research and clinical applications. Thus, the FSAP dcs activity assay can represent a valuable complement or alternative for FSAP testing in future studies.
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http://dx.doi.org/10.1515/CCLM.2011.199DOI Listing
July 2011

Coagulation assays based on the Luminescent Oxygen Channeling Immunoassay technology 1).

Clin Chem Lab Med 2011 May 3;49(5):855-60. Epub 2011 Feb 3.

Siemens Healthcare Diagnostics Products GmbH, Marburg, Germany.

Background: The Luminescent Oxygen Channeling Immunoassay (LOCI) technology is a well-established homogeneous assay format that allows for fast, accurate, and highly sensitive quantitation of analytes. We set out to develop and prove a novel concept to establish a LOCI format that should principally allow for the determination of the activity of coagulation factors and anticoagulants of clinical relevance.

Methods: The concept is based on the linkage of LOCI nano-beads by a peptide that can be cleaved by a coagulation factor. To prove the principle, we used a peptide that can be cleaved by thrombin.

Results: We were able to show that coagulation activation of plasma or whole blood samples that were combined with the LOCI components degraded the thrombin-sensitive peptide and consequently, led to a reduction of the LOCI signal. Signal reduction was proportional to the amount of active thrombin generated. The research prototype assay allowed for the detection of factor deficiencies in both the extrinsic and intrinsic coagulation pathways, and for the quantification of hirudin, a direct thrombin inhibitor.

Conclusions: Taken together, we conclude that the LOCI technology has the potential for extension to functional blood coagulation assays.
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http://dx.doi.org/10.1515/CCLM.2011.132DOI Listing
May 2011

Quantification of coagulation factor XIII activity by a thio-NADH based assay using factor XIII immuno-depleted plasma as a diluent for calibration.

Clin Chem Lab Med 2010 Dec 10;48(12):1739-43. Epub 2010 Sep 10.

Siemens Healthcare Diagnostics Products GmbH, Marburg, Germany.

Background: Accurate determination of factor XIII (FXIII) activity is crucial for replacement therapy. FXIII activity is typically determined using a coupled enzymatic reaction that measures nicotinamide adenine dinucleotide hydride (NADH) consumption at 340 nm.

Methods: Here, we describe the development of a prototype for a novel FXIII activity assay for detection at 405 nm by replacing NADH with thio-NADH, and the application of FXIII immuno-depleted plasma as a diluent for calibration.

Results: Performance data show up to two-fold lower susceptibility of the prototype assay to interferences from hemolyzed, icteric, and lipemic samples when compared to a NADH assay format. In addition, the use of FXIII immuno-depleted plasma as diluent for calibration improved recovery almost two-fold in the lower measurement range. The novel prototype assay correlates well with a conventional assay (r=0.98, y=0.99·x+2.17% FXIII, n=173).

Conclusions: The described prototype assay has the potential to (a) increase trueness of measurement of low levels of FXIII, (b) improve robustness due to reduction from interferences, and (c) can be used on a broad range of coagulation instruments due to its detection at 405 nm.
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http://dx.doi.org/10.1515/CCLM.2010.339DOI Listing
December 2010

Qualitative detection of the Marburg I alloenzyme of factor VII-activating protease by an immunoassay and its comparison to PCR testing.

Clin Chem Lab Med 2010 Dec 10;48(12):1745-9. Epub 2010 Sep 10.

Siemens Healthcare Diagnostics Products GmbH, Marburg, Germany.

Background: The Marburg I (MRI) single nucleotide polymorphism (SNP) of the factor VII-activating protease (FSAP) gene has been associated with thrombophilia, thromboembolism, atherosclerosis, and the incidence and progression of carotid stenosis. At present, MRI SNP testing is mainly performed using costly nucleic acid analysis. The ratio between FSAP activity and antigen concentrations in citrated plasma has been used to assess the FSAP genotype.

Methods: This article describes the development of a prototype ELISA for the detection of the MRI FSAP alloenzyme, and its correlation to FSAP genotypes to assess whether a positive MRI FSAP ELISA result may be used as a surrogate marker for the presence of the MRI SNP.

Results: ELISA results were correlated with FSAP genotypes from 523 blood donors measured using PCR. Diagnostic sensitivity and specificity of the assay for determination of the genotype were 100% (95% confidence interval [CI]: 93.36-100) and 99.79% (95% CI: 98.80-99.96), respectively. Maximum run-to-run, within-run, and total coefficients of variation were 7.8%, 7.9%, and 9.9%, respectively. No cross-reactivities with homologues of the MRI FSAP alloenzyme were observed. Test performance was not affected by typical interfering compounds.

Conclusions: The data demonstrate that an immunoassay applying antibodies specific to the MRI FSAP alloenzyme can provide sufficiently accurate detection of the MRI SNP. This will significantly simplify MRI FSAP testing, particularly in large cohorts.
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http://dx.doi.org/10.1515/CCLM.2010.334DOI Listing
December 2010

Development of high-throughput chemical extraction techniques and quantitative HPLC-MS/MS (SRM) assays for clinically relevant plasma proteins.

J Proteome Res 2010 Jan;9(1):333-40

Quotient Bioresearch Ltd, Newmarket Road, Fordham, Cambridgeshire CB7 5WW, United Kingdom.

The clinical application of targeted plasma protein analysis by selective reaction monitoring of peptides using LC-MS/MS requires the development of robust, inexpensive protein extraction techniques with the potential for high-throughput applications. We present the development of a novel mixed-mode solid phase extraction (SPE) technique for the removal of high abundance and high molecular weight proteins from plasma. This technique, coupled with fused-core HPLC-MS/MS analysis is compared to a previously developed extraction method to study a range of proteins in plasma, including routinely measured biomarkers of growth hormone action. To further validate this technique, it was used for the quantification of insulin-like growth factor I (IGF-I) levels and compared to a state-of-the-art immunoassay on a fully automated analyzer. Clinical reference materials were applied for method development to allow for further interlaboratory comparisons. The LC-MS/MS approach quantified IGF-I in plasma with an accuracy that is within the guidelines for macromolecular assays in a regulated laboratory environment. Furthermore, IGF-I levels determined using the SPE and ACN methods with LC-MS/MS analysis correlated well with the immunoassay results. This demonstrates the applicability of mixed-mode SPE coupled with fused-core HPLC-MS/MS to quantify plasma proteins with results suitable for clinical applications.
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http://dx.doi.org/10.1021/pr900658dDOI Listing
January 2010

Tests for the measurement of factor VII-activating protease (FSAP) activity and antigen levels in citrated plasma, their correlation to PCR testing, and utility for the detection of the Marburg I-polymorphism of FSAP.

Clin Chem Lab Med 2008 ;46(8):1109-16

Dade Behring Marburg GmbH, A Siemens Company, Marburg, Germany.

Background: The single nucleotide Marburg I (MRI) polymorphism of the factor VII-activating protease (FSAP) gene, the prourokinase-activating activity of FSAP, and antigen levels of FSAP in plasma have been associated with incidence and progression of carotid stenosis and venous thromboembolism. However, more information on the extent of these associations, potential further ones, and respective clinical utilities remain to be determined. At present, testing is performed mainly by PCR assays based on probes or SYBR Green I. Some studies include testing for antigen levels of total FSAP and its ability to activate prourokinase. To test large cohorts, it is beneficial to rely on assays that are cost-effective, reliable, easy to use, rapid to perform, and that may eventually be automated. In addition, it appears advantageous to use functional tests or tests that determine antigen levels as they may relate more closely to the phenotype than the genotype does.

Methods: Tests for the measurements of antigen levels of FSAP and its prourokinase-activating activity were improved and performance characteristics assessed. To determine the FSAP genotypes, an amplification created restriction site (ACRS) PCR test was developed.

Results: Key performance characteristics of the FSAP activity and antigen tests were as follows: measuring range: 350-1400 mPEU/mL and 1.8-120 ng/mL, total coefficients of variation (CV): 5%-20% and 5%-14%, within-run CV: 4%-11% and 2.3%-12%, and run-to-run CV: 2%-17% and 4.3%-8.3%, respectively. The ratio of the activity and antigen level of FSAP correctly identified the FSAP genotypes of 126 samples tested.

Conclusions: The ACRS PCR test is useful for laboratories that do not have the equipment to perform probe or SYBR Green I based real-time PCR. Furthermore, the tests developed for the determination of FSAP activity and antigen levels are convenient for determining clinical correlations, even for large population studies. The ratio of activity and antigen level of FSAP appears to be a promising and efficient alternative to molecular diagnostic techniques to detect the MRI polymorphism of FSAP.
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http://dx.doi.org/10.1515/CCLM.2008.218DOI Listing
October 2008

Factor VII-activating protease in patients with acute deep venous thrombosis.

Thromb Res 2008 18;122(6):848-53. Epub 2008 Apr 18.

Institute of Public Health, University of Southern Denmark, Niels Bohrs Vej 9, DK-6700 Esbjerg, Denmark.

Factor VII-activating protease (FSAP) is involved in haemostasis and inflammation. FSAP cleaves single chain urokinase-type plasminogen activator (scu-PA). The 1601GA genotype of the 1601G/A polymorphism in the FSAP gene leads to the expression of a FSAP variant with reduced ability to activate scu-PA, without affecting the ability to activate coagulation Factor VII (FVII). Previous studies have investigated the association of the 1601GA genotype with incidence and progression of carotid stenosis and deep venous thrombosis (DVT). The present study is the first to evaluate the potential association between the FSAP phenotype and DVT. We studied the association between the 1601G/A polymorphism, FSAP activity, FSAP antigen, Factor VIIa (FVIIa), prothrombin fragment 1+2 (F1+2), and C-reactive protein (CRP) in plasmas of 170 patients suspected for DVT. FSAP genotypes were equally distributed in patients with (n=64) and without DVT (n=106), (P=0.94). The 1601GA genotype was associated with significant reduction of FSAP activity (P<0.001) and FSAP antigen levels (P=0.04). Patients with DVT showed significantly higher FSAP activity (P=0.008), FSAP antigen (P=0.003), and F1+2 levels (P<0.001) than patients without DVT. The association between the FSAP measures and DVT disappeared when adjusted for CRP levels. F1+2 correlated positively to FSAP antigen (P=0.01), while FVIIa-levels were comparable in patients with and without DVT. We conclude that even though FSAP measures are significantly increased in patients with acute DVT, alterations in the scu-PA activating properties of FSAP are presumably not markedly involved in the development of acute DVT, and that the association between FSAP and DVT disappears after adjustment for CRP.
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http://dx.doi.org/10.1016/j.thromres.2008.02.002DOI Listing
December 2008

Metrological sharp shooting for plasma proteins and peptides: The need for reference materials for accurate measurements in clinical proteomics and in vitro diagnostics to generate reliable results.

Proteomics Clin Appl 2007 Sep 10;1(9):1016-35. Epub 2007 Aug 10.

Dade Behring Marburg GmbH, Technology Assessment & External Cooperations, Marburg, Germany.

Reliable study results are necessary for the assessment of discoveries, including those from proteomics. Reliable study results are also crucial to increase the likelihood of making a successful choice of biomarker candidates for verification and subsequent validation studies, a current bottleneck for the transition to in vitro diagnostic (IVD). In this respect, a major need for improvement in proteomics appears to be accuracy of measurements, including both trueness and precision of measurement. Standardization and total quality management systems (TQMS) help to provide accurate measurements and reliable results. Reference materials are an essential part of standardization and TQMS in IVD and are crucial to provide metrological correct measurements and for the overall quality assurance process. In this article we give an overview on how reference materials are defined, prepared and what role they play in standardization and TQMS to support the generation of reliable results. We discuss how proteomics can support the establishment of reference materials and biomarker tests for IVD applications, how current reference materials used in IVD may be beneficially applied in proteomics, and we provide considerations on the establishment of reference materials specific for proteomics. For clarity, we solely focus on reference materials related to serum and plasma.
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http://dx.doi.org/10.1002/prca.200700223DOI Listing
September 2007

Effects of preanalytical variables on peptide and protein measurements in human serum and plasma: implications for clinical proteomics.

Expert Rev Proteomics 2006 Aug;3(4):409-26

Memorial Sloan Kettering Cancer Center, Department of Clinical Laboratories, 1275 York Avenue, Box 88, New York, NY 10021, USA.

There is a wealth of knowledge in the field of in vitro diagnostics with regard to preanalytical variables and their impact on the determination of peptide and protein analytes in human serum and plasma. This information is applicable to clinical proteomics investigations, which utilize the same sample types. Studies have demonstrated that the majority of variations and errors in in vitro diagnostics seem to occur in the preanalytical phase prior to specimen analysis. Preanalytical processes include study design, compliance of the subjects investigated, compliance of the technical staff in adherence to protocols, choice of specimens utilized and sample collection and processing. These variables can have a dramatic impact on the determination of analytes and can affect result outcomes, reproducibility and the validity of investigations. By drawing analogies to in vitro diagnostics practices, specific variables that are likely to impact the results of proteomics studies can be identified. Recognition of such variables is the first step towards their understanding and, eventually, controlling their impact. In this article, we will review preanalytical variables, provide examples for their effects on the determination of distinct peptides and proteins and discuss potential implications for clinical proteomics investigations.
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http://dx.doi.org/10.1586/14789450.3.4.409DOI Listing
August 2006

Proteomics: from basic research to diagnostic application. A review of requirements & needs.

J Proteome Res 2005 Jul-Aug;4(4):1086-97

Dade Behring Marburg GmbH, Emil-von-Behring-Strasse 76, PO Box 1149, 35041 Marburg, Germany.

For several years proteomics research has been expected to lead to the finding of new markers that will translate into clinical tests applicable to samples such as serum, plasma and urine: so-called in vitro diagnostics (IVDs). Attempts to implement technologies applied in proteomics, in particular protein arrays and surface-enhanced laser desorption ionization time-of-flight mass spectrometry (SELDI-TOF MS), as IVD instruments have initiated constructive discussions on opportunities and challenges inherent in such a translation process also with respect to the use of multi-marker profiling approaches and pattern signatures in IVD. Taking into account the role that IVD plays in health care, we describe IVD requirements and needs. Subject to stringent costs versus benefit analyses, IVD has to provide reliable information about a person's condition, prognosis or risk to suffer a disease, thus supporting decisions on treatment or prevention. It is mandatory to fulfill requirements in routine IVD, including disease prevention, diagnosis, prognosis, and treatment monitoring or follow up among others. To fulfill IVD requirements, it is essential to (1) provide diagnostic tests that allow for definite and reliable diagnosis tied to a decision on interventions (prevention, treatment, or nontreatment), (2) meet stringent performance characteristics for each analyte (in particular test accuracy, including both precision of the measurement and trueness of the measurement), and (3) provide adequate diagnostic accuracy, i.e., diagnostic sensitivity and diagnostic specificity, determined by the desired positive and negative predictive values which depend on disease frequency. The fulfillment of essential IVD requirements is mandatory in the regulated environment of modern diagnostics. Addressing IVD needs at an early stage can support a timely and effective transition of findings and developments into routine diagnosis. IVD needs reflect features that are useful in clinical practice. This helps to generate acceptance and assists the implementation process. On the basis of IVD requirements and needs, we outline potential implications for clinical proteomics focused on applied research activities.
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http://dx.doi.org/10.1021/pr050080bDOI Listing
October 2005

A proteomic study of the HUPO Plasma Proteome Project's pilot samples using an accurate mass and time tag strategy.

Proteomics 2005 Aug;5(13):3454-66

Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA.

Characterization of the human blood plasma proteome is critical to the discovery of routinely useful clinical biomarkers. We used an accurate mass and time (AMT) tag strategy with high-resolution mass accuracy cLC-FT-ICR MS to perform a global proteomic analysis of pilot study samples as part of the HUPO Plasma Proteome Project. HUPO reference serum and citrated plasma samples from African Americans, Asian Americans, and Caucasian Americans were analyzed, in addition to a Pacific Northwest National Laboratory reference serum and plasma. The AMT tag strategy allowed us to leverage two previously published "shotgun" proteomics experiments to perform global analyses on these samples in triplicate in less than 4 days total analysis time. A total of 722 (22% with multiple peptide identifications) International Protein Index redundant proteins, or 377 protein families by ProteinProphet, were identified over the six individual HUPO serum and plasma samples. The samples yielded a similar number of identified redundant proteins in the plasma samples (average 446 +/- 23) as found in the serum samples (average 440 +/- 20). These proteins were identified by an average of 956 +/- 35 unique peptides in plasma and 930 +/- 11 unique peptides in serum. In addition to this high-throughput analysis, the AMT tag approach was used with a Z-score normalization to compare relative protein abundances. This analysis highlighted both known differences in serum and citrated plasma such as fibrinogens, and reproducible differences in peptide abundances from proteins such as soluble activin receptor-like kinase 7b and glycoprotein m6b. The AMT tag strategy not only improved our sample throughput but also provided a basis for estimated quantitation.
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http://dx.doi.org/10.1002/pmic.200401333DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2041806PMC
August 2005

HUPO Plasma Proteome Project specimen collection and handling: towards the standardization of parameters for plasma proteome samples.

Proteomics 2005 Aug;5(13):3262-77

The Johns Hopkins University School of Medicine, Department of Pathology, Division of Clinical Chemistry, Baltimore, MD 21287-7065, USA.

There is a substantial list of pre-analytical variables that can alter the analysis of blood-derived samples. We have undertaken studies on some of these issues including choice of sample type, stability during storage, use of protease inhibitors, and clinical standardization. As there is a wide range of sample variables and a broad spectrum of analytical techniques in the HUPO PPP effort, it is not possible to define a single list of pre-analytical standards for samples or their processing. We present here a compendium of observations, drawing on actual results and sound clinical theories and practices. Based on our data, we find that (1) platelet-depleted plasma is preferable to serum for certain peptidomic studies; (2) samples should be aliquoted and stored preferably in liquid nitrogen; (3) the addition of protease inhibitors is recommended, but should be incorporated early and used judiciously, as some form non specific protein adducts and others interfere with peptide studies. Further, (4) the diligent tracking of pre-analytical variables and (5) the use of reference materials for quality control and quality assurance, are recommended. These findings help provide guidance on sample handling issues, with the overall suggestion being to be conscious of all possible pre-analytical variables as a prerequisite of any proteomic study.
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http://dx.doi.org/10.1002/pmic.200401245DOI Listing
August 2005

Immunoassay and antibody microarray analysis of the HUPO Plasma Proteome Project reference specimens: systematic variation between sample types and calibration of mass spectrometry data.

Proteomics 2005 Aug;5(13):3278-91

The Van Andel Research Institute, Grand Rapids, MI 49503, USA.

Four different immunoassay and antibody microarray methods performed at four different sites were used to measure the levels of a broad range of proteins (N = 323 assays; 39, 88, 168, and 28 assays at the respective sites; 237 unique analytes) in the human serum and plasma reference specimens distributed by the Plasma Proteome Project (PPP) of the HUPO. The methods provided a means to (1) assess the level of systematic variation in protein abundances associated with blood preparation methods (serum, citrate-anticoagulated-plasma, EDTA-anticoagulated-plasma, or heparin-anticoagulated-plasma) and (2) evaluate the dependence on concentration of MS-based protein identifications from data sets using the HUPO specimens. Some proteins, particularly cytokines, had highly variable concentrations between the different sample preparations, suggesting specific effects of certain anticoagulants on the stability or availability of these proteins. The linkage of antibody-based measurements from 66 different analytes with the combined MS/MS data from 18 different laboratories showed that protein detection and the quality of MS data increased with analyte concentration. The conclusions from these initial analyses are that the optimal blood preparation method is variable between analytes and that the discovery of blood proteins by MS can be extended to concentrations below the ng/mL range under certain circumstances. Continued developments in antibody-based methods will further advance the scientific goals of the PPP.
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http://dx.doi.org/10.1002/pmic.200401276DOI Listing
August 2005

Investigations on DNA intercalation and surface binding by SYBR Green I, its structure determination and methodological implications.

Nucleic Acids Res 2004 Jul 12;32(12):e103. Epub 2004 Jul 12.

Laboratory of Biochemistry, Institute for Interfacial Engineering, University of Stuttgart, 70569 Stuttgart, Germany.

The detection of double-stranded (ds) DNA by SYBR Green I (SG) is important in many molecular biology methods including gel electrophoresis, dsDNA quantification in solution and real-time PCR. Biophysical studies at defined dye/base pair ratios (dbprs) were used to determine the structure-property relationships that affect methods applying SG. These studies revealed the occurrence of intercalation, followed by surface binding at dbprs above approximately 0.15. Only the latter led to a significant increase in fluorescence. Studies with poly(dA)* poly(dT) and poly(dG)* poly(dC) homopolymers showed sequence-specific binding of SG. Also, salts had a marked impact on SG fluorescence. We also noted binding of SG to single-stranded (ss) DNA, although SG/ssDNA fluorescence was at least approximately 11-fold lower than with dsDNA. To perform these studies, we determined the structure of SG by mass spectrometry and NMR analysis to be [2-[N-(3-dimethylaminopropyl)-N-propylamino]-4-[2,3-dihydro-3-methyl-(benzo-1,3-thiazol-2-yl)-methylidene]-1-phenyl-quinolinium]. For comparison, the structure of PicoGreen (PG) was also determined and is [2-[N-bis-(3-dimethylaminopropyl)-amino]-4-[2,3-dihydro-3-methyl-(benzo-1,3-thiazol-2-yl)-methylidene]-1-phenyl-quinolinium]+. These structure-property relationships help in the design of methods that use SG, in particular dsDNA quantification in solution and real-time PCR.
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http://dx.doi.org/10.1093/nar/gnh101DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC484200PMC
July 2004

Mechanisms underlying the impact of humic acids on DNA quantification by SYBR Green I and consequences for the analysis of soils and aquatic sediments.

Nucleic Acids Res 2003 Apr;31(7):e39

Laboratory of Biochemistry, Chair for Interfacial Engineering, University of Stuttgart and Fraunhofer IGB, Nobelstrasse 12, D-70569 Stuttgart, Germany.

DNA quantification of soils and sediments is useful for the investigation of microbial communities and for the acquisition of their genomes that are exploited for the production of natural products. However, in such samples DNA quantification is impaired by humic acids (HA). Due to its lack of specificity and sensitivity, UV spectrophotometry cannot be applied. Consequently, fluorimetric assays applying Hoechst (H) 33258 or PicoGreen (PG) are used. Here, we investigated the SYBR Green I (SG) assay, which was also affected by HA, but was found to be 25- and 1.7-fold more sensitive compared to the H 33258 and PG assays, respectively. Spectrophotometric, fluorimetric and quenching studies as well as gel mobility shift assays suggested that the effect of HA on the SG assay was based on an inner filter effect, collisional quenching and binding of SG to HA. As to the latter finding, the standard 6250-fold dilution of the SG reagent was optimised to a 2000-fold dilution. Although the sensitivity of the optimised SG assay was reduced by a factor of 1.3, the interfering effect of HA could be reduced up to 22-fold. A significant reduction of HA interferences by lowering the pH of the assay was not observed. Finally, the performance of the modified SG assay and the corresponding evaluation methods were verified by the determination of DNA recoveries and concentrations of standards and environmental samples in comparison to the PG assay.
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC152824PMC
http://dx.doi.org/10.1093/nar/gng039DOI Listing
April 2003