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Liang K, Li Q, Song Z, Zhao K, Su R, Huang S, Guo X, Li Y. Endogenous Plasma Peptides Modulated by Protease in a Time-Dependent Manner as Effective Biomarkers for Preanalytical Quality Control. J Proteome Res 2023; 22:3029-3039. [PMID: 37530177 DOI: 10.1021/acs.jproteome.3c00335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/03/2023]
Abstract
Non-cryopreservation temperature exposure (NCE) is a vital preanalytical factor for assessing plasma quality. NCE can introduce undesirable errors in clinical diagnosis or when developing biomarkers of diseases. Biomarkers that can effectively indicate the changes in sample quality caused by long-term NCE (0-several days) are limited. Low-molecular-weight (LMW) peptides in the plasma are modulated by endogenous proteases. These protease activities are significantly correlated with NCE temperatures and duration, indicating a potential link of these protease reactions with the preanalytical quality of plasma samples. In this study, two groups of plasma samples were aged at room temperature (RT, 57 samples) and 4 °C (69 samples) for different durations (0, 1, 2, 5, and 10 days), and LMW peptidomics were analyzed through nanopore-assisted matrix-assisted laser desorption ionization time-of-flight mass spectrometry. The analysis revealed 10 peptides that consistently exhibited time-dependent changes, which were used to develop multiple-variable models for predicting the changes in sample quality resulting from extended NCE. These biomarker models exhibited outstanding performance in distinguishing poor-quality samples aged at both RT and 4 °C. To validate the findings, tests on samples from validation sets were conducted by analysts who were blinded to the detailed conditions, which revealed a high specificity (94.3-96.9%) and sensitivity (90.5-99.3%). These results indicate the potential of these peptides as novel biomarkers of quality control.
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Affiliation(s)
- Kai Liang
- Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- Western Institute of Health Data Science, Chongqin 400050, China
| | - Qianqian Li
- Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhijing Song
- Western Institute of Health Data Science, Chongqin 400050, China
| | - Keli Zhao
- Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Rong Su
- Foshan Hospital of Traditional Chinese Medicine, Foshan 528000, China
| | - Shengchun Huang
- Foshan Hospital of Traditional Chinese Medicine, Foshan 528000, China
| | - Xueyan Guo
- Foshan Hospital of Traditional Chinese Medicine, Foshan 528000, China
| | - Yan Li
- Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- Western Institute of Health Data Science, Chongqin 400050, China
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Popp D, Diekmann R, Binder L, Asif AR, Nussbeck SY. Liquid materials for biomedical research: a highly IT-integrated and automated biobanking solution. J LAB MED 2019. [DOI: 10.1515/labmed-2017-0118] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
AbstractVarious information technology (IT) infrastructures for biobanking, networks of biobanks and biomaterial management are described in the literature. As pre-analytical variables play a major role in the downstream interpretation of clinical as well as research results, their documentation is essential. A description for mainly automated documentation of the complete life-cycle of each biospecimen is lacking so far. Here, the example taken is from the University Medical Center Göttingen (UMG), where the workflow of liquid biomaterials is standardized between the central laboratory and the central biobank. The workflow of liquid biomaterials from sample withdrawal to long-term storage in a biobank was analyzed. Essential data such as time and temperature for processing and freezing can be automatically collected. The proposed solution involves only one major interface between the main IT systems of the laboratory and the biobank. It is key to talk to all the involved stakeholders to ensure a functional and accepted solution. Although IT components differ widely between clinics, the proposed way of documenting the complete life-cycle of each biospecimen can be transferred to other university medical centers. The complete documentation of the life-cycle of each biospecimen ensures a good interpretability of downstream routine as well as research results.
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Findeisen P, Hemanna S, Maharjan RS, Mindt S, Costina V, Hofheinz R, Neumaier M. Mass spectrometry based analytical quality assessment of serum and plasma specimens with patterns of endo- and exogenous peptides. Clin Chem Lab Med 2019; 57:668-678. [DOI: 10.1515/cclm-2018-0811] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Accepted: 11/05/2018] [Indexed: 12/23/2022]
Abstract
Abstract
Background
Inappropriate preanalytical sample handling is a major threat for any biomarker discovery approach. Blood specimens have a genuine proteolytic activity that leads to a time dependent decay of peptidic quality control markers (QCMs). The aim of this study was to identify QCMs for direct assessment of sample quality (DASQ) of serum and plasma specimens.
Methods
Serum and plasma specimens of healthy volunteers and tumor patients were spiked with two synthetic reporter peptides (exogenous QCMs) and aged under controlled conditions for up to 24 h. The proteolytic fragments of endogenous and exogenous QCMs were monitored for each time point by mass spectrometry (MS). The decay pattern of peptides was used for supervised classification of samples according to their respective preanalytical quality.
Results
The classification accuracy for fresh specimens (1 h) was 96% and 99% for serum and plasma specimens, respectively, when endo- and exogenous QCMs were used for the calculations. However, classification of older specimens was more difficult and overall classification accuracy decreased to 79%.
Conclusions
MALDI-TOF MS is a simple and robust method that can be used for DASQ of serum and plasma specimens in a high throughput manner. We propose DASQ as a fast and simple step that can be included in multicentric large-scale projects to ensure the homogeneity of sample quality.
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Kong FMS, Zhao L, Wang L, Chen Y, Hu J, Fu X, Bai C, Wang L, Lawrence TS, Anscher MS, Dicker A, Okunieff P. Ensuring sample quality for blood biomarker studies in clinical trials: a multicenter international study for plasma and serum sample preparation. Transl Lung Cancer Res 2017; 6:625-634. [PMID: 29218266 DOI: 10.21037/tlcr.2017.09.13] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Background Sample quality is critical for biomarker detection in oncology, and platelet degradation and contamination in plasma have a remarkable impact on the ability to accurately quantify many blood-based biomarkers. Platelet factor 4 (PF4) can be used as an indicator to monitor sample quality. This multicenter study aimed to determine the impact of critical components of the blood sample handling process on platelet degradation/contamination and to establish an optimal method for collecting platelet-poor plasma samples. Methods At each of six participating centers, blood samples were drawn from 12-13 healthy volunteers. Serum and plasma samples were prepared from whole blood samples using nine different methods that have been commonly used in ongoing multicenter trials. PF4 levels in the prepared samples were measured by enzyme-linked immunosorbent assay (ELISA). Paired t-tests were used for statistical analysis. Results Blood samples were collected from 74 subjects enrolled in six centers. PF4 levels were significantly higher in serum samples than in plasma samples (P<0.001), in plasma samples from blood that sat at room temperature for 5 minutes (P=0.021), in plasma samples prepared at an insufficient centrifugal force (P<0.001), and in plasma samples prepared from blood that sat for longer than 4 hours on ice (P=0.001). For each method, the PF4 levels did not differ significantly among the centers or between Chinese and American subjects. The methods that resulted in normal levels of PF4 involved keeping blood samples on ice for 30 minutes to <4 hours and centrifugation at 2,500-3,000 ×g for 30 min. Conclusions This multicenter study evaluated multiple blood sample handling conditions for minimizing platelet degradation during plasma serum preparation and determined an optimal method for preparing platelet-poor plasma. The findings of this study can be applied in future blood biomarker studies.
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Affiliation(s)
- Feng-Ming Spring Kong
- Department of Radiation Oncology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Lujun Zhao
- Department of Radiation Oncology, Tianjin Medical University Cancer Hospital, Tianjin 300060, China
| | - Luhua Wang
- Department of Radiation Oncology, Cancer Institute and Hospital, Chinese Academy of Science, Peking Union Medical College, Beijing 100021, China
| | - Yuhchyau Chen
- Deapartment of Radiation Oncology, University of Rochester, Rochester, NY, USA
| | - Jie Hu
- Department of Pulmonary Medicine, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Xiaolong Fu
- Department of Radiation Oncology, Chest Hospital, Jiaotong University, Shanghai 200030, China
| | - Chunxue Bai
- Department of Pulmonary Medicine, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Li Wang
- Department of Radiation Oncology, UT MD Anderson Cancer Center, Houston, TX, USA
| | - Theodore S Lawrence
- Department of Radiation Oncology, University of Michigan, Ann Arbor, Michigan, USA
| | - Mitchell S Anscher
- Department of Radiation Oncology, UT MD Anderson Cancer Center, Houston, TX, USA
| | - Adam Dicker
- Department of Radiation Oncology, Thomas Jefferson Hospital, Philadelphia, PA, USA
| | - Paul Okunieff
- Department of Radiation Oncology, University of Florida, Gainesville, FL, USA
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Mateos J, Carneiro I, Corrales F, Elortza F, Paradela A, Del Pino MS, Iloro I, Marcilla M, Mora MI, Valero L, Ciordia S, Fernández V, Fortuño MA, García-Sánchez I, Martínez R, Muñoz MA, Rodriguez C, Doménech N. Multicentric study of the effect of pre-analytical variables in the quality of plasma samples stored in biobanks using different complementary proteomic methods. J Proteomics 2016; 150:109-120. [PMID: 27620695 DOI: 10.1016/j.jprot.2016.09.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Revised: 09/06/2016] [Accepted: 09/07/2016] [Indexed: 12/27/2022]
Abstract
Analytical proteomics has experienced exponential progress in the last decade and can be expected to lead research studies on diagnostic and therapeutic biomarkers in the near future. Because the development of this type of analysis requires the use of a large number of human samples with a minimum of quality requirements, our objective was to identify appropriate indicators for quality control of plasma samples stored in biobanks for research in proteomics. To accomplish this, plasma samples from 100 healthy donors were obtained and processed according to the pre-analytical variables of: a) time delay for the first centrifugation of the original blood sample (4 or 24h) and b) number of freeze/thaw cycles (1, 2 or 3) of the processed plasma samples. The analyses of samples were performed by different and complementary methods such as SPE MALDI-TOF, DIGE, shotgun (iTRAQ, nLC MALDI TOF/TOF) and targeted nLC MS/MS proteomic techniques (SRM). In general, because the distribution of proteins in all samples was found to be very similar, the results shown that delayed processing of blood samples and the number of freeze/thaw cycles has little or no effect on the integrity of proteins in the plasma samples. SIGNIFICANCE The results of the present work indicate that blood proteins in plasma are broadly insensitive to such preanalytical variables as delayed processing or freeze/thaw cycles when analyzed at the peptide level. Although there are other studies related to protein stability of clinical samples with similar results, what is remarkable about our work is the large number of plasma samples examined and that our analyses assessed protein integrity by combining a wide set of complementary proteomic approaches performed at different proteomic platform participating laboratories that all yielded similar results. We believe our study is the most comprehensive performed to date to determine the changes in proteins induced by delayed sample processing and plasma freeze/thaw cycles.
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Affiliation(s)
- Jesús Mateos
- Plataforma de Proteómica, Instituto de Investigación Biomédica (INIBIC), A Coruña, Spain
| | | | - Fernando Corrales
- Centro de Investigación en Medicina Aplicada (CIMA)-UN, Pamplona, Spain
| | - Felix Elortza
- Centro de Investigación Cooperativa en Biociencias CICbioGUNE, Derio, Spain
| | | | | | - Ibon Iloro
- Centro de Investigación Cooperativa en Biociencias CICbioGUNE, Derio, Spain
| | | | - Maria Isabel Mora
- Centro de Investigación en Medicina Aplicada (CIMA)-UN, Pamplona, Spain
| | - Luz Valero
- Universidad de Valencia (UV), Valencia, Spain
| | - Sergio Ciordia
- Centro Nacional de Biotecnología (CNB)-CSIC, Madrid, Spain
| | - Verónica Fernández
- Biobanco HCB-IDIBAPS, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | | | | | | | | | - Clara Rodriguez
- Biobanco Vasco/Centro Vasco de Transfusiones, Barakaldo, Spain
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Herpel E, Schmitt S, Kiehntopf M. Qualität von Biomaterialien im Biobanking von Flüssig- und Gewebeproben. Bundesgesundheitsblatt Gesundheitsforschung Gesundheitsschutz 2016; 59:325-35. [PMID: 26753866 DOI: 10.1007/s00103-015-2294-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Affiliation(s)
- Esther Herpel
- Pathologisches Institut, Universitätsklinikum Heidelberg, Heidelberg, Deutschland
- Gewebebank des Nationalen Centrums für Tumorerkrankungen (NCT), Universitätsklinikum Heidelberg, Heidelberg, Deutschland
| | - Sabrina Schmitt
- Gewebebank des Nationalen Centrums für Tumorerkrankungen (NCT), Universitätsklinikum Heidelberg, Heidelberg, Deutschland
| | - Michael Kiehntopf
- Institut für Klinische Chemie und Laboratoriumsdiagnostik, Universitätsklinikum Jena, Jena, Deutschland.
- Integrierte Biobank Jena (IBBJ), Universitätsklinikum Jena, Jena, Deutschland.
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Reumer A, Maes E, Mertens I, Cho WCS, Landuyt B, Valkenborg D, Schoofs L, Baggerman G. Colorectal cancer biomarker discovery and validation using LC-MS/MS-based proteomics in blood: truth or dare? Expert Rev Proteomics 2014; 11:449-463. [PMID: 24702250 DOI: 10.1586/14789450.2014.905743] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
Globally, colorectal cancer (CRC) is the third most common malignant neoplasm. However, highly sensitive, specific, noninvasive tests that allow CRC diagnosis at an early stage are still needed. As circulatory blood reflects the physiological status of an individual and/or the disease status for several disorders, efforts have been undertaken to identify candidate diagnostic CRC markers in plasma and serum. In this review, the challenges, bottlenecks and promising properties of mass spectrometry (MS)-based proteomics in blood are discussed. More specifically, important aspects in clinical design, sample retrieval, sample preparation, and MS analysis are presented. The recent developments in targeted MS approaches in plasma or serum are highlighted as well.
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Affiliation(s)
- Ank Reumer
- KU Leuven, Animal Physiology and Neurobiology Section, Naamsestraat 59, BE-3000 Leuven, Belgium
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Yepes D, Costina V, Pilz LR, Hofheinz R, Neumaier M, Findeisen P. Multiplex profiling of tumor-associated proteolytic activity in serum of colorectal cancer patients. Proteomics Clin Appl 2014; 8:308-16. [PMID: 24616428 DOI: 10.1002/prca.201300103] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2013] [Revised: 01/19/2014] [Accepted: 03/05/2014] [Indexed: 01/05/2023]
Abstract
PURPOSE The monitoring of tumor-associated protease activity in blood specimens has recently been proposed as new diagnostic tool in cancer research. In this paper, we describe the screening of a peptide library for identification of reporter peptides (RPs) that are selectively cleaved in serum specimens from colorectal cancer patients and investigate the benefits of RP multiplexing. EXPERIMENTAL DESIGN A library of 144 RPs was constructed that contained amino acid sequences of abundant plasma proteins. Proteolytic cleavage of RPs was monitored with MS. Five RPs that were selectively cleaved in serum specimens from tumor patients were selected for further validation in serum specimens of colorectal tumor patients (n = 30) and nonmalignant controls (n = 60). RESULTS RP spiking and subsequent quantification of proteolytic fragments with LC-MS showed good reproducibility with CVs always below 26%. The linear discriminant analysis and PCA revealed that a combination of RPs for diagnostic classification is superior to single markers. Classification accuracy reached 88% (79/90) when all five markers were combined. CONCLUSIONS AND CLINICAL RELEVANCE Functional protease profiling with RPs might improve the laboratory-based diagnosis, monitoring and prognosis of malignant disease, and has to be evaluated thoroughly in future studies.
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Affiliation(s)
- Diego Yepes
- Institute for Clinical Chemistry, Medical Faculty Mannheim of the University of Heidelberg, University Hospital Mannheim, Mannheim, Germany
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Patrie SM, Roth MJ, Plymire DA, Maresh E, Zhang J. Measurement of Blood Protease Kinetic Parameters with Self-Assembled Monolayer Ligand Binding Assays and Label-Free MALDI-TOF MS. Anal Chem 2013; 85:10597-604. [DOI: 10.1021/ac402739z] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Steven M. Patrie
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9072
| | - Michael J. Roth
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9072
| | - Daniel A. Plymire
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9072
| | - Erica Maresh
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9072
| | - Junmei Zhang
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9072
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