1
|
Katrukha IA, Riabkova NS, Kogan AE, Vylegzhanina AV, Mukharyamova KS, Bogomolova AP, Zabolotskii AI, Koshkina EV, Bereznikova AV, Katrukha AG. Fragmentation of human cardiac troponin T after acute myocardial infarction. Clin Chim Acta 2023; 542:117281. [PMID: 36918061 DOI: 10.1016/j.cca.2023.117281] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Revised: 02/18/2023] [Accepted: 03/06/2023] [Indexed: 03/13/2023]
Abstract
BACKGROUND Blood measurement of cardiac troponin T (cTnT) is one of the most widespread methods of acute myocardial infarction (MI) diagnosis. cTnT degradation may have a significant influence on the precision of cTnT immunodetection; however, there are no consistent data describing the level and sites of cTnT proteolysis in the blood of MI patients. In this study, we bordered major cTnT fragments and quantified their relative abundance in the blood at different times after MI. METHODS Serial heparin plasma samples were collected from 37 MI patients 2-37 h following the onset of MI. cTnT and its fragments were studied by western blotting and immunofluorescence analysis using monoclonal antibodies specific to various cTnT epitopes. RESULTS cTnT was present in the blood of MI patients as 23 proteolytic fragments with an apparent molecular mass of ∼ 8-37 kDa. Two major sites of cTnT degradation were identified: between amino acid residues (aar) 68 and 69 and between aar 189 and 223. Analysis of the abundance of cTnT fragments showed an increase in the fraction of free central fragments in the first few hours after MI, while the fraction of the C-terminal fragments of cTnT remained almost unchanged. CONCLUSION cTnT progressively degrades after MI and appears in the blood as a mixture of 23 proteolytic fragments. The cTnT region approximately bordered by aar 69-158 is a promising target for antibodies used for measurement of total cTnT.
Collapse
Affiliation(s)
- Ivan A Katrukha
- HyTest Ltd., Turku, Finland; Department of Biochemistry, School of Biology, Moscow State University, Moscow, Russia.
| | - Natalia S Riabkova
- HyTest Ltd., Turku, Finland; Department of Biochemistry, School of Biology, Moscow State University, Moscow, Russia
| | - Alexander E Kogan
- HyTest Ltd., Turku, Finland; Department of Biochemistry, School of Biology, Moscow State University, Moscow, Russia
| | | | | | - Agnessa P Bogomolova
- HyTest Ltd., Turku, Finland; Department of Biochemistry, School of Biology, Moscow State University, Moscow, Russia
| | - Artur I Zabolotskii
- Department of Biochemistry, School of Biology, Moscow State University, Moscow, Russia
| | | | - Anastasia V Bereznikova
- HyTest Ltd., Turku, Finland; Department of Biochemistry, School of Biology, Moscow State University, Moscow, Russia
| | - Alexey G Katrukha
- HyTest Ltd., Turku, Finland; Department of Biochemistry, School of Biology, Moscow State University, Moscow, Russia
| |
Collapse
|
2
|
Ito H, Matsui T, Konno R, Itakura M, Kodera Y. LC-MS peak assignment based on unanimous selection by six machine learning algorithms. Sci Rep 2021; 11:23411. [PMID: 34862414 PMCID: PMC8642397 DOI: 10.1038/s41598-021-02899-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 11/24/2021] [Indexed: 11/13/2022] Open
Abstract
Recent mass spectrometry (MS)-based techniques enable deep proteome coverage with relative quantitative analysis, resulting in increased identification of very weak signals accompanied by increased data size of liquid chromatography (LC)–MS/MS spectra. However, the identification of weak signals using an assignment strategy with poorer performance results in imperfect quantification with misidentification of peaks and ratio distortions. Manually annotating a large number of signals within a very large dataset is not a realistic approach. In this study, therefore, we utilized machine learning algorithms to successfully extract a higher number of peptide peaks with high accuracy and precision. Our strategy evaluated each peak identified using six different algorithms; peptide peaks identified by all six algorithms (i.e., unanimously selected) were subsequently assigned as true peaks, which resulted in a reduction in the false-positive rate. Hence, exact and highly quantitative peptide peaks were obtained, providing better performance than obtained applying the conventional criteria or using a single machine learning algorithm.
Collapse
Affiliation(s)
- Hiroaki Ito
- Department of Physics, School of Science, Kitasato University, 1-15-1 Kitasato, Minami-ku, Sagamihara, Kanagawa, 252-0373, Japan
| | - Takashi Matsui
- Department of Physics, School of Science, Kitasato University, 1-15-1 Kitasato, Minami-ku, Sagamihara, Kanagawa, 252-0373, Japan.,Center for Disease Proteomics, School of Science, Kitasato University, 1-15-1 Kitasato, Minami-ku, Sagamihara, 252-0373, Japan
| | - Ryo Konno
- Department of Physics, School of Science, Kitasato University, 1-15-1 Kitasato, Minami-ku, Sagamihara, Kanagawa, 252-0373, Japan
| | - Makoto Itakura
- Center for Disease Proteomics, School of Science, Kitasato University, 1-15-1 Kitasato, Minami-ku, Sagamihara, 252-0373, Japan.,Department of Biochemistry, School of Medicine, Kitasato University, 1-15-1 Kitasato, Minami-ku , Sagamihara, 252-0373, Japan
| | - Yoshio Kodera
- Department of Physics, School of Science, Kitasato University, 1-15-1 Kitasato, Minami-ku, Sagamihara, Kanagawa, 252-0373, Japan. .,Center for Disease Proteomics, School of Science, Kitasato University, 1-15-1 Kitasato, Minami-ku, Sagamihara, 252-0373, Japan.
| |
Collapse
|
3
|
Carbonara K, Andonovski M, Coorssen JR. Proteomes Are of Proteoforms: Embracing the Complexity. Proteomes 2021; 9:38. [PMID: 34564541 PMCID: PMC8482110 DOI: 10.3390/proteomes9030038] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Revised: 08/24/2021] [Accepted: 08/29/2021] [Indexed: 12/17/2022] Open
Abstract
Proteomes are complex-much more so than genomes or transcriptomes. Thus, simplifying their analysis does not simplify the issue. Proteomes are of proteoforms, not canonical proteins. While having a catalogue of amino acid sequences provides invaluable information, this is the Proteome-lite. To dissect biological mechanisms and identify critical biomarkers/drug targets, we must assess the myriad of proteoforms that arise at any point before, after, and between translation and transcription (e.g., isoforms, splice variants, and post-translational modifications [PTM]), as well as newly defined species. There are numerous analytical methods currently used to address proteome depth and here we critically evaluate these in terms of the current 'state-of-the-field'. We thus discuss both pros and cons of available approaches and where improvements or refinements are needed to quantitatively characterize proteomes. To enable a next-generation approach, we suggest that advances lie in transdisciplinarity via integration of current proteomic methods to yield a unified discipline that capitalizes on the strongest qualities of each. Such a necessary (if not revolutionary) shift cannot be accomplished by a continued primary focus on proteo-genomics/-transcriptomics. We must embrace the complexity. Yes, these are the hard questions, and this will not be easy…but where is the fun in easy?
Collapse
Affiliation(s)
| | | | - Jens R. Coorssen
- Faculties of Applied Health Sciences and Mathematics & Science, Departments of Health Sciences and Biological Sciences, Brock University, 1812 Sir Isaac Brock Way, St. Catharines, ON L2S 3A1, Canada; (K.C.); (M.A.)
| |
Collapse
|
4
|
Ma H, Cassedy A, O'Kennedy R. The role of antibody-based troponin detection in cardiovascular disease: A critical assessment. J Immunol Methods 2021; 497:113108. [PMID: 34329690 PMCID: PMC8412434 DOI: 10.1016/j.jim.2021.113108] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 07/13/2021] [Accepted: 07/24/2021] [Indexed: 01/19/2023]
Abstract
Cardiovascular disease has remained the world's biggest killer for 30 years. To aid in the diagnosis and prognosis of patients suffering cardiovascular-related disease accurate detection methods are essential. For over 20 years, the cardiac-specific troponins, I (cTnI) and T (cTnT), have acted as sensitive and specific biomarkers to assist in the diagnosis of various types of heart diseases. Various cardiovascular complications were commonly detected in patients with COVID-19, where cTn elevation is detectable, which suggested potential great prognostic value of cTn in COVID-19-infected patients. Detection of these biomarkers circulating in the bloodstream is generally facilitated by immunoassays employing cTnI- and/or cTnT-specific antibodies. While several anti-troponin assays are commercially available, there are still obstacles to overcome to achieve optimal troponin detection. Such obstacles include the proteolytic degradation of N and C terminals on cTnI, epitope occlusion of troponin binding-sites by the cTnI/cTnT complex, cross reactivity of antibodies with skeletal troponins or assay interference caused by human anti-species antibodies. Therefore, further research into multi-antibody based platforms, multi-epitope targeting and rigorous validation of immunoassays is required to ensure accurate measurements. Moreover, with combination and modification of various latest technical (e.g. microfluidics), antibody-based troponin detection systems can be more specific, sensitive and rapid which could be incorporated into portable biosensor systems to be used at point-of care.
Collapse
Affiliation(s)
- Hui Ma
- School of Biotechnology, Dublin City University, Dublin 9 D09 V2O9, Ireland
| | - Arabelle Cassedy
- School of Biotechnology, Dublin City University, Dublin 9 D09 V2O9, Ireland
| | - Richard O'Kennedy
- School of Biotechnology, Dublin City University, Dublin 9 D09 V2O9, Ireland; Qatar Foundation and Hamad Bin Khalifa University, Research Complex, Education City, Doha, Qatar.
| |
Collapse
|
5
|
de Boer D, Streng AS, van Doorn WPTM, Vroemen WHM, Bekers O, Wodzig WKWH, Mingels AMA. Cardiac Troponin T: The Impact of Posttranslational Modifications on Analytical Immunoreactivity in Blood up to the Excretion in Urine. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1306:41-59. [PMID: 33959905 DOI: 10.1007/978-3-030-63908-2_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Cardiac troponin T (cTnT) is a sensitive and specific biomarker for detecting cardiac muscle injury. Its concentration in blood can be significantly elevated outside the normal reference range under several pathophysiological conditions. The classical analytical method in routine clinical analysis to detect cTnT in serum or plasma is a single commercial immunoassay, which is designed to quantify the intact cTnT molecule. The targeted epitopes are located in the central region of the cTnT molecule. However, in blood cTnT exists in different biomolecular complexes and proteoforms: bound (to cardiac troponin subunits or to immunoglobulins) or unbound (as intact protein or as proteolytic proteoforms). While proteolysis is a principal posttranslational modification (PTM), other confirmed PTMs of the proteoforms include N-terminal initiator methionine removal, N-acetylation, O-phosphorylation, O-(N-acetyl)-glucosaminylation, N(ɛ)-(carboxymethyl)lysine modification and citrullination. The immunoassay probably detects several of those cTnT biomolecular complexes and proteoforms, as long as they have the centrally targeted epitopes in common. While analytical cTnT immunoreactivity has been studied predominantly in blood, it can also be detected in urine, although it is unclear in which proteoform cTnT immunoreactivity is present in urine. This review presents an overview of the current knowledge on the pathophysiological lifecycle of cTnT. It provides insight into the impact of PTMs, not only on the analytical immunoreactivity, but also on the excretion of cTnT in urine as one of the waste routes in that lifecycle. Accordingly, and after isolating the proteoforms from urine of patients suffering from proteinuria and acute myocardial infarction, the structures of some possible cTnT proteoforms are reconstructed using mass spectrometry and presented.
Collapse
Affiliation(s)
- Douwe de Boer
- Unit of Clinical Chemistry, Central Diagnostic Laboratory, Maastricht University Medical Center, Maastricht, The Netherlands.
- NUTRIM, School of Nutrition and Translational Research in Metabolism, Medicine and Life Sciences (FHML) of Maastricht University (UM), Maastricht University Medical Center, Maastricht, The Netherlands.
| | - Alexander S Streng
- Unit of Clinical Chemistry, Central Diagnostic Laboratory, Maastricht University Medical Center, Maastricht, The Netherlands
| | - William P T M van Doorn
- Unit of Clinical Chemistry, Central Diagnostic Laboratory, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Wim H M Vroemen
- Unit of Clinical Chemistry, Central Diagnostic Laboratory, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Otto Bekers
- Unit of Clinical Chemistry, Central Diagnostic Laboratory, Maastricht University Medical Center, Maastricht, The Netherlands
- CARIM, School for Cardiovascular Diseases, Faculty of Health, Medicine and Life Sciences (FHML) of Maastricht University (UM), Maastricht University Medical Center, Maastricht, The Netherlands
| | - Will K W H Wodzig
- Unit of Clinical Chemistry, Central Diagnostic Laboratory, Maastricht University Medical Center, Maastricht, The Netherlands
- NUTRIM, School of Nutrition and Translational Research in Metabolism, Medicine and Life Sciences (FHML) of Maastricht University (UM), Maastricht University Medical Center, Maastricht, The Netherlands
| | - Alma M A Mingels
- Unit of Clinical Chemistry, Central Diagnostic Laboratory, Maastricht University Medical Center, Maastricht, The Netherlands
- CARIM, School for Cardiovascular Diseases, Faculty of Health, Medicine and Life Sciences (FHML) of Maastricht University (UM), Maastricht University Medical Center, Maastricht, The Netherlands
| |
Collapse
|
6
|
Starnberg K, Fridén V, Muslimovic A, Ricksten SE, Nyström S, Forsgard N, Lindahl B, Vukusic K, Sandstedt J, Dellgren G, Hammarsten O. A Possible Mechanism behind Faster Clearance and Higher Peak Concentrations of Cardiac Troponin I Compared with Troponin T in Acute Myocardial Infarction. Clin Chem 2020; 66:333-341. [PMID: 32040581 DOI: 10.1093/clinchem/hvz003] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Accepted: 09/20/2019] [Indexed: 12/15/2022]
Abstract
BACKGROUND Although cardiac troponin I (cTnI) and troponin T (cTnT) form a complex in the human myocardium and bind to thin filaments in the sarcomere, cTnI often reaches higher concentrations and returns to normal concentrations faster than cTnT in patients with acute myocardial infarction (MI). METHODS We compared the overall clearance of cTnT and cTnI in rats and in patients with heart failure and examined the release of cTnT and cTnI from damaged human cardiac tissue in vitro. RESULTS Ground rat heart tissue was injected into the quadriceps muscle in rats to simulate myocardial damage with a defined onset. cTnT and cTnI peaked at the same time after injection. cTnI returned to baseline concentrations after 54 h, compared with 168 h for cTnT. There was no difference in the rate of clearance of solubilized cTnT or cTnI after intravenous or intramuscular injection. Renal clearance of cTnT and cTnI was similar in 7 heart failure patients. cTnI was degraded and released faster and reached higher concentrations than cTnT when human cardiac tissue was incubated in 37°C plasma. CONCLUSION Once cTnI and cTnT are released to the circulation, there seems to be no difference in clearance. However, cTnI is degraded and released faster than cTnT from necrotic cardiac tissue. Faster degradation and release may be the main reason why cTnI reaches higher peak concentrations and returns to normal concentrations faster in patients with MI.
Collapse
Affiliation(s)
- Karin Starnberg
- Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Vincent Fridén
- Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Aida Muslimovic
- Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Sven-Erik Ricksten
- Department of Anesthesiology and Intensive Care Medicine, Institute of Clinical Sciences at the Sahlgrenska Academy, University of Gothenburg, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Susanne Nyström
- Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Niklas Forsgard
- Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Bertil Lindahl
- Department of Medical Sciences, Uppsala University, Uppsala, Sweden.,Uppsala Clinical Research Center, Uppsala University, Uppsala, Sweden
| | - Kristina Vukusic
- Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Joakim Sandstedt
- Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Göran Dellgren
- Department of Cardiothoracic Surgery, Sahlgrenska University Hospital, Gothenburg, Sweden.,Department of Molecular and Clinical Medicine, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Ola Hammarsten
- Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Sahlgrenska University Hospital, Gothenburg, Sweden
| |
Collapse
|
7
|
Adem S, Jain S, Sveiven M, Zhou X, O'Donoghue AJ, Hall DA. Giant magnetoresistive biosensors for real-time quantitative detection of protease activity. Sci Rep 2020; 10:7941. [PMID: 32409675 PMCID: PMC7224196 DOI: 10.1038/s41598-020-62910-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 03/18/2020] [Indexed: 12/19/2022] Open
Abstract
Proteases are enzymes that cleave proteins and are crucial to physiological processes such as digestion, blood clotting, and wound healing. Unregulated protease activity is a biomarker of several human diseases. Synthetic peptides that are selectively hydrolyzed by a protease of interest can be used as reporter substrates of unregulated protease activity. We developed an activity-based protease sensor by immobilizing magnetic nanoparticles (MNPs) to the surface of a giant magnetoresistive spin-valve (GMR SV) sensor using peptides. Cleavage of these peptides by a protease releases the magnetic nanoparticles resulting in a time-dependent change in the local magnetic field. Using this approach, we detected a significant release of MNPs after 3.5 minutes incubation using just 4 nM of the cysteine protease, papain. In addition, we show that proteases in healthy human urine do not release the MNPs, however addition of 20 nM of papain to the urine samples resulted in a time-dependent change in magnetoresistance. This study lays the foundation for using GMR SV sensors as a platform for real-time, quantitative detection of protease activity in biological fluids.
Collapse
Affiliation(s)
- Sandeep Adem
- University of California - San Diego, Department of Bioengineering, La Jolla, CA, 92093, USA
| | - Sonal Jain
- University of California - San Diego, Department of Bioengineering, La Jolla, CA, 92093, USA
| | - Michael Sveiven
- University of California - San Diego, Department of Bioengineering, La Jolla, CA, 92093, USA
| | - Xiahan Zhou
- University of California - San Diego, Department of Electrical and Computer Engineering, La Jolla, CA, 92093, USA
| | - Anthony J O'Donoghue
- University of California - San Diego, Skaggs School of Pharmacy and Pharmaceutical Sciences, La Jolla, CA, 92093, USA.
| | - Drew A Hall
- University of California - San Diego, Department of Bioengineering, La Jolla, CA, 92093, USA.
- University of California - San Diego, Department of Electrical and Computer Engineering, La Jolla, CA, 92093, USA.
| |
Collapse
|
8
|
Liu H, Lu XJ, Chen J. Full-length and a smaller globular fragment of adiponectin have opposite roles in regulating monocyte/macrophage functions in ayu, Plecoglossus altivelis. FISH & SHELLFISH IMMUNOLOGY 2018; 82:319-329. [PMID: 30130657 DOI: 10.1016/j.fsi.2018.08.041] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Revised: 08/17/2018] [Accepted: 08/18/2018] [Indexed: 06/08/2023]
Abstract
Adiponectin (ADP), a regulator of the innate immune system, plays a role in the progression of inflammation and metabolic disorders in mammals. However, the role of ADP in fish is poorly understood. Here, we cloned the cDNA sequence of a ADP homolog (PaADP) gene from ayu. Multiple sequence alignment revealed that PaADP presented typical characteristics of ADPs. Phylogenetic tree analysis showed that PaADP was most closely related to that of rainbow trout. In healthy ayu, the transcripts of PaADP were detected in most of the tested tissues and cells, with the highest level in the adipose tissue. Upon V. anguillarum infection, the mRNA expression of PaADP was significantly up-regulated in the tissues and cells except adipose tissue. Subsequently, the full-length mature PaADP (fPaADP) and the globular domain fragment (gPaADP) were prokaryotically expressed in bacteria and purified, and anti-PaADP antibodies were produced. Western blot analysis revealed that three fragments including fPaADP and gPaADP were existed in ayu serum. The recombinant fPaADP (rfPaADP) had an anti-inflammatory effect on ayu MO/MФ by upregulating anti-inflammatory cytokine expressions, downregulating pro-inflammatory cytokine expressions, inhibiting the phagocytosis and subsequent bacterial killing. In contrast, the recombinant gPaADP (rgPaADP) presented a pro-inflammatory effect on ayu MO/MФ by upregulating pro-inflammatory cytokine expression, downregulating anti-inflammatory cytokine expressions, enhancing the phagocytosis and subsequent bacterial killing. These results suggested that fPaADP and gPaADP have opposite roles in the regulation of MO/MФ functions in ayu.
Collapse
Affiliation(s)
- He Liu
- Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo 315211, China
| | - Xin-Jiang Lu
- Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo 315211, China
| | - Jiong Chen
- Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo 315211, China; Key Laboratory of Applied Marine Biotechnology of Ministry of Education, Ningbo University, Ningbo 315211, China.
| |
Collapse
|
9
|
Hammarsten O, Mair J, Möckel M, Lindahl B, Jaffe AS. Possible mechanisms behind cardiac troponin elevations. Biomarkers 2018; 23:725-734. [DOI: 10.1080/1354750x.2018.1490969] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Ola Hammarsten
- Department of Clinical Chemistry and Transfusion Medicine, University of Gothenburg, Gothenburg, Sweden
| | - Johannes Mair
- Department of Internal Medicine III – Cardiology and Angiology, Heart Center, Medical University of Innsbruck, Innsbruck, Austria
| | - Martin Möckel
- Division of Emergency Medicine and Department of Cardiology, Charité – Universitätsmedizin Berlin, Berlin, Germany
| | - Bertil Lindahl
- Department of Medical Sciences, Uppsala University and Uppsala Clinical Research Center, Uppsala, Sweden
| | - Allan S. Jaffe
- Department of Cardiovascular Medicine, Mayo Clinic and Medical School, Rochester, MN, USA
| |
Collapse
|
10
|
Vizovišek M, Vidmar R, Drag M, Fonović M, Salvesen GS, Turk B. Protease Specificity: Towards In Vivo Imaging Applications and Biomarker Discovery. Trends Biochem Sci 2018; 43:829-844. [PMID: 30097385 DOI: 10.1016/j.tibs.2018.07.003] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Revised: 06/05/2018] [Accepted: 07/12/2018] [Indexed: 02/06/2023]
Abstract
Proteases are considered of major importance in biomedical research because of their crucial roles in health and disease. Their ability to hydrolyze their protein and peptide substrates at single or multiple sites, depending on their specificity, makes them unique among the enzymes. Understanding protease specificity is therefore crucial to understand their biology as well as to develop tools and drugs. Recent advancements in the fields of proteomics and chemical biology have improved our understanding of protease biology through extensive specificity profiling and identification of physiological protease substrates. There are growing efforts to transfer this knowledge into clinical modalities, but their success is often limited because of overlapping protease features, protease redundancy, and chemical tools lacking specificity. Herein, we discuss the current trends and challenges in protease research and how to exploit the growing information on protease specificities for understanding protease biology, as well as for development of selective substrates, cleavable linkers, and activity-based probes and for biomarker discovery.
Collapse
Affiliation(s)
- Matej Vizovišek
- Jozef Stefan Institute, Department of Biochemistry and Molecular and Structural Biology, Jamova 39, SI-1000 Ljubljana, Slovenia; These authors contributed equally to this work
| | - Robert Vidmar
- Jozef Stefan Institute, Department of Biochemistry and Molecular and Structural Biology, Jamova 39, SI-1000 Ljubljana, Slovenia; These authors contributed equally to this work
| | - Marcin Drag
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - Marko Fonović
- Jozef Stefan Institute, Department of Biochemistry and Molecular and Structural Biology, Jamova 39, SI-1000 Ljubljana, Slovenia
| | - Guy S Salvesen
- NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA.
| | - Boris Turk
- Jozef Stefan Institute, Department of Biochemistry and Molecular and Structural Biology, Jamova 39, SI-1000 Ljubljana, Slovenia; Faculty of Chemistry and Chemical Technology, University of Ljubljana, Vecna pot 113, SI-1000 Ljubljana, Slovenia.
| |
Collapse
|
11
|
Ankney JA, Muneer A, Chen X. Relative and Absolute Quantitation in Mass Spectrometry-Based Proteomics. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2018; 11:49-77. [PMID: 29894226 DOI: 10.1146/annurev-anchem-061516-045357] [Citation(s) in RCA: 104] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Mass spectrometry-based quantitative proteomics is a powerful tool for gaining insights into function and dynamics of biological systems. However, peptides with different sequences have different ionization efficiencies, and their intensities in a mass spectrum are not correlated with their abundances. Therefore, various label-free or stable isotope label-based quantitation methods have emerged to assist mass spectrometry to perform comparative proteomic experiments, thus enabling nonbiased identification of thousands of proteins differentially expressed in healthy versus diseased cells. Here, we discuss the most widely used label-free and metabolic-, enzymatic-, and chemical labeling-based proteomic strategies for relative and absolute quantitation. We summarize the specific strengths and weaknesses of each technique in terms of quantification accuracy, proteome coverage, multiplexing capability, and robustness. Applications of each strategy for solving specific biological complexities are also presented.
Collapse
Affiliation(s)
- J Astor Ankney
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, North Carolina 27599, USA;
| | - Adil Muneer
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, North Carolina 27599, USA;
| | - Xian Chen
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, North Carolina 27599, USA;
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| |
Collapse
|
12
|
Streng AS, van der Linden N, Kocken JMM, Bekers O, Bouwman FG, Mariman ECM, Meex SJR, Wodzig WKWH, de Boer D. Mass Spectrometric Identification of Cardiac Troponin T in Urine of Patients Suffering from Acute Myocardial Infarction. J Appl Lab Med 2018; 2:857-867. [PMID: 33636816 DOI: 10.1373/jalm.2017.024224] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Accepted: 08/30/2017] [Indexed: 11/06/2022]
Abstract
BACKGROUND Because of its high cardiospecificity, cardiac troponin T (cTnT) is one of the first-choice biomarkers to diagnose acute myocardial infarction (AMI). cTnT is extensively fragmented in serum of patients suffering from AMI. However, it is currently unknown whether all cTnT is completely degraded in the body or whether some cTnT fragments can leave the body via urine. The aim of the present study is to develop a method for the detection of cTnT in urine and to examine whether cTnT is detectable in patient urine. METHODS Proteins in urine samples of 20 patients were precipitated using a cTnT-specific immunoprecipitation technique and a nonspecific acetonitrile protein precipitation. After in-solution digestion of the precipitated proteins, the resulting peptides were separated and analyzed using HPLC and mass spectrometry with a targeted selected ion monitoring assay with data-dependent tandem mass spectrometry (t-SIM/dd-MS2). RESULTS The t-SIM/dd-MS2 assay was validated using a synthetic peptide standard containing 10 specific cTnT peptides of interest and with purified human intact cTnT spiked in urine from healthy individuals. Using this assay, 6 different cTnT-specific peptides were identified in urine samples from 3 different patients, all suffering from AMI. CONCLUSIONS We show here for the first time that cTnT can be present in the urine of AMI patients using a targeted LC-MS/MS assay. Whether the presence of cTnT in urine reflects a physiological or pathophysiological process still needs to be elucidated.
Collapse
Affiliation(s)
- Alexander S Streng
- Department of Clinical Chemistry, Central Diagnostic Laboratory, Maastricht University Medical Center, Maastricht, the Netherlands
| | - Noreen van der Linden
- Department of Clinical Chemistry, Central Diagnostic Laboratory, Maastricht University Medical Center, Maastricht, the Netherlands
| | - Jordy M M Kocken
- Department of Clinical Chemistry, Central Diagnostic Laboratory, Maastricht University Medical Center, Maastricht, the Netherlands
| | - Otto Bekers
- Department of Clinical Chemistry, Central Diagnostic Laboratory, Maastricht University Medical Center, Maastricht, the Netherlands
| | - Freek G Bouwman
- Department of Human Biology, Maastricht University, Maastricht, the Netherlands
| | - Edwin C M Mariman
- Department of Human Biology, Maastricht University, Maastricht, the Netherlands
| | - Steven J R Meex
- Department of Clinical Chemistry, Central Diagnostic Laboratory, Maastricht University Medical Center, Maastricht, the Netherlands
| | - Will K W H Wodzig
- Department of Clinical Chemistry, Central Diagnostic Laboratory, Maastricht University Medical Center, Maastricht, the Netherlands
| | - Douwe de Boer
- Department of Clinical Chemistry, Central Diagnostic Laboratory, Maastricht University Medical Center, Maastricht, the Netherlands
| |
Collapse
|
13
|
Greco V, Piras C, Pieroni L, Urbani A. Direct Assessment of Plasma/Serum Sample Quality for Proteomics Biomarker Investigation. Methods Mol Biol 2018; 1619:3-21. [PMID: 28674873 DOI: 10.1007/978-1-4939-7057-5_1] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Blood proteome analysis for biomarker discovery represents one of the most challenging tasks to be achieved through clinical proteomics due to the sample complexity, such as the extreme heterogeneity of proteins in very dynamic concentrations, and to the observation of proper sampling and storage conditions. Quantitative and qualitative proteomics profiling of plasma and serum could be useful both for the early detection of diseases and for the evaluation of pathological status. Two main sources of variability can affect the precision and accuracy of the quantitative experiments designed for biomarker discovery and validation. These sources are divided into two categories, pre-analytical and analytical, and are often ignored; however, they can contribute to consistent errors and misunderstanding in biomarker research. In this chapter, we review critical pre-analytical and analytical variables that can influence quantitative proteomics. According to guidelines accepted by proteomics community, we propose some recommendations and strategies for a proper proteomics analysis addressed to biomarker studies.
Collapse
Affiliation(s)
- Viviana Greco
- Proteomics and metabonomics unit, Fondazione Santa Lucia, IRCCS, Rome, Italy
| | - Cristian Piras
- Department of Veterinary Medicine, University of Milan, Milan, Italy
| | - Luisa Pieroni
- Proteomics and metabonomics unit, Fondazione Santa Lucia, IRCCS, Rome, Italy
| | - Andrea Urbani
- Proteomics and metabonomics unit, Fondazione Santa Lucia, IRCCS, Rome, Italy. .,Institute of Biochemistry and Clinical Biochemistry, Catholic University of Sacred Heart, Rome, Italy.
| |
Collapse
|
14
|
Borràs E, Sabidó E. What is targeted proteomics? A concise revision of targeted acquisition and targeted data analysis in mass spectrometry. Proteomics 2017; 17. [PMID: 28719092 DOI: 10.1002/pmic.201700180] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2017] [Revised: 07/06/2017] [Accepted: 07/11/2017] [Indexed: 12/14/2022]
Abstract
Targeted proteomics has gained significant popularity in mass spectrometry-based protein quantification as a method to detect proteins of interest with high sensitivity, quantitative accuracy and reproducibility. However, with the emergence of a wide variety of targeted proteomics methods, some of them with high-throughput capabilities, it is easy to overlook the essence of each method and to determine what makes each of them a targeted proteomics method. In this viewpoint, we revisit the main targeted proteomics methods and classify them in four categories differentiating those methods that perform targeted data acquisition from targeted data analysis, and those methods that are based on peptide ion data (MS1 targeted methods) from those that rely on the peptide fragments (MS2 targeted methods).
Collapse
Affiliation(s)
- Eva Borràs
- Proteomics Unit, Centre de Regulació Genòmica, Barcelona Institute of Science and Technology, Barcelona, Spain.,Universitat Pompeu Fabra, Barcelona, Spain
| | - Eduard Sabidó
- Proteomics Unit, Centre de Regulació Genòmica, Barcelona Institute of Science and Technology, Barcelona, Spain.,Universitat Pompeu Fabra, Barcelona, Spain
| |
Collapse
|
15
|
Savickas S, Auf dem Keller U. Targeted degradomics in protein terminomics and protease substrate discovery. Biol Chem 2017; 399:47-54. [PMID: 28850541 DOI: 10.1515/hsz-2017-0187] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Accepted: 08/21/2017] [Indexed: 02/06/2023]
Abstract
Targeted degradomics integrates positional information into mass spectrometry (MS)-based targeted proteomics workflows and thereby enables analysis of proteolytic cleavage events with unprecedented specificity and sensitivity. Rapid progress in the establishment of protease-substrate relations provides extensive degradomics target lists that now can be tested with help of selected and parallel reaction monitoring (S/PRM) in complex biological systems, where proteases act in physiological environments. In this minireview, we describe the general principles of targeted degradomics, outline the generic experimental workflow of the methodology and highlight recent and future applications in protease research.
Collapse
Affiliation(s)
- Simonas Savickas
- Institute of Molecular Health Sciences, ETH Zurich, Otto-Stern-Weg 7, CH-8093 Zurich, Switzerland
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Anker Engelunds Vej, Building 301, DK-2800 Kgs. Lyngby, Denmark
| | - Ulrich Auf dem Keller
- Institute of Molecular Health Sciences, ETH Zurich, Otto-Stern-Weg 7, CH-8093 Zurich, Switzerland
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Anker Engelunds Vej, Building 301, DK-2800 Kgs. Lyngby, Denmark
| |
Collapse
|
16
|
Katrukha IA, Kogan AE, Vylegzhanina AV, Koshkina EV, Bereznikova AV, Katrukha AG. In Reply. Clin Chem 2017; 63:1769-1770. [DOI: 10.1373/clinchem.2017.280800] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Ivan A Katrukha
- HyTest Ltd., Turku, Finland
- Department of Biochemistry School of Biology Moscow State University Moscow, Russia
| | - Alexander E Kogan
- HyTest Ltd., Turku, Finland
- Department of Biochemistry School of Biology Moscow State University Moscow, Russia
| | | | | | - Anastasia V Bereznikova
- HyTest Ltd., Turku, Finland
- Department of Biochemistry School of Biology Moscow State University Moscow, Russia
| | - Alexey G Katrukha
- HyTest Ltd., Turku, Finland
- Department of Biochemistry School of Biology Moscow State University Moscow, Russia
| |
Collapse
|
17
|
Halvorsen TG, Reubsaet L. Antibody based affinity capture LC-MS/MS in quantitative determination of proteins in biological matrices. Trends Analyt Chem 2017. [DOI: 10.1016/j.trac.2017.08.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
|
18
|
Bodor GS. Cardiac Troponins: Molecules of Many Surprises. Clin Chem 2017; 63:1059-1060. [DOI: 10.1373/clinchem.2017.273094] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2017] [Accepted: 03/20/2017] [Indexed: 11/06/2022]
Affiliation(s)
- Geza S Bodor
- Department of Pathology, University of Colorado Denver, School of Medicine, Denver, CO
| |
Collapse
|
19
|
Fridén V, Starnberg K, Muslimovic A, Ricksten SE, Bjurman C, Forsgard N, Wickman A, Hammarsten O. Clearance of cardiac troponin T with and without kidney function. Clin Biochem 2017; 50:468-474. [DOI: 10.1016/j.clinbiochem.2017.02.007] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Revised: 02/07/2017] [Accepted: 02/09/2017] [Indexed: 01/29/2023]
|
20
|
Katrukha IA, Kogan AE, Vylegzhanina AV, Serebryakova MV, Koshkina EV, Bereznikova AV, Katrukha AG. Thrombin-Mediated Degradation of Human Cardiac Troponin T. Clin Chem 2017; 63:1094-1100. [PMID: 28428352 DOI: 10.1373/clinchem.2016.266635] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Accepted: 01/26/2017] [Indexed: 11/06/2022]
Abstract
BACKGROUND Cardiac troponin T (cTnT) is an acknowledged biomarker of acute myocardial infarction (AMI) that is known to be prone to proteolytic degradation in serum. Such degradation is usually explained by the action of μ-calpain, although there could be other candidates for that role. In the current study, we explored the hypothesis that thrombin-mediated cTnT cleavage occurs as a result of the serum sample preparation. METHODS cTnT degradation was studied by using immunoblotting and mass spectrometry (MS) analysis. RESULTS The comparison of cTnT isolated from AMI heparin plasma and serum samples showed that cTnT in the plasma samples was mainly present as the full-sized molecule (approximately 35 kDa), while in serum samples it was present as a 29-kDa fragment. The incubation of recombinant cTnT, or native ternary cardiac troponin complex with thrombin or in normal human serum (NHS), resulted in the formation of a 29-kDa product that was similar to that detected in AMI serum samples. No cTnT degradation was observed when thrombin or NHS was pretreated with hirudin, a specific inhibitor of thrombin, or during incubation of troponin in normal heparin plasma. When the products of thrombin-mediated cTnT proteolysis were analyzed by MS, 2 fragments consisting of amino acid residues (aar) 2-68 and 69-288 were identified, which suggests that thrombin cleaves cTnT between R68 and S69. CONCLUSIONS The results of this study suggest that the 29-kDa fragment of cTnT in AMI serum samples mainly appears due to the cleavage by thrombin during serum sample preparation.
Collapse
Affiliation(s)
- Ivan A Katrukha
- HyTest Ltd., Turku, Finland; .,Department of Biochemistry, School of Biology, Moscow State University, Moscow, Russia
| | - Alexander E Kogan
- HyTest Ltd., Turku, Finland.,Department of Biochemistry, School of Biology, Moscow State University, Moscow, Russia
| | | | - Marina V Serebryakova
- Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow, Russia
| | | | - Anastasia V Bereznikova
- HyTest Ltd., Turku, Finland.,Department of Biochemistry, School of Biology, Moscow State University, Moscow, Russia
| | - Alexey G Katrukha
- HyTest Ltd., Turku, Finland.,Department of Biochemistry, School of Biology, Moscow State University, Moscow, Russia
| |
Collapse
|
21
|
Chutipongtanate S, Chatchen S, Svasti J. Plasma prefractionation methods for proteomic analysis and perspectives in clinical applications. Proteomics Clin Appl 2017; 11. [DOI: 10.1002/prca.201600135] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Revised: 01/24/2017] [Accepted: 02/10/2017] [Indexed: 12/16/2022]
Affiliation(s)
- Somchai Chutipongtanate
- Pediatric Translational Research Unit, Department of Pediatrics, Faculty of Medicine Ramathibodi Hospital; Mahidol University; Salaya Thailand
| | - Supawat Chatchen
- Department of Tropical Pediatrics, Faculty of Tropical Medicine; Mahidol University; Salaya Thailand
| | - Jisnuson Svasti
- Laboratory of Biochemistry; Chulabhorn Research Institute, Krung Thep Maha Nakhon; Thailand
- Applied Biological Sciences Program; Chulabhorn Graduate Institute; Thailand
| |
Collapse
|
22
|
Streng AS, de Boer D, van Doorn WPTM, Bouwman FG, Mariman ECM, Bekers O, van Dieijen-Visser MP, Wodzig WKWH. Identification and Characterization of Cardiac Troponin T Fragments in Serum of Patients Suffering from Acute Myocardial Infarction. Clin Chem 2016; 63:563-572. [PMID: 27940450 DOI: 10.1373/clinchem.2016.261511] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Accepted: 09/06/2016] [Indexed: 12/22/2022]
Abstract
BACKGROUND Cardiac troponin T (cTnT) is the preferred biomarker for the diagnosis of acute myocardial infarction (AMI). It has been suggested that cTnT is present predominantly in fragmented forms in human serum following AMI. In this study, we have used a targeted mass spectrometry assay and epitope mapping using Western blotting to confirm this hypothesis. METHODS cTnT was captured from the serum of 12 patients diagnosed with AMI using an immunoprecipitation technique employing the M11.7 catcher antibody and fractionated with SDS-PAGE. Coomassie-stained bands of 4 patients at 37, 29, and 16 kDa were excised from the gel, digested with trypsin, and analyzed on a Q Exactive instrument set on targeted Selected Ion Monitoring mode with data-dependent tandem mass spectrometry (MS/MS) for identification. Western blotting employing 3 different antibodies was used for epitope mapping. RESULTS Ten cTnT peptides of interest were targeted. By using MS/MS, all of these peptides were identified in the 37-kDa, intact, cTnT band. In the 29- and 16-kDa fragment bands, 8 and 4 cTnT-specific peptides were identified, respectively. Some of these peptides were "semitryptic," meaning that their C-termini were not formed by trypsin cleavage. The C-termini of these semitryptic peptides represent the C-terminal end of the cTnT molecules present in these bands. These results were confirmed independently by epitope mapping. CONCLUSIONS Using LC-MS, we have succeeded in positively identifying the 29- and 16-kDa fragment bands as cTnT-derived products. The amino acid sequences of the 29- and 16-kDa fragments are Ser79-Trp297 and Ser79-Gln199, respectively.
Collapse
Affiliation(s)
- Alexander S Streng
- Department of Clinical Chemistry, Central Diagnostic Laboratory, Maastricht University Medical Centre, Maastricht, the Netherlands
| | - Douwe de Boer
- Department of Clinical Chemistry, Central Diagnostic Laboratory, Maastricht University Medical Centre, Maastricht, the Netherlands
| | - William P T M van Doorn
- Department of Clinical Chemistry, Central Diagnostic Laboratory, Maastricht University Medical Centre, Maastricht, the Netherlands
| | - Freek G Bouwman
- Department of Human Biology, Maastricht University, Maastricht, the Netherlands
| | - Edwin C M Mariman
- Department of Human Biology, Maastricht University, Maastricht, the Netherlands
| | - Otto Bekers
- Department of Clinical Chemistry, Central Diagnostic Laboratory, Maastricht University Medical Centre, Maastricht, the Netherlands
| | - Marja P van Dieijen-Visser
- Department of Clinical Chemistry, Central Diagnostic Laboratory, Maastricht University Medical Centre, Maastricht, the Netherlands
| | - Will K W H Wodzig
- Department of Clinical Chemistry, Central Diagnostic Laboratory, Maastricht University Medical Centre, Maastricht, the Netherlands;
| |
Collapse
|
23
|
Streng AS, de Boer D, van Doorn WP, Kocken JM, Bekers O, Wodzig WK. Cardiac troponin T degradation in serum is catalysed by human thrombin. Biochem Biophys Res Commun 2016; 481:165-168. [DOI: 10.1016/j.bbrc.2016.10.149] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Accepted: 10/31/2016] [Indexed: 12/21/2022]
|
24
|
Streng AS, de Boer D, Bouwman FG, Mariman ECM, Scholten A, van Dieijen-Visser MP, Wodzig WKWH. Validation, optimisation, and application data in support of the development of a targeted selected ion monitoring assay for degraded cardiac troponin T. Data Brief 2016; 7:397-405. [PMID: 26977445 PMCID: PMC4782000 DOI: 10.1016/j.dib.2016.02.051] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Revised: 02/03/2016] [Accepted: 02/19/2016] [Indexed: 11/30/2022] Open
Abstract
Cardiac troponin T (cTnT) fragmentation in human serum was investigated using a newly developed targeted selected ion monitoring assay, as described in the accompanying article: “Development of a targeted selected ion monitoring assay for the elucidation of protease induced structural changes in cardiac troponin T” [1]. This article presents data describing aspects of the validation and optimisation of this assay. The data consists of several figures, an excel file containing the results of a sequence identity search, and a description of the raw mass spectrometry (MS) data files, deposited in the ProteomeXchange repository with id PRIDE: PXD003187.
Collapse
Affiliation(s)
- Alexander S Streng
- Central Diagnostic Laboratory, Maastricht University Medical Centre, Maastricht, the Netherlands
| | - Douwe de Boer
- Central Diagnostic Laboratory, Maastricht University Medical Centre, Maastricht, the Netherlands
| | - Freek G Bouwman
- Department of Human Biology, Maastricht University, Maastricht, the Netherlands
| | - Edwin C M Mariman
- Department of Human Biology, Maastricht University, Maastricht, the Netherlands
| | - Arjen Scholten
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Centre for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, the Netherlands; Netherlands Proteomics Centre, Utrecht University, Utrecht, the Netherlands; Current working address: Janssen, Pharmaceutical Companies of Johnson&Johnson, Infectious Diseases and Vaccines, Leiden, the Netherlands
| | | | - Will K W H Wodzig
- Central Diagnostic Laboratory, Maastricht University Medical Centre, Maastricht, the Netherlands
| |
Collapse
|