1
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Richard V, Mitsa G, Eshghi A, Chaplygina D, Mohammed Y, Goodlett DR, Zahedi RP, Thevis M, Borchers CH. Establishing Personalized Blood Protein Reference Ranges Using Noninvasive Microsampling and Targeted Proteomics: Implications for Antidoping Strategies. J Proteome Res 2024; 23:1779-1787. [PMID: 38655860 PMCID: PMC11077581 DOI: 10.1021/acs.jproteome.4c00020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 03/28/2024] [Accepted: 04/05/2024] [Indexed: 04/26/2024]
Abstract
To prevent doping practices in sports, the World Anti-Doping Agency implemented the Athlete Biological Passport (ABP) program, monitoring biological variables over time to indirectly reveal the effects of doping rather than detect the doping substance or the method itself. In the context of this program, a highly multiplexed mass spectrometry-based proteomics assay for 319 peptides corresponding to 250 proteins was developed, including proteins associated with blood-doping practices. "Baseline" expression profiles of these potential biomarkers in capillary blood (dried blood spots (DBS)) were established using multiple reaction monitoring (MRM). Combining DBS microsampling with highly multiplexed MRM assays is the best-suited technology to enhance the effectiveness of the ABP program, as it represents a cost-effective and robust alternative analytical method with high specificity and selectivity of targets in the attomole range. DBS data were collected from 10 healthy athlete volunteers over a period of 140 days (28 time points per participant). These comprehensive findings provide a personalized targeted blood proteome "fingerprint" showcasing that the targeted proteome is unique to an individual and likely comparable to a DNA fingerprint. The results can serve as a baseline for future studies investigating doping-related perturbations.
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Affiliation(s)
- Vincent
R. Richard
- Segal
Cancer Proteomics Centre, Lady Davis Institute
for Medical Research, Jewish General Hospital, Montréal, Quebec H3T 1E2, Canada
| | - Georgia Mitsa
- Segal
Cancer Proteomics Centre, Lady Davis Institute
for Medical Research, Jewish General Hospital, Montréal, Quebec H3T 1E2, Canada
- Division
of Experimental Medicine, McGill University, Montréal, Quebec H4A 3J1, Canada
| | - Azad Eshghi
- University
of Victoria-Genome BC Proteomics Centre, Victoria, British Columbia V8Z 7X8, Canada
| | - Daria Chaplygina
- Segal
Cancer Proteomics Centre, Lady Davis Institute
for Medical Research, Jewish General Hospital, Montréal, Quebec H3T 1E2, Canada
| | - Yassene Mohammed
- Center
for Proteomics and Metabolomics, Leiden
University Medical Center, Leiden 2333 ZC, The Netherlands
| | - David R. Goodlett
- University
of Victoria-Genome BC Proteomics Centre, Victoria, British Columbia V8Z 7X8, Canada
| | - Rene P. Zahedi
- Manitoba
Centre for Proteomics and Systems Biology, Winnipeg, Manitoba R3E 3P4, Canada
- Department
of Internal Medicine, University of Manitoba, Winnipeg, Manitoba R3E 3P4, Canada
- Department
of Biochemistry and Medical Genetics, University
of Manitoba, Winnipeg, Manitoba R3E 0J9, Canada
- CancerCare
Manitoba Research Institute, Winnipeg, Manitoba R3E 0V9, Canada
| | - Mario Thevis
- Institute
of Biochemistry, Center for Preventive Doping Research, German Sport University Cologne, Cologne 50933, Germany
- European
Monitoring Center for Emerging Doping Agents (EuMoCEDA), Cologne/Bonn 50933, Germany
| | - Christoph H. Borchers
- Segal
Cancer Proteomics Centre, Lady Davis Institute
for Medical Research, Jewish General Hospital, Montréal, Quebec H3T 1E2, Canada
- Division
of Experimental Medicine, McGill University, Montréal, Quebec H4A 3J1, Canada
- Gerald
Bronfman Department of Oncology, McGill
University, Montréal, Quebec H4A 3T2, Canada
- Department
of Pathology, McGill University, Montréal, Quebec H4A 3J1, Canada
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2
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Farkona S, Pastrello C, Konvalinka A. Proteomics: Its Promise and Pitfalls in Shaping Precision Medicine in Solid Organ Transplantation. Transplantation 2023; 107:2126-2142. [PMID: 36808112 DOI: 10.1097/tp.0000000000004539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Abstract
Solid organ transplantation is an established treatment of choice for end-stage organ failure. However, all transplant patients are at risk of developing complications, including allograft rejection and death. Histological analysis of graft biopsy is still the gold standard for evaluation of allograft injury, but it is an invasive procedure and prone to sampling errors. The past decade has seen an increased number of efforts to develop minimally invasive procedures for monitoring allograft injury. Despite the recent progress, limitations such as the complexity of proteomics-based technology, the lack of standardization, and the heterogeneity of populations that have been included in different studies have hindered proteomic tools from reaching clinical transplantation. This review focuses on the role of proteomics-based platforms in biomarker discovery and validation in solid organ transplantation. We also emphasize the value of biomarkers that provide potential mechanistic insights into the pathophysiology of allograft injury, dysfunction, or rejection. Additionally, we forecast that the growth of publicly available data sets, combined with computational methods that effectively integrate them, will facilitate a generation of more informed hypotheses for potential subsequent evaluation in preclinical and clinical studies. Finally, we illustrate the value of combining data sets through the integration of 2 independent data sets that pinpointed hub proteins in antibody-mediated rejection.
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Affiliation(s)
- Sofia Farkona
- Toronto General Hospital Research Institute, University Health Network, Toronto, ON, Canada
- Soham and Shaila Ajmera Family Transplant Centre, University Health Network, Toronto, ON, Canada
| | - Chiara Pastrello
- Osteoarthritis Research Program, Division of Orthopedic Surgery, Schroeder Arthritis Institute University Health Network, Toronto, ON, Canada
- Data Science Discovery Centre for Chronic Diseases, Krembil Research Institute, Toronto Western Hospital, University Health Network, Toronto, ON, Canada
| | - Ana Konvalinka
- Toronto General Hospital Research Institute, University Health Network, Toronto, ON, Canada
- Soham and Shaila Ajmera Family Transplant Centre, University Health Network, Toronto, ON, Canada
- Department of Medicine, Division of Nephrology, University Health Network, Toronto, ON, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
- Institute of Medical Science, University of Toronto, Toronto, ON, Canada
- Canadian Donation and Transplantation Research Program, Edmonton, AB, Canada
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3
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Novikova S, Soloveva N, Farafonova T, Tikhonova O, Shimansky V, Kugushev I, Zgoda V. Proteomic Shotgun and Targeted Mass Spectrometric Datasets of Cerebrospinal Fluid (Liquor) Derived from Patients with Vestibular Schwannoma. DATA 2023. [DOI: 10.3390/data8040071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/08/2023] Open
Abstract
Vestibular schwannomas are relatively rare intracranial tumors compared to other brain tumors. Data on the molecular features, especially on schwannoma proteome, are scarce. The 41 cerebrospinal fluid (liquor) samples were obtained during the surgical removal of vestibular schwannoma. Obtained peptide samples were analyzed by shotgun LC-MS/MS high-resolution mass spectrometry. The same peptide samples were spiked with 148 stable isotopically labeled peptide standards (SIS) followed by alkaline fractionation and scheduled multiple reaction monitoring (MRM) for quantitative analysis. The natural counterparts of SIS peptides were mapped onto 111 proteins that were Food and Drug Administration (FDA)-approved for diagnostic use. As a result, 525 proteins were identified by shotgun LC-MS/MS with high confidence (at least two peptides per protein, FDR < 1%) in liquor samples. Absolute quantitative concentrations were obtained for 54 FDA-approved proteins detected in at least five experimental samples. Since there is lack of data on the molecular landscape of vestibular schwannoma, the obtained datasets are unique and one of the first in its field.
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Affiliation(s)
| | | | | | - Olga Tikhonova
- Institute of Biomedical Chemistry, 119121 Moscow, Russia
| | - Vadim Shimansky
- N.N. Burdenko National Scientific and Practical Center for Neurosurgery, 125047 Moscow, Russia
| | - Ivan Kugushev
- N.N. Burdenko National Scientific and Practical Center for Neurosurgery, 125047 Moscow, Russia
| | - Victor Zgoda
- Institute of Biomedical Chemistry, 119121 Moscow, Russia
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4
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Mohammed Y, Goodlett D, Borchers CH. Absolute Quantitative Targeted Proteomics Assays for Plasma Proteins. Methods Mol Biol 2023; 2628:439-473. [PMID: 36781801 DOI: 10.1007/978-1-0716-2978-9_27] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023]
Abstract
Preclinical and clinical trials require rapid, precise, and multiplexed analytical methods to characterize the complex samples and to allow high-throughput biomarker monitoring with low consumption of sample material. Targeted proteomics has been used to address these challenges when quantifying protein abundances in complex biological matrices. In many of these studies, blood plasma is collected either as the main research or diagnostic sample or in combination with other specimens. Mass spectrometry (MS)-based targeted proteomics using multiple reaction monitoring (MRM) or parallel reaction monitoring (PRM) with stable isotope-labeled internal standard (SIS) peptides allows robust characterization of blood plasma protein via absolute quantification. Compared to other commonly used technologies like enzyme-linked immunosorbent assay (ELISA), targeted proteomics is faster, more sensitive, and more cost-effective. Here we describe a protocol for the quantification of proteins in blood plasma using targeted MRM proteomics with heavy-labeled internal standards. The 270-protein panel allows rapid and robust absolute quantitative proteomic characterization of blood plasma in a 1 h gradient. The method we describe here works for non-depleted plasma, which makes it simple and easy to implement. Moreover, the protocol works with the two most commonly used blood plasma collection methods used in practice, namely, either K2EDTA or sodium citrate as anticoagulants.
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Affiliation(s)
- Yassene Mohammed
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands. .,University of Victoria - Genome BC Proteomics Centre, Victoria, BC, Canada.
| | - David Goodlett
- University of Victoria - Genome BC Proteomics Centre, Victoria, BC, Canada.,Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada.,University of Gdansk, International Centre for Cancer Vaccine Science, Gdansk, Poland
| | - Christoph H Borchers
- Proteomics Centre, Segal Cancer Centre, Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, QC, Canada.,Gerald Bronfman Department of Oncology, Jewish General Hospital, Montreal, QC, Canada.,Division of Experimental Medicine, McGill University, Montreal, QC, Canada.,Department of Pathology, McGill University, Montreal, QC, Canada
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5
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Kong W, Hui HWH, Peng H, Goh WWB. Dealing with missing values in proteomics data. Proteomics 2022; 22:e2200092. [PMID: 36349819 DOI: 10.1002/pmic.202200092] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 09/15/2022] [Accepted: 10/11/2022] [Indexed: 11/10/2022]
Abstract
Proteomics data are often plagued with missingness issues. These missing values (MVs) threaten the integrity of subsequent statistical analyses by reduction of statistical power, introduction of bias, and failure to represent the true sample. Over the years, several categories of missing value imputation (MVI) methods have been developed and adapted for proteomics data. These MVI methods perform their tasks based on different prior assumptions (e.g., data is normally or independently distributed) and operating principles (e.g., the algorithm is built to address random missingness only), resulting in varying levels of performance even when dealing with the same dataset. Thus, to achieve a satisfactory outcome, a suitable MVI method must be selected. To guide decision making on suitable MVI method, we provide a decision chart which facilitates strategic considerations on datasets presenting different characteristics. We also bring attention to other issues that can impact proper MVI such as the presence of confounders (e.g., batch effects) which can influence MVI performance. Thus, these too, should be considered during or before MVI.
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Affiliation(s)
- Weijia Kong
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore.,School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Harvard Wai Hann Hui
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore.,School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Hui Peng
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore.,School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Wilson Wen Bin Goh
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore.,School of Biological Sciences, Nanyang Technological University, Singapore, Singapore.,Centre for Biomedical Informatics, Nanyang Technological University, Singapore, Singapore
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6
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Gabriel W, The M, Zolg DP, Bayer FP, Shouman O, Lautenbacher L, Schnatbaum K, Zerweck J, Knaute T, Delanghe B, Huhmer A, Wenschuh H, Reimer U, Médard G, Kuster B, Wilhelm M. Prosit-TMT: Deep Learning Boosts Identification of TMT-Labeled Peptides. Anal Chem 2022; 94:7181-7190. [PMID: 35549156 DOI: 10.1021/acs.analchem.1c05435] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The prediction of fragment ion intensities and retention time of peptides has gained significant attention over the past few years. However, the progress shown in the accurate prediction of such properties focused primarily on unlabeled peptides. Tandem mass tags (TMT) are chemical peptide labels that are coupled to free amine groups usually after protein digestion to enable the multiplexed analysis of multiple samples in bottom-up mass spectrometry. It is a standard workflow in proteomics ranging from single-cell to high-throughput proteomics. Particularly for TMT, increasing the number of confidently identified spectra is highly desirable as it provides identification and quantification information with every spectrum. Here, we report on the generation of an extensive resource of synthetic TMT-labeled peptides as part of the ProteomeTools project and present the extension of the deep learning model Prosit to accurately predict the retention time and fragment ion intensities of TMT-labeled peptides with high accuracy. Prosit-TMT supports CID and HCD fragmentation and ion trap and Orbitrap mass analyzers in a single model. Reanalysis of published TMT data sets show that this single model extracts substantial additional information. Applying Prosit-TMT, we discovered that the expression of many proteins in human breast milk follows a distinct daily cycle which may prime the newborn for nutritional or environmental cues.
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Affiliation(s)
- Wassim Gabriel
- Computational Mass Spectrometry, Technical University of Munich, 85354 Freising, Germany
| | - Matthew The
- Chair of Proteomics and Bioanalytics, Technical University of Munich, 85354 Freising, Germany
| | - Daniel P Zolg
- Chair of Proteomics and Bioanalytics, Technical University of Munich, 85354 Freising, Germany
| | - Florian P Bayer
- Chair of Proteomics and Bioanalytics, Technical University of Munich, 85354 Freising, Germany
| | - Omar Shouman
- Computational Mass Spectrometry, Technical University of Munich, 85354 Freising, Germany
| | - Ludwig Lautenbacher
- Computational Mass Spectrometry, Technical University of Munich, 85354 Freising, Germany
| | | | | | - Tobias Knaute
- JPT Peptide Technologies GmbH, 12489 Berlin, Germany
| | | | - Andreas Huhmer
- Thermo Fisher Scientific, San Jose, California 95134, United States
| | | | - Ulf Reimer
- JPT Peptide Technologies GmbH, 12489 Berlin, Germany
| | - Guillaume Médard
- Chair of Proteomics and Bioanalytics, Technical University of Munich, 85354 Freising, Germany
| | - Bernhard Kuster
- Chair of Proteomics and Bioanalytics, Technical University of Munich, 85354 Freising, Germany.,Bavarian Center for Biomolecular Mass Spectrometry, 85354 Freising, Germany
| | - Mathias Wilhelm
- Computational Mass Spectrometry, Technical University of Munich, 85354 Freising, Germany
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7
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Proteomic Analysis of Maternal Urine for the Early Detection of Preeclampsia and Fetal Growth Restriction. J Clin Med 2021; 10:jcm10204679. [PMID: 34682802 PMCID: PMC8537852 DOI: 10.3390/jcm10204679] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Revised: 10/05/2021] [Accepted: 10/06/2021] [Indexed: 12/30/2022] Open
Abstract
Background: To explore the use of maternal urine proteome for the identification of preeclampsia biomarkers. Methods: Maternal urine samples from women with and without preeclampsia were used for protein discovery followed by a validation study. The targeted proteins of interest were then measured in urine samples collected at 20–24 and 30–34 weeks among nine women who developed preeclampsia, one woman with fetal growth restriction, and 20 women with uncomplicated pregnancies from a longitudinal study. Protein identification and quantification was obtained using liquid chromatography–tandem mass spectrometry (LC–MS/MS). Results: Among the 1108 urine proteins quantified in the discovery study, 21 were upregulated in preeclampsia and selected for validation. Nineteen (90%) proteins were confirmed as upregulated in preeclampsia cases. Among them, two proteins, ceruloplasmin and serpin A7, were upregulated at 20–24 weeks and 30–34 weeks of gestation (p < 0.05) in cases of preeclampsia, and could have served to identify 60% of women who subsequently developed preeclampsia and/or fetal growth restriction at 20–24 weeks of gestation, and 78% at 30–34 weeks, for a false-positive rate of 10%. Conclusions: Proteomic profiling of maternal urine can differentiate women with and without preeclampsia. Several proteins including ceruloplasmin and serpin A7 are upregulated in maternal urine before the diagnosis of preeclampsia and potentially fetal growth restriction.
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8
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Anderson P, Gadgil R, Johnson WA, Schwab E, Davidson JM. Reducing variability of breast cancer subtype predictors by grounding deep learning models in prior knowledge. Comput Biol Med 2021; 138:104850. [PMID: 34536702 DOI: 10.1016/j.compbiomed.2021.104850] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 08/31/2021] [Accepted: 09/05/2021] [Indexed: 12/23/2022]
Abstract
Deep learning neural networks have improved performance in many cancer informatics problems, including breast cancer subtype classification. However, many networks experience underspecificationwheremultiplecombinationsofparametersachievesimilarperformance, bothin training and validation. Additionally, certain parameter combinations may perform poorly when the test distribution differs from the training distribution. Embedding prior knowledge from the literature may address this issue by boosting predictive models that provide crucial, in-depth information about a given disease. Breast cancer research provides a wealth of such knowledge, particularly in the form of subtype biomarkers and genetic signatures. In this study, we draw on past research on breast cancer subtype biomarkers, label propagation, and neural graph machines to present a novel methodology for embedding knowledge into machine learning systems. We embed prior knowledge into the loss function in the form of inter-subject distances derived from a well-known published breast cancer signature. Our results show that this methodology reduces predictor variability on state-of-the-art deep learning architectures and increases predictor consistency leading to improved interpretation. We find that pathway enrichment analysis is more consistent after embedding knowledge. This novel method applies to a broad range of existing studies and predictive models. Our method moves the traditional synthesis of predictive models from an arbitrary assignment of weights to genes toward a more biologically meaningful approach of incorporating knowledge.
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Affiliation(s)
- Paul Anderson
- Department of Computer Science and Software Engineering, California Polytechnic State University, San Luis Obispo, CA, USA
| | - Richa Gadgil
- Department of Computer Science and Software Engineering, California Polytechnic State University, San Luis Obispo, CA, USA
| | - William A Johnson
- Department of Biology, California Polytechnic State University, San Luis Obispo, CA, USA
| | - Ella Schwab
- Department of Biology, California Polytechnic State University, San Luis Obispo, CA, USA
| | - Jean M Davidson
- Department of Biology, California Polytechnic State University, San Luis Obispo, CA, USA.
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9
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Gao J, Ulvik A, McCann A, Ueland PM, Meyer K. Microheterogeneity and preanalytical stability of protein biomarkers of inflammation and renal function. Talanta 2021; 223:121774. [PMID: 33303176 DOI: 10.1016/j.talanta.2020.121774] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 10/09/2020] [Accepted: 10/11/2020] [Indexed: 02/01/2023]
Abstract
Protein biomarker microheterogeneity has attracted increasing attention in epidemiological and clinical research studies. Knowledge concerning the preanalytical stability of proteins is paramount to assess the biological significance of their proteoforms. We investigated the stability of the inflammatory markers C-reactive protein (CRP), serum amyloid A (SAA), and calprotectin (S100A8/9), and the renal function marker, cystatin C (CnC). In total 16 proteoforms were quantified by immuno-MALDI-TOF MS in EDTA plasma and serum samples from 15 healthy volunteers. Prior to analysis blood samples were stored at either room temperature from 1 h up to 8 days, or underwent up to 9 consecutive freeze/thaw cycles. Pearson's correlation coefficient and t-test, intra-class correlation coefficient (ICC), and Autoregressive Integrated Moving-Average (ARIMA) models were used to investigate the stability of proteoform concentrations and distributions in blood. Plasma and serum concentrations of CRP and SAA proteoforms were highly stable during room temperature exposure and repeated freeze/thaw cycles, demonstrating excellent reproducibility (ICC > 0.75), no serial dependency in ARIMA models, and stable distribution of proteoforms. Stability analyses for proteoforms of S100A8/9 and CnC identified only minor preanalytical changes in concentrations and distributions, and none of the proteoforms were produced during prolonged exposure to room temperature or repeated freezing/thawing. The four proteins and their proteoforms are stable during sub-optimal sample handling, and represent robust biomarker candidates for future biobank studies aimed at investigating the microheterogeneity of SAA, S100A8/9, and CnC in relation to inflammation, renal dysfunction and various clinical outcomes.
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Affiliation(s)
- Jie Gao
- Department of Clinical Science, University of Bergen, 5021, Bergen, Norway.
| | - Arve Ulvik
- Bevital AS, Jonas Lies veg 87, Laboratory building, 5021, Bergen, Norway
| | - Adrian McCann
- Bevital AS, Jonas Lies veg 87, Laboratory building, 5021, Bergen, Norway
| | - Per Magne Ueland
- Bevital AS, Jonas Lies veg 87, Laboratory building, 5021, Bergen, Norway
| | - Klaus Meyer
- Bevital AS, Jonas Lies veg 87, Laboratory building, 5021, Bergen, Norway
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10
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Bramer LM, Irvahn J, Piehowski PD, Rodland KD, Webb-Robertson BJM. A Review of Imputation Strategies for Isobaric Labeling-Based Shotgun Proteomics. J Proteome Res 2020; 20:1-13. [PMID: 32929967 DOI: 10.1021/acs.jproteome.0c00123] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The throughput efficiency and increased depth of coverage provided by isobaric-labeled proteomics measurements have led to increased usage of these techniques. However, the structure of missing data is different than unlabeled studies, which prompts the need for this review to compare the efficacy of nine imputation methods on large isobaric-labeled proteomics data sets to guide researchers on the appropriateness of various imputation methods. Imputation methods were evaluated by accuracy, statistical hypothesis test inference, and run time. In general, expectation maximization and random forest imputation methods yielded the best performance, and constant-based methods consistently performed poorly across all data set sizes and percentages of missing values. For data sets with small sample sizes and higher percentages of missing data, results indicate that statistical inference with no imputation may be preferable. On the basis of the findings in this review, there are core imputation methods that perform better for isobaric-labeled proteomics data, but great care and consideration as to whether imputation is the optimal strategy should be given for data sets comprised of a small number of samples.
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Affiliation(s)
- Lisa M Bramer
- Computing & Analytics Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Jan Irvahn
- Boeing, Seattle, Washington 98055, United States
| | - Paul D Piehowski
- Biological Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Blvd., Richland, Washington 99354, United States
| | - Karin D Rodland
- Biological Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Blvd., Richland, Washington 99354, United States
| | - Bobbie-Jo M Webb-Robertson
- Biological Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Blvd., Richland, Washington 99354, United States
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11
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Eshghi A, Pistawka AJ, Liu J, Chen M, Sinclair NJT, Hardie DB, Elliott M, Chen L, Newman R, Mohammed Y, Borchers CH. Concentration Determination of >200 Proteins in Dried Blood Spots for Biomarker Discovery and Validation. Mol Cell Proteomics 2020; 19:540-553. [PMID: 31896676 PMCID: PMC7050112 DOI: 10.1074/mcp.tir119.001820] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 12/06/2019] [Indexed: 12/26/2022] Open
Abstract
The use of protein biomarkers as surrogates for clinical endpoints requires extensive multilevel validation including development of robust and sensitive assays for precise measurement of protein concentration. Multiple reaction monitoring (MRM) is a well-established mass-spectrometric method that can be used for reproducible protein-concentration measurements in biological specimens collected via microsampling. The dried blood spot (DBS) microsampling technique can be performed non-invasively without the expertise of a phlebotomist, and can enhance analyte stability which facilitate the application of this technique in retrospective studies while providing lower storage and shipping costs, because cold-chain logistics can be eliminated. Thus, precise, sensitive, and multiplexed methods for measuring protein concentrations in DBSs can be used for de novo biomarker discovery and for biomarker quantification or verification experiments. To achieve this goal, MRM assays were developed for multiplexed concentration measurement of proteins in DBSs.The lower limit of quantification (LLOQ) was found to have a median total coefficient of variation (CV) of 18% for 245 proteins, whereas the median LLOQ was 5 fmol of peptide injected on column, and the median inter-day CV over 4 days for measuring endogenous protein concentration was 8%. The majority (88%) of the assays displayed parallelism, whereas the peptide standards remained stable throughout the assay workflow and after exposure to multiple freeze-thaw cycles. For 190 proteins, the measured protein concentrations remained stable in DBS stored at ambient laboratory temperature for up to 2 months. Finally, the developed assays were used to measure the concentration ranges for 200 proteins in twenty same sex, same race and age matched individuals.
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Affiliation(s)
- Azad Eshghi
- University of Victoria - Genome BC Proteomics Centre, University of Victoria, Victoria, British Columbia V8Z 7X8, Canada.
| | - Adam J Pistawka
- University of Victoria - Genome BC Proteomics Centre, University of Victoria, Victoria, British Columbia V8Z 7X8, Canada
| | - Jun Liu
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia V6T 2B5, Canada
| | - Michael Chen
- Island Medical Program, Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia V6T 2B5, Canada
| | - Nicholas J T Sinclair
- University of Victoria - Genome BC Proteomics Centre, University of Victoria, Victoria, British Columbia V8Z 7X8, Canada
| | - Darryl B Hardie
- University of Victoria - Genome BC Proteomics Centre, University of Victoria, Victoria, British Columbia V8Z 7X8, Canada
| | - Monica Elliott
- University of Victoria - Genome BC Proteomics Centre, University of Victoria, Victoria, British Columbia V8Z 7X8, Canada
| | - Lei Chen
- University of Victoria - Genome BC Proteomics Centre, University of Victoria, Victoria, British Columbia V8Z 7X8, Canada
| | - Rachael Newman
- University of Victoria - Genome BC Proteomics Centre, University of Victoria, Victoria, British Columbia V8Z 7X8, Canada
| | - Yassene Mohammed
- University of Victoria - Genome BC Proteomics Centre, University of Victoria, Victoria, British Columbia V8Z 7X8, Canada; Center for Proteomics and Metabolomics, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, The Netherlands
| | - Christoph H Borchers
- University of Victoria - Genome BC Proteomics Centre, University of Victoria, Victoria, British Columbia V8Z 7X8, Canada; Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia V8P 5C2, Canada; Segal Cancer Proteomics Centre, Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, Quebec H3T 1E2, Canada; Gerald Bronfman Department of Oncology, Jewish General Hospital, McGill University, Montreal, Quebec H3T 1E2, Canada; Department of Data Intensive Science and Engineering, Skolkovo Institute of Science and Technology, Skolkovo Innovation Center, Nobel St., Moscow143026, Russia.
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12
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Teclemariam ET, Pergande MR, Cologna SM. Considerations for mass spectrometry-based multi-omic analysis of clinical samples. Expert Rev Proteomics 2020; 17:99-107. [PMID: 31996049 DOI: 10.1080/14789450.2020.1724540] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Introduction: The role of mass spectrometry in biomolecule analysis has become paramount over the last several decades ranging in the analysis across model systems and human specimens. Accordingly, the presence of mass spectrometers in clinical laboratories has also expanded alongside the number of researchers investigating the protein, lipid, and metabolite composition of an array of biospecimens. With this increase in the number of omic investigations, it is important to consider the entire experimental strategy from sample collection and storage, data collection and analysis.Areas covered: In this short review, we outline considerations for working with clinical (e.g. human) specimens including blood, urine, and cerebrospinal fluid, with emphasis on sample handling, profiling composition, targeted measurements and relevance to disease. Discussions of integrated genomic or transcriptomic datasets are not included. A brief commentary is also provided regarding new technologies with clinical relevance.Expert opinion: The role of mass spectrometry to investigate clinically related specimens is on the rise and the ability to integrate multiple omics datasets from mass spectrometry measurements will be crucial to further understanding human health and disease.
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Affiliation(s)
- Esei T Teclemariam
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL, USA
| | - Melissa R Pergande
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL, USA
| | - Stephanie M Cologna
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL, USA.,Laboratory of Integrated Neuroscience, University of Illinois at Chicago, Chicago, IL, USA
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13
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Sobsey CA, Ibrahim S, Richard VR, Gaspar V, Mitsa G, Lacasse V, Zahedi RP, Batist G, Borchers CH. Targeted and Untargeted Proteomics Approaches in Biomarker Development. Proteomics 2020; 20:e1900029. [DOI: 10.1002/pmic.201900029] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 10/10/2019] [Indexed: 01/24/2023]
Affiliation(s)
- Constance A. Sobsey
- Segal Cancer Proteomics CentreLady Davis InstituteJewish General HospitalMcGill University Montreal Quebec H3T 1E2 Canada
| | - Sahar Ibrahim
- Segal Cancer Proteomics CentreLady Davis InstituteJewish General HospitalMcGill University Montreal Quebec H3T 1E2 Canada
| | - Vincent R. Richard
- Segal Cancer Proteomics CentreLady Davis InstituteJewish General HospitalMcGill University Montreal Quebec H3T 1E2 Canada
| | - Vanessa Gaspar
- Segal Cancer Proteomics CentreLady Davis InstituteJewish General HospitalMcGill University Montreal Quebec H3T 1E2 Canada
| | - Georgia Mitsa
- Segal Cancer Proteomics CentreLady Davis InstituteJewish General HospitalMcGill University Montreal Quebec H3T 1E2 Canada
| | - Vincent Lacasse
- Segal Cancer Proteomics CentreLady Davis InstituteJewish General HospitalMcGill University Montreal Quebec H3T 1E2 Canada
| | - René P. Zahedi
- Segal Cancer Proteomics CentreLady Davis InstituteJewish General HospitalMcGill University Montreal Quebec H3T 1E2 Canada
| | - Gerald Batist
- Gerald Bronfman Department of OncologyJewish General HospitalMcGill University Montreal Quebec H4A 3T2 Canada
| | - Christoph H. Borchers
- Segal Cancer Proteomics CentreLady Davis InstituteJewish General HospitalMcGill University Montreal Quebec H3T 1E2 Canada
- Gerald Bronfman Department of OncologyJewish General HospitalMcGill University Montreal Quebec H4A 3T2 Canada
- Department of Data Intensive Science and EngineeringSkolkovo Institute of Science and TechnologySkolkovo Innovation Center Moscow 143026 Russia
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14
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Gaither C, Popp R, Mohammed Y, Borchers CH. Determination of the concentration range for 267 proteins from 21 lots of commercial human plasma using highly multiplexed multiple reaction monitoring mass spectrometry. Analyst 2020; 145:3634-3644. [DOI: 10.1039/c9an01893j] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Multiple reaction monitoring (MRM) is a key tool for biomarker validation and the translation of potential biomarkers into the clinic.
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Affiliation(s)
| | | | - Yassene Mohammed
- University of Victoria – Genome British Columbia Proteomics Centre
- University of Victoria
- Victoria
- Canada
- Center for Proteomics and Metabolomics
| | - Christoph H. Borchers
- University of Victoria – Genome British Columbia Proteomics Centre
- University of Victoria
- Victoria
- Canada
- Department of Biochemistry and Microbiology
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15
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Richard C, Fakhfouri A, Colditz M, Striggow F, Kronstein-Wiedemann R, Tonn T, Medina-Sánchez M, Schmidt OG, Gemming T, Winkler A. Blood platelet enrichment in mass-producible surface acoustic wave (SAW) driven microfluidic chips. LAB ON A CHIP 2019; 19:4043-4051. [PMID: 31723953 DOI: 10.1039/c9lc00804g] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The ability to separate specific biological components from cell suspensions is indispensable for liquid biopsies, and for personalized diagnostics and therapy. This paper describes an advanced surface acoustic wave (SAW) based device designed for the enrichment of platelets (PLTs) from a dispersion of PLTs and red blood cells (RBCs) at whole blood concentrations, opening new possibilities for diverse applications involving cell manipulation with high throughput. The device is made of patterned SU-8 photoresist that is lithographically defined on the wafer scale with a new proposed methodology. The blood cells are initially focused and subsequently separated by an acoustic radiation force (ARF) applied through standing SAWs (SSAWs). By means of flow cytometric analysis, the PLT concentration factor was found to be 7.7, and it was proven that the PLTs maintain their initial state. A substantially higher cell throughput and considerably lower applied powers than comparable devices from literature were achieved. In addition, fully coupled 3D numerical simulations based on SAW wave field measurements were carried out to anticipate the coupling of the wave field into the fluid, and to obtain the resulting pressure field. A comparison to the acoustically simpler case of PDMS channel walls is given. The simulated results show an ideal match to the experimental observations and offer the first insights into the acoustic behavior of SU-8 as channel wall material. The proposed device is compatible with current (Lab-on-a-Chip) microfabrication techniques allowing for mass-scale, reproducible chip manufacturing which is crucial to push the technology from lab-based to real-world applications.
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Affiliation(s)
- Cynthia Richard
- Leibniz-IFW Dresden, Helmholtzstr. 20, 01069 Dresden, Germany.
| | | | - Melanie Colditz
- Leibniz-IFW Dresden, Helmholtzstr. 20, 01069 Dresden, Germany.
| | | | - Romy Kronstein-Wiedemann
- Experimentelle Transfusionsmedizin, Medizinische Fakultät Carl Gustav Carus der Technischen Universität Dresden/DRK-Blutspendedienst Nord-Ost gGmbH, Blasewitzer str. 68/70, 01370 Dresden, Germany
| | - Torsten Tonn
- Experimentelle Transfusionsmedizin, Medizinische Fakultät Carl Gustav Carus der Technischen Universität Dresden/DRK-Blutspendedienst Nord-Ost gGmbH, Blasewitzer str. 68/70, 01370 Dresden, Germany
| | | | | | - Thomas Gemming
- Leibniz-IFW Dresden, Helmholtzstr. 20, 01069 Dresden, Germany.
| | - Andreas Winkler
- Leibniz-IFW Dresden, Helmholtzstr. 20, 01069 Dresden, Germany.
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16
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Kim KH, Kim JY, Yoo JS. Mass spectrometry analysis of glycoprotein biomarkers in human blood of hepatocellular carcinoma. Expert Rev Proteomics 2019; 16:553-568. [DOI: 10.1080/14789450.2019.1626235] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Kwang Hoe Kim
- Biomedical Omics Group, Korea Basic Science Institute, Cheongju, Republic of Korea
| | - Jin Young Kim
- Biomedical Omics Group, Korea Basic Science Institute, Cheongju, Republic of Korea
| | - Jong Shin Yoo
- Biomedical Omics Group, Korea Basic Science Institute, Cheongju, Republic of Korea
- Graduate School of Analytical Science and Technology, Chungnam National University, Daejeon, Republic of Korea
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17
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Development and comparative analysis of yeast protein extraction protocols for mass spectrometry. Anal Biochem 2019; 567:90-95. [DOI: 10.1016/j.ab.2018.10.028] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Revised: 10/25/2018] [Accepted: 10/29/2018] [Indexed: 11/22/2022]
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Abstract
Targeted proteomics detects proteins of interest with high sensitivity, quantitative accuracy, and reproducibility. In a targeted proteomics assay, surrogate peptides are generated by proteolytic digestion of target proteins and selected reaction monitoring (SRM) assays are developed to quantify these peptides using liquid chromatography-tandem mass spectrometry (LC-MS/MS). In this report, we describe the details of quantitative analysis of target protein in cells and tissue samples.
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Affiliation(s)
- Yun Chen
- School of Pharmacy, Nanjing Medical University, Nanjing, China.
| | - Liang Liu
- School of Pharmacy, Nanjing Medical University, Nanjing, China
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19
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Kaushal P, Kwon Y, Ju S, Lee C. An SDS-PAGE based proteomic approach for N-terminome profiling. Analyst 2019; 144:7001-7009. [DOI: 10.1039/c9an01616c] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Schematic diagram of the SDS-PAGE based N-termini enrichment (GelNrich) workflow.
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Affiliation(s)
- Prashant Kaushal
- Center for Theragnosis
- Korea Institute of Science and Technology
- Seoul 02792
- Korea
- Division of Bio-Medical Science & Technology
| | - Yumi Kwon
- Center for Theragnosis
- Korea Institute of Science and Technology
- Seoul 02792
- Korea
- Department of Life Science and Research Institute for Natural Sciences
| | - Shinyeong Ju
- Center for Theragnosis
- Korea Institute of Science and Technology
- Seoul 02792
- Korea
- Department of Life Science and Research Institute for Natural Sciences
| | - Cheolju Lee
- Center for Theragnosis
- Korea Institute of Science and Technology
- Seoul 02792
- Korea
- Division of Bio-Medical Science & Technology
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20
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Identification of differentially expressed proteins in rats with spinal cord injury during the transitional phase using an iTRAQ-based quantitative analysis. Gene 2018; 677:66-76. [PMID: 30036659 DOI: 10.1016/j.gene.2018.07.050] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Revised: 07/13/2018] [Accepted: 07/16/2018] [Indexed: 12/24/2022]
Abstract
BACKGROUND Spinal cord injury (SCI) is a disease associated with high disability and mortality rates. The transitional phase from subacute phase to intermediate phase may play a major role in the process of secondary injury. Changes in protein expression levels have been shown to play key roles in many central nervous system (CNS) diseases. Nevertheless, the roles of proteins in the transitional phase of SCI are not clear. METHODS We examined protein expression in a rat model 2 weeks after SCI and identified differentially expressed proteins (DEPs) using isobaric tagging for relative and absolute protein quantification (iTRAQ). Gene Ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis of DEPs were performed. Furthermore, we constructed a protein-protein interaction (PPI) network, and the top 10 high-degree core nodes were identified. Meanwhile, we validated protein level changes of five high-degree core regulated proteins using Western blots. RESULTS A total of 162 DEPs were identified between the injury group and the control, of which 101 (62.35%) were up-regulated and 61 (37.65%) were down-regulated in the transitional phase of SCI. Key molecular function, cellular components, biological process terms and pathways were identified and may be important mechanisms in the transitional phase of SCI. Alb, Calm1, Vim, Apoe, Syp, P4hb, Cd68, Eef1a2, Rab3a and Lgals3 were the top 10 high-degree core nodes. Western blot analysis performed on five of these proteins showed the same trend as iTRAQ results. CONCLUSION The current study may provide novel insights into how proteins regulate the pathogenesis of the transitional phase after SCI.
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21
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Fu Y, Wang Z, Lu B, Zhao S, Zhang Y, Zhao Z, Zhang C, Li J, Zhou B, Guo Z, Qian J, Liu L. Immune response and differentially expressed proteins in the lung tissue of BALB/c mice challenged by aerosolized Brucella melitensis 5. J Int Med Res 2018; 46:4740-4752. [PMID: 30282518 PMCID: PMC6259401 DOI: 10.1177/0300060518799879] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Objective This study was performed to develop a murine aerosol infection model of brucellosis to investigate the pathogenicity and immune reactions induced by aerosolized Brucella and to identify key proteins associated with Brucella infection in lung tissue. Methods BALB/c mice were exposed to aerosolized Brucella melitensis 5 (M5) for 30 minutes and killed at 1, 3, 7, and 15 days post-exposure. Clinical observation, pathological analysis of lung tissue, and cytokine expression detection were then performed. Proteomic analysis based on two-dimensional electrophoresis and mass spectrometry was used to identify proteins exhibiting significant changes in expression in lung tissues during Brucella infection. Results Pathological analysis revealed alveolar wall thickening, telangiectasia with hyperemia, inflammatory cell infiltration, large areas of congestion and bleeding, and areas of focal necrosis. The T-helper 1 type immune response played an important role during aerosol infection, and 12 differentially expressed proteins were involved in the infectious process in lung tissue. Conclusion These results contribute to our understanding of the pathogenic process of Brucella in the lung tissue of BALB/c mice challenged with aerosolized Brucella. Some of the identified proteins may be potential targets in future therapeutic strategies.
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Affiliation(s)
- Yingying Fu
- Academy of Military Medical Sciences, Beijing, China
| | - Zhongyi Wang
- Academy of Military Medical Sciences, Beijing, China
| | - Bing Lu
- Academy of Military Medical Sciences, Beijing, China
| | - Siyan Zhao
- Academy of Military Medical Sciences, Beijing, China
| | - Yi Zhang
- Academy of Military Medical Sciences, Beijing, China
| | | | - Chunmao Zhang
- Academy of Military Medical Sciences, Beijing, China
| | - Jiaming Li
- Academy of Military Medical Sciences, Beijing, China
| | - Bo Zhou
- Academy of Military Medical Sciences, Beijing, China
| | - Zhendong Guo
- Academy of Military Medical Sciences, Beijing, China
| | - Jun Qian
- Academy of Military Medical Sciences, Beijing, China
| | - Linna Liu
- Academy of Military Medical Sciences, Beijing, China
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22
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Selby PJ, Banks RE, Gregory W, Hewison J, Rosenberg W, Altman DG, Deeks JJ, McCabe C, Parkes J, Sturgeon C, Thompson D, Twiddy M, Bestall J, Bedlington J, Hale T, Dinnes J, Jones M, Lewington A, Messenger MP, Napp V, Sitch A, Tanwar S, Vasudev NS, Baxter P, Bell S, Cairns DA, Calder N, Corrigan N, Del Galdo F, Heudtlass P, Hornigold N, Hulme C, Hutchinson M, Lippiatt C, Livingstone T, Longo R, Potton M, Roberts S, Sim S, Trainor S, Welberry Smith M, Neuberger J, Thorburn D, Richardson P, Christie J, Sheerin N, McKane W, Gibbs P, Edwards A, Soomro N, Adeyoju A, Stewart GD, Hrouda D. Methods for the evaluation of biomarkers in patients with kidney and liver diseases: multicentre research programme including ELUCIDATE RCT. PROGRAMME GRANTS FOR APPLIED RESEARCH 2018. [DOI: 10.3310/pgfar06030] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
BackgroundProtein biomarkers with associations with the activity and outcomes of diseases are being identified by modern proteomic technologies. They may be simple, accessible, cheap and safe tests that can inform diagnosis, prognosis, treatment selection, monitoring of disease activity and therapy and may substitute for complex, invasive and expensive tests. However, their potential is not yet being realised.Design and methodsThe study consisted of three workstreams to create a framework for research: workstream 1, methodology – to define current practice and explore methodology innovations for biomarkers for monitoring disease; workstream 2, clinical translation – to create a framework of research practice, high-quality samples and related clinical data to evaluate the validity and clinical utility of protein biomarkers; and workstream 3, the ELF to Uncover Cirrhosis as an Indication for Diagnosis and Action for Treatable Event (ELUCIDATE) randomised controlled trial (RCT) – an exemplar RCT of an established test, the ADVIA Centaur® Enhanced Liver Fibrosis (ELF) test (Siemens Healthcare Diagnostics Ltd, Camberley, UK) [consisting of a panel of three markers – (1) serum hyaluronic acid, (2) amino-terminal propeptide of type III procollagen and (3) tissue inhibitor of metalloproteinase 1], for liver cirrhosis to determine its impact on diagnostic timing and the management of cirrhosis and the process of care and improving outcomes.ResultsThe methodology workstream evaluated the quality of recommendations for using prostate-specific antigen to monitor patients, systematically reviewed RCTs of monitoring strategies and reviewed the monitoring biomarker literature and how monitoring can have an impact on outcomes. Simulation studies were conducted to evaluate monitoring and improve the merits of health care. The monitoring biomarker literature is modest and robust conclusions are infrequent. We recommend improvements in research practice. Patients strongly endorsed the need for robust and conclusive research in this area. The clinical translation workstream focused on analytical and clinical validity. Cohorts were established for renal cell carcinoma (RCC) and renal transplantation (RT), with samples and patient data from multiple centres, as a rapid-access resource to evaluate the validity of biomarkers. Candidate biomarkers for RCC and RT were identified from the literature and their quality was evaluated and selected biomarkers were prioritised. The duration of follow-up was a limitation but biomarkers were identified that may be taken forward for clinical utility. In the third workstream, the ELUCIDATE trial registered 1303 patients and randomised 878 patients out of a target of 1000. The trial started late and recruited slowly initially but ultimately recruited with good statistical power to answer the key questions. ELF monitoring altered the patient process of care and may show benefits from the early introduction of interventions with further follow-up. The ELUCIDATE trial was an ‘exemplar’ trial that has demonstrated the challenges of evaluating biomarker strategies in ‘end-to-end’ RCTs and will inform future study designs.ConclusionsThe limitations in the programme were principally that, during the collection and curation of the cohorts of patients with RCC and RT, the pace of discovery of new biomarkers in commercial and non-commercial research was slower than anticipated and so conclusive evaluations using the cohorts are few; however, access to the cohorts will be sustained for future new biomarkers. The ELUCIDATE trial was slow to start and recruit to, with a late surge of recruitment, and so final conclusions about the impact of the ELF test on long-term outcomes await further follow-up. The findings from the three workstreams were used to synthesise a strategy and framework for future biomarker evaluations incorporating innovations in study design, health economics and health informatics.Trial registrationCurrent Controlled Trials ISRCTN74815110, UKCRN ID 9954 and UKCRN ID 11930.FundingThis project was funded by the NIHR Programme Grants for Applied Research programme and will be published in full inProgramme Grants for Applied Research; Vol. 6, No. 3. See the NIHR Journals Library website for further project information.
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Affiliation(s)
- Peter J Selby
- Clinical and Biomedical Proteomics Group, Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, UK
- Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | - Rosamonde E Banks
- Clinical and Biomedical Proteomics Group, Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, UK
| | - Walter Gregory
- Leeds Institute of Clinical Trials Research, University of Leeds, Leeds, UK
| | - Jenny Hewison
- Leeds Institute of Health Sciences, University of Leeds, Leeds, UK
| | - William Rosenberg
- Institute for Liver and Digestive Health, Division of Medicine, University College London, London, UK
| | - Douglas G Altman
- Centre for Statistics in Medicine, University of Oxford, Oxford, UK
| | - Jonathan J Deeks
- Institute of Applied Health Research, University of Birmingham, Birmingham, UK
| | - Christopher McCabe
- Department of Emergency Medicine, University of Alberta Hospital, Edmonton, AB, Canada
| | - Julie Parkes
- Primary Care and Population Sciences Academic Unit, University of Southampton, Southampton, UK
| | | | | | - Maureen Twiddy
- Leeds Institute of Health Sciences, University of Leeds, Leeds, UK
| | - Janine Bestall
- Leeds Institute of Health Sciences, University of Leeds, Leeds, UK
| | | | - Tilly Hale
- LIVErNORTH Liver Patient Support, Newcastle upon Tyne, UK
| | - Jacqueline Dinnes
- Institute of Applied Health Research, University of Birmingham, Birmingham, UK
| | - Marc Jones
- Leeds Institute of Clinical Trials Research, University of Leeds, Leeds, UK
| | | | | | - Vicky Napp
- Leeds Institute of Clinical Trials Research, University of Leeds, Leeds, UK
| | - Alice Sitch
- Institute of Applied Health Research, University of Birmingham, Birmingham, UK
| | - Sudeep Tanwar
- Institute for Liver and Digestive Health, Division of Medicine, University College London, London, UK
| | - Naveen S Vasudev
- Clinical and Biomedical Proteomics Group, Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, UK
- Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | - Paul Baxter
- Leeds Institute of Cardiovascular and Metabolic Medicine, University of Leeds, Leeds, UK
| | - Sue Bell
- Leeds Institute of Clinical Trials Research, University of Leeds, Leeds, UK
| | - David A Cairns
- Clinical and Biomedical Proteomics Group, Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, UK
| | | | - Neil Corrigan
- Leeds Institute of Clinical Trials Research, University of Leeds, Leeds, UK
| | - Francesco Del Galdo
- Leeds Institute of Rheumatic and Musculoskeletal Medicine, University of Leeds, Leeds, UK
| | - Peter Heudtlass
- Leeds Institute of Clinical Trials Research, University of Leeds, Leeds, UK
| | - Nick Hornigold
- Clinical and Biomedical Proteomics Group, Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, UK
| | - Claire Hulme
- Leeds Institute of Health Sciences, University of Leeds, Leeds, UK
| | - Michelle Hutchinson
- Clinical and Biomedical Proteomics Group, Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, UK
| | - Carys Lippiatt
- Department of Specialist Laboratory Medicine, Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | | | - Roberta Longo
- Leeds Institute of Health Sciences, University of Leeds, Leeds, UK
| | - Matthew Potton
- Leeds Institute of Clinical Trials Research, University of Leeds, Leeds, UK
| | - Stephanie Roberts
- Clinical and Biomedical Proteomics Group, Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, UK
| | - Sheryl Sim
- Clinical and Biomedical Proteomics Group, Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, UK
| | - Sebastian Trainor
- Clinical and Biomedical Proteomics Group, Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, UK
| | - Matthew Welberry Smith
- Clinical and Biomedical Proteomics Group, Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, UK
- Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | - James Neuberger
- University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK
| | | | - Paul Richardson
- Royal Liverpool and Broadgreen University Hospitals NHS Trust, Liverpool, UK
| | - John Christie
- Royal Devon and Exeter NHS Foundation Trust, Exeter, UK
| | - Neil Sheerin
- Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - William McKane
- Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield, UK
| | - Paul Gibbs
- Portsmouth Hospitals NHS Trust, Portsmouth, UK
| | | | - Naeem Soomro
- Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | | | - Grant D Stewart
- NHS Lothian, Edinburgh, UK
- Academic Urology Group, University of Cambridge, Cambridge, UK
| | - David Hrouda
- Charing Cross Hospital, Imperial College Healthcare NHS Trust, London, UK
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Mohammed Y, Pan J, Zhang S, Han J, Borchers CH. ExSTA: External Standard Addition Method for Accurate High-Throughput Quantitation in Targeted Proteomics Experiments. Proteomics Clin Appl 2018; 12:1600180. [PMID: 28895300 PMCID: PMC6084352 DOI: 10.1002/prca.201600180] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Revised: 08/09/2017] [Indexed: 11/08/2022]
Abstract
PURPOSE Targeted proteomics using MRM with stable-isotope-labeled internal-standard (SIS) peptides is the current method of choice for protein quantitation in complex biological matrices. Better quantitation can be achieved with the internal standard-addition method, where successive increments of synthesized natural form (NAT) of the endogenous analyte are added to each sample, a response curve is generated, and the endogenous concentration is determined at the x-intercept. Internal NAT-addition, however, requires multiple analyses of each sample, resulting in increased sample consumption and analysis time. EXPERIMENTAL DESIGN To compare the following three methods, an MRM assay for 34 high-to-moderate abundance human plasma proteins is used: classical internal SIS-addition, internal NAT-addition, and external NAT-addition-generated in buffer using NAT and SIS peptides. Using endogenous-free chicken plasma, the accuracy is also evaluated. RESULTS The internal NAT-addition outperforms the other two in precision and accuracy. However, the curves derived by internal vs. external NAT-addition differ by only ≈3.8% in slope, providing comparable accuracies and precision with good CV values. CONCLUSIONS AND CLINICAL RELEVANCE While the internal NAT-addition method may be "ideal", this new external NAT-addition can be used to determine the concentration of high-to-moderate abundance endogenous plasma proteins, providing a robust and cost-effective alternative for clinical analyses or other high-throughput applications.
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Affiliation(s)
- Yassene Mohammed
- University of Victoria ‐ Genome British Columbia Proteomics CentreVictoriaCanada
- Center for Proteomics and MetabolomicsLeiden University Medical CenterLeidenthe Netherlands
| | - Jingxi Pan
- University of Victoria ‐ Genome British Columbia Proteomics CentreVictoriaCanada
| | - Suping Zhang
- MRM Proteomics Inc.VictoriaBritish ColumbiaCanada
| | - Jun Han
- University of Victoria ‐ Genome British Columbia Proteomics CentreVictoriaCanada
| | - Christoph H. Borchers
- University of Victoria ‐ Genome British Columbia Proteomics CentreVictoriaCanada
- University of VictoriaDepartment of Biochemistry and MicrobiologyVictoriaBCCanada
- Gerald Bronfman Department of OncologyJewish General HospitalMcGill UniversityMontrealQuebecCanada
- Proteomics CentreSegal Cancer CentreLady Davis InstituteJewish General HospitalMcGill UniversityMontrealQuebecCanada
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24
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Politis A, Schmidt C. Structural characterisation of medically relevant protein assemblies by integrating mass spectrometry with computational modelling. J Proteomics 2018; 175:34-41. [DOI: 10.1016/j.jprot.2017.04.019] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Revised: 04/13/2017] [Accepted: 04/18/2017] [Indexed: 01/14/2023]
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25
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Chavis AE, Brady KT, Hatmaker GA, Angevine CE, Kothalawala N, Dass A, Robertson JWF, Reiner JE. Single Molecule Nanopore Spectrometry for Peptide Detection. ACS Sens 2017; 2:1319-1328. [PMID: 28812356 PMCID: PMC11274829 DOI: 10.1021/acssensors.7b00362] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Sensing and characterization of water-soluble peptides is of critical importance in a wide variety of bioapplications. Single molecule nanopore spectrometry (SMNS) is based on the idea that one can use biological protein nanopores to resolve different sized molecules down to limits set by the blockade duration and noise. Previous work has shown that this enables discrimination between polyethylene glycol (PEG) molecules that differ by a single monomer unit. This paper describes efforts to extend SMNS to a variety of biologically relevant, water-soluble peptides. We describe the use of Au25(SG)18 clusters, previously shown to improve PEG detection, to increase the on- and off-rate of peptides to the pore. In addition, we study the role that fluctuations play in the single molecule nanopore spectrometry (SMNS) methodology and show that modifying solution conditions to increase peptide flexibility (via pH or chaotropic salt) leads to a nearly 2-fold reduction in the current blockade fluctuations and a corresponding narrowing of the peaks in the blockade distributions. Finally, a model is presented that connects the current blockade depths to the mass of the peptides, which shows that our enhanced SMNS detection improves the mass resolution of the nanopore sensor more than 2-fold for the largest cationic peptides studied.
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Affiliation(s)
- Amy E. Chavis
- Department of Physics, Virginia Commonwealth University, Richmond, Virginia 23284, United States
| | - Kyle T. Brady
- Department of Physics, Virginia Commonwealth University, Richmond, Virginia 23284, United States
| | - Grace A. Hatmaker
- Department of Physics, Virginia Commonwealth University, Richmond, Virginia 23284, United States
| | - Christopher E. Angevine
- Department of Physics, Virginia Commonwealth University, Richmond, Virginia 23284, United States
| | - Nuwan Kothalawala
- Department of Chemistry and Biochemistry, University of Mississippi, University, Mississippi 38677, United States
| | - Amala Dass
- Department of Chemistry and Biochemistry, University of Mississippi, University, Mississippi 38677, United States
| | - Joseph W. F. Robertson
- Physical Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, Maryland 20899-8120, United States
| | - Joseph E. Reiner
- Department of Physics, Virginia Commonwealth University, Richmond, Virginia 23284, United States
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26
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Kumar A, Gangadharan B, Cobbold J, Thursz M, Zitzmann N. Absolute quantitation of disease protein biomarkers in a single LC-MS acquisition using apolipoprotein F as an example. Sci Rep 2017; 7:12072. [PMID: 28935895 PMCID: PMC5608892 DOI: 10.1038/s41598-017-12229-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Accepted: 09/06/2017] [Indexed: 11/22/2022] Open
Abstract
LC-MS and immunoassay can detect protein biomarkers. Immunoassays are more commonly used but can potentially be outperformed by LC-MS. These techniques have limitations including the necessity to generate separate calibration curves for each biomarker. We present a rapid mass spectrometry-based assay utilising a universal calibration curve. For the first time we analyse clinical samples using the HeavyPeptide IGNIS kit which establishes a 6-point calibration curve and determines the biomarker concentration in a single LC-MS acquisition. IGNIS was tested using apolipoprotein F (APO-F), a potential biomarker for non-alcoholic fatty liver disease (NAFLD). Human serum and IGNIS prime peptides were digested and the IGNIS assay was used to quantify APO-F in clinical samples. Digestion of IGNIS prime peptides was optimised using trypsin and SMART Digest™. IGNIS was 9 times faster than the conventional LC-MS method for determining the concentration of APO-F in serum. APO-F decreased across NAFLD stages. Inter/intra-day variation and stability post sample preparation for one of the peptides was ≤13% coefficient of variation (CV). SMART Digest™ enabled complete digestion in 30 minutes compared to 24 hours using in-solution trypsin digestion. We have optimised the IGNIS kit to quantify APO-F as a NAFLD biomarker in serum using a single LC-MS acquisition.
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Affiliation(s)
- Abhinav Kumar
- Oxford Antiviral Drug Discovery Unit, Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, United Kingdom.
| | - Bevin Gangadharan
- Oxford Antiviral Drug Discovery Unit, Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, United Kingdom
| | - Jeremy Cobbold
- Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Headley Way, Headington, Oxford, OX3 9DU, United Kingdom
| | - Mark Thursz
- Division of Digestive Diseases, Imperial College, St Mary's Hospital Campus, Norfolk Place, London, W2 1NY, United Kingdom
| | - Nicole Zitzmann
- Oxford Antiviral Drug Discovery Unit, Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, United Kingdom
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Li H, Popp R, Frohlich B, Chen MX, Borchers CH. Peptide and Protein Quantification Using Automated Immuno-MALDI (iMALDI). J Vis Exp 2017. [PMID: 28872133 DOI: 10.3791/55933] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Mass spectrometry (MS) is one of the most commonly used technologies for quantifying proteins in complex samples, with excellent assay specificity as a result of the direct detection of the mass-to-charge ratio of each target molecule. However, MS-based proteomics, like most other analytical techniques, has a bias towards measuring high-abundance analytes, so it is challenging to achieve detection limits of low ng/mL or pg/mL in complex samples, and this is the concentration range for many disease-relevant proteins in biofluids such as human plasma. To assist in the detection of low-abundance analytes, immuno-enrichment has been integrated into the assay to concentrate and purify the analyte before MS measurement, significantly improving assay sensitivity. In this work, the immuno- Matrix-Assisted Laser Desorption/Ionization (iMALDI) technology is presented for the quantification of proteins and peptides in biofluids, based on immuno-enrichment on beads, followed by MALDI-MS measurement without prior elution. The anti-peptide antibodies are functionalized on magnetic beads, and incubated with samples. After washing, the beads are directly transferred onto a MALDI target plate, and the signals are measured by a MALDI-Time of Flight (MALDI-TOF) instrument after the matrix solution has been applied to the beads. The sample preparation procedure is simplified compared to other immuno-MS assays, and the MALDI measurement is fast. The whole sample preparation is automated with a liquid handling system, with improved assay reproducibility and higher throughput. In this article, the iMALDI assay is used for determining the peptide angiotensin I (Ang I) concentration in plasma, which is used clinically as readout of plasma renin activity for the screening of primary aldosteronism (PA).
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Affiliation(s)
- Huiyan Li
- University of Victoria-Genome BC Proteomics Centre
| | - Robert Popp
- University of Victoria-Genome BC Proteomics Centre
| | | | | | - Christoph H Borchers
- University of Victoria-Genome BC Proteomics Centre; Dept of Biochemistry and Microbiology, University of Victoria; Proteomics Centre, Segal Cancer Centre, Lady Davis Institute, Jewish General Hospital, McGill University; Gerald Bronfman Department of Oncology, Jewish General Hospital;
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28
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Duran-Ortiz S, Brittain AL, Kopchick JJ. The impact of growth hormone on proteomic profiles: a review of mouse and adult human studies. Clin Proteomics 2017; 14:24. [PMID: 28670222 PMCID: PMC5492507 DOI: 10.1186/s12014-017-9160-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Accepted: 06/20/2017] [Indexed: 12/17/2022] Open
Abstract
Growth hormone (GH) is a protein that is known to stimulate postnatal growth, counter regulate insulin's action and induce expression of insulin-like growth factor-1. GH exerts anabolic or catabolic effects depending upon on the targeted tissue. For instance, GH increases skeletal muscle and decreases adipose tissue mass. Our laboratory has spent the past two decades studying these effects, including the effects of GH excess and depletion, on the proteome of several mouse and human tissues. This review first discusses proteomic techniques that are commonly used for these types of studies. We then examine the proteomic differences found in mice with excess circulating GH (bGH mice) or mice with disruption of the GH receptor gene (GHR-/-). We also describe the effects of increased and decreased GH action on the proteome of adult patients with either acromegaly, GH deficiency or patients after short-term GH treatment. Finally, we explain how these proteomic studies resulted in the discovery of potential biomarkers for GH action, particularly those related with the effects of GH on aging, glucose metabolism and body composition.
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Affiliation(s)
- Silvana Duran-Ortiz
- Edison Biotechnology Institute, Ohio University, Athens, OH USA.,Department of Biological Sciences, College of Arts and Sciences, Ohio University, Athens, OH USA.,Molecular and Cellular Biology Program, Ohio University, Athens, OH USA
| | - Alison L Brittain
- Edison Biotechnology Institute, Ohio University, Athens, OH USA.,Department of Biological Sciences, College of Arts and Sciences, Ohio University, Athens, OH USA.,Molecular and Cellular Biology Program, Ohio University, Athens, OH USA.,Department of Biomedical Sciences, Heritage College of Osteopathic Medicine, Ohio University, Athens, OH 45701 USA
| | - John J Kopchick
- Edison Biotechnology Institute, Ohio University, Athens, OH USA.,Molecular and Cellular Biology Program, Ohio University, Athens, OH USA.,Department of Biomedical Sciences, Heritage College of Osteopathic Medicine, Ohio University, Athens, OH 45701 USA
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29
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Li H, Han J, Pan J, Liu T, Parker CE, Borchers CH. Current trends in quantitative proteomics - an update. JOURNAL OF MASS SPECTROMETRY : JMS 2017; 52:319-341. [PMID: 28418607 DOI: 10.1002/jms.3932] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Revised: 03/28/2017] [Accepted: 04/06/2017] [Indexed: 05/11/2023]
Abstract
Proteins can provide insights into biological processes at the functional level, so they are very promising biomarker candidates. The quantification of proteins in biological samples has been routinely used for the diagnosis of diseases and monitoring the treatment. Although large-scale protein quantification in complex samples is still a challenging task, a great amount of effort has been made to advance the technologies that enable quantitative proteomics. Seven years ago, in 2009, we wrote an article about the current trends in quantitative proteomics. In writing this current paper, we realized that, today, we have an even wider selection of potential tools for quantitative proteomics. These tools include new derivatization reagents, novel sampling formats, new types of analyzers and scanning techniques, and recently developed software to assist in assay development and data analysis. In this review article, we will discuss these innovative methods, and their current and potential applications in proteomics. Copyright © 2017 John Wiley & Sons, Ltd.
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Affiliation(s)
- H Li
- University of Victoria - Genome British Columbia Proteomics Centre, University of Victoria, Victoria, BC, V8Z 7X8, Canada
| | - J Han
- University of Victoria - Genome British Columbia Proteomics Centre, University of Victoria, Victoria, BC, V8Z 7X8, Canada
| | - J Pan
- University of Victoria - Genome British Columbia Proteomics Centre, University of Victoria, Victoria, BC, V8Z 7X8, Canada
| | - T Liu
- University of Victoria - Genome British Columbia Proteomics Centre, University of Victoria, Victoria, BC, V8Z 7X8, Canada
| | - C E Parker
- University of Victoria - Genome British Columbia Proteomics Centre, University of Victoria, Victoria, BC, V8Z 7X8, Canada
| | - C H Borchers
- University of Victoria - Genome British Columbia Proteomics Centre, University of Victoria, Victoria, BC, V8Z 7X8, Canada
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, V8P 5C2, Canada
- Proteomics Centre, Segal Cancer Centre, Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, QC, H3T 1E2, Canada
- Gerald Bronfman Department of Oncology, Jewish General Hospital, Montreal, Quebec, H3T 1E2, Canada
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30
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Li H, Popp R, Borchers CH. Affinity-mass spectrometric technologies for quantitative proteomics in biological fluids. Trends Analyt Chem 2017. [DOI: 10.1016/j.trac.2017.02.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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31
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Jagadeesan KK, Rossetti C, Abdel Qader A, Reubsaet L, Sellergren B, Laurell T, Ekström S. Filter Plate-Based Screening of MIP SPE Materials for Capture of the Biomarker Pro-Gastrin-Releasing Peptide. SLAS DISCOVERY 2017; 22:1253-1261. [PMID: 28346098 DOI: 10.1177/2472555216689494] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Affinity-based solid-phase extraction (SPE) is an attractive low-cost sample preparation strategy for biomarker analysis. Molecularly imprinted polymers (MIPs) as affinity sorbents offer unique opportunities for affinity SPE, due to their low manufacturing cost and high robustness. A limitation is the prediction of their affinity; therefore, screening of analyte recovery and specificity within a large range of SPE conditions is important in order to ensure high-sensitivity detection and assay reproducibility. Here, a µ-SPE method for screening of the MIP-SPE materials using a commercial 384-well filter plate is presented. The method allows for rapid and automated screening using 10-30 µL of packed SPE sorbent per well and sample volumes in the range of 10-70 µL. This enables screening of many different SPE sorbents while simultaneously identifying optimal SPE conditions. In addition, the 384-well format also facilitates detection with a multitude of analytical platforms. Performance of the µ-MIP-SPE method was investigated using a series of MIPs designed to capture pro-gastrin-releasing peptide (ProGRP). Fractions coming from sample load, cartridge wash, and elution were collected and analyzed using mass spectrometry (MS). The top-performing MIPs were identified, together with proper SPE conditions.
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Affiliation(s)
| | - Cecilia Rossetti
- 2 Department of Pharmaceutical Chemistry, School of Pharmacy, University of Oslo, Oslo, Norway
| | - Abed Abdel Qader
- 3 Department of Environmental Chemistry and Analytical Chemistry, Institute for Environmental Research (INFU), Technical University of Dortmund, Dortmund, Germany
| | - Léon Reubsaet
- 2 Department of Pharmaceutical Chemistry, School of Pharmacy, University of Oslo, Oslo, Norway
| | - Börje Sellergren
- 4 Department of Biomedical Sciences, Faculty of Health and Society, University of Malmö, Malmö, Sweden
| | - Thomas Laurell
- 1 Department of Biomedical Engineering, Lund University, Lund, Sweden
| | - Simon Ekström
- 1 Department of Biomedical Engineering, Lund University, Lund, Sweden
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Soboleva A, Modzel M, Didio A, Płóciennik H, Kijewska M, Grischina T, Karonova T, Bilova T, Stefanov V, Stefanowicz P, Frolov A. Quantification of prospective type 2 diabetes mellitus biomarkers by stable isotope dilution with bi-labeled standard glycated peptides. ANALYTICAL METHODS 2017; 9:409-418. [DOI: 10.1039/c6ay02483a] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/02/2024]
Abstract
A new analytical approach is proposed for quantification of multiple glycated peptides in human plasma tryptic digests.
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Affiliation(s)
- Alena Soboleva
- Department of Biochemistry
- St. Petersburg State University
- Russian Federation
- Department of Bioorganic Chemistry
- Leibniz Institute of Plant Biochemistry
| | | | - Anna Didio
- Department of Biochemistry
- St. Petersburg State University
- Russian Federation
- Department of Bioorganic Chemistry
- Leibniz Institute of Plant Biochemistry
| | | | | | - Tatiana Grischina
- Department of Biochemistry
- St. Petersburg State University
- Russian Federation
| | - Tatiana Karonova
- Federal Almazov North-West Medical Research Centre
- Russian Federation
- The First Pavlov St. Petersburg State Medical University
- Russian Federation
| | - Tatiana Bilova
- Department of Plant Physiology and Biochemistry
- St. Petersburg State University
- Russian Federation
| | - Vasily Stefanov
- Department of Biochemistry
- St. Petersburg State University
- Russian Federation
| | | | - Andrej Frolov
- Department of Bioorganic Chemistry
- Leibniz Institute of Plant Biochemistry
- Halle/Saale
- Germany
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33
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High precision quantification of human plasma proteins using the automated SISCAPA Immuno-MS workflow. N Biotechnol 2016; 33:494-502. [DOI: 10.1016/j.nbt.2015.12.008] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Revised: 12/22/2015] [Accepted: 12/29/2015] [Indexed: 11/24/2022]
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34
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Multiplexed longitudinal measurement of protein biomarkers in DBS using an automated SISCAPA workflow. Bioanalysis 2016; 8:1597-1609. [PMID: 27420772 DOI: 10.4155/bio-2016-0059] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND The use of DBS for quantitative protein biomarker measurement has been hindered by issues associated with blood hematocrit variations and lack of detection sensitivity, particularly when multiple biomarkers are measured. MATERIALS & METHODS An automated, multiplexed SISCAPA analysis was used to normalize blood volume variations in DBS and quantify proteins of varying abundance in longitudinal specimens. CONCLUSION The results showed that after normalizing the spot-to-spot hematocrit variations, peptide surrogates of protein biomarkers could be accurately quantitated in DBS. This allowed the establishment of baselines for a variety of biomarkers in multiple individuals and enabled detection of changes over time, thus offering an effective solution for longitudinal personal monitoring of biomarkers relevant in health and disease.
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35
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Mass Spectrometry-Based Metabolomic and Proteomic Strategies in Organic Acidemias. BIOMED RESEARCH INTERNATIONAL 2016; 2016:9210408. [PMID: 27403441 PMCID: PMC4923558 DOI: 10.1155/2016/9210408] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Accepted: 05/15/2016] [Indexed: 12/17/2022]
Abstract
Organic acidemias (OAs) are inherited metabolic disorders caused by deficiency of enzymatic activities in the catabolism of amino acids, carbohydrates, or lipids. These disorders result in the accumulation of mono-, di-, or tricarboxylic acids, generally referred to as organic acids. The OA outcomes can involve different organs and/or systems. Some OA disorders are easily managed if promptly diagnosed and treated, whereas, in others cases, such as propionate metabolism-related OAs (propionic acidemia, PA; methylmalonic acidemia, MMA), neither diet, vitamin therapy, nor liver transplantation appears to prevent multiorgan impairment. Here, we review the recent developments in dissecting molecular bases of OAs by using integration of mass spectrometry- (MS-) based metabolomic and proteomic strategies. MS-based techniques have facilitated the rapid and economical evaluation of a broad spectrum of metabolites in various body fluids, also collected in small samples, like dried blood spots. This approach has enabled the timely diagnosis of OAs, thereby facilitating early therapeutic intervention. Besides providing an overview of MS-based approaches most frequently used to study the molecular mechanisms underlying OA pathophysiology, we discuss the principal challenges of metabolomic and proteomic applications to OAs.
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36
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Lee H, Mun DG, Bae J, Kim H, Oh SY, Park YS, Lee JH, Lee SW. A simple dual online ultra-high pressure liquid chromatography system (sDO-UHPLC) for high throughput proteome analysis. Analyst 2016; 140:5700-6. [PMID: 26153568 DOI: 10.1039/c5an00639b] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
We report a new and simple design of a fully automated dual-online ultra-high pressure liquid chromatography system. The system employs only two nano-volume switching valves (a two-position four port valve and a two-position ten port valve) that direct solvent flows from two binary nano-pumps for parallel operation of two analytical columns and two solid phase extraction (SPE) columns. Despite the simple design, the sDO-UHPLC offers many advantageous features that include high duty cycle, back flushing sample injection for fast and narrow zone sample injection, online desalting, high separation resolution and high intra/inter-column reproducibility. This system was applied to analyze proteome samples not only in high throughput deep proteome profiling experiments but also in high throughput MRM experiments.
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Affiliation(s)
- Hangyeore Lee
- Department of Chemistry, Research Institute for Natural Sciences, Korea University, Seoul 136-701, South Korea.
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37
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Knoop A, Thomas A, Fichant E, Delahaut P, Schänzer W, Thevis M. Qualitative identification of growth hormone-releasing hormones in human plasma by means of immunoaffinity purification and LC-HRMS/MS. Anal Bioanal Chem 2016; 408:3145-53. [PMID: 26879649 PMCID: PMC4830873 DOI: 10.1007/s00216-016-9377-3] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Revised: 01/18/2016] [Accepted: 01/28/2016] [Indexed: 11/24/2022]
Abstract
The use of growth hormone-releasing hormones (GHRHs) is prohibited in sports according to the regulations of the World Anti-Doping Agency (WADA). The aim of the present study was to develop a method for the simultaneous detection of four different GHRHs and respective metabolites from human plasma by means of immunoaffinity purification and subsequent nano-ultrahigh performance liquid chromatography-high resolution/high accuracy (tandem) mass spectrometry. The target analytes included Geref (Sermorelin), CJC-1293, CJC-1295, and Egrifta (Tesamorelin) as well as two metabolites of Geref and CJC-1293, which were captured from plasma samples using a polyclonal GHRH antibody in concert with protein A/G monolithic MSIA™ D.A.R.T.'S® (Disposable Automation Research Tips) prior to separation and detection. The method was fully validated and found to be fit for purpose considering the parameters specificity, linearity, recovery (19-37%), lower limit of detection (<50 pg/mL), imprecision (<20%), and ion suppression/enhancement effects. The analytes' stability and metabolism were elucidated using in vitro and in vivo approaches. EDTA blood samples were collected from rats 2, 4, and 8 h after intravenous administration of GHRH (one compound per test animal). All intact substances were detected for at least 4 h but no anticipated metabolite was confirmed in laboratory rodents' samples; conversely, a Geref metabolite (GHRH3-29) was found in a human plasma sample collected after subcutaneous injection of the drug to a healthy male volunteer. The obtained results demonstrate that GHRHs are successfully detected in plasma using an immunoaffinity-mass spectrometry-based method, which can be applied to sports drug testing samples. Further studies are however required and warranted to account for potential species-related differences in metabolism and elimination of the target analytes.
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Affiliation(s)
- Andre Knoop
- Institute for Biochemistry-Center for Preventive Doping Research, German Sport University Cologne, Am Sportpark Müngersdorf 6, 50933, Cologne, Germany
| | - Andreas Thomas
- Institute for Biochemistry-Center for Preventive Doping Research, German Sport University Cologne, Am Sportpark Müngersdorf 6, 50933, Cologne, Germany
| | - Eric Fichant
- Laboratoire d'Hormonologie, C.E.R. Groupe-Département Santé, Rue du Point du jour 8, 6900, Marloie, Belgium
| | - Philippe Delahaut
- Laboratoire d'Hormonologie, C.E.R. Groupe-Département Santé, Rue du Point du jour 8, 6900, Marloie, Belgium
| | - Wilhelm Schänzer
- Institute for Biochemistry-Center for Preventive Doping Research, German Sport University Cologne, Am Sportpark Müngersdorf 6, 50933, Cologne, Germany
| | - Mario Thevis
- Institute for Biochemistry-Center for Preventive Doping Research, German Sport University Cologne, Am Sportpark Müngersdorf 6, 50933, Cologne, Germany. .,European Monitoring Center for Emerging Doping Agents (EuMoCEDA), Cologne/Bonn, Germany.
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38
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Application of streptavidin mass spectrometric immunoassay tips for immunoaffinity based antibody phage display panning. J Microbiol Methods 2016; 120:6-14. [DOI: 10.1016/j.mimet.2015.11.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Revised: 11/09/2015] [Accepted: 11/09/2015] [Indexed: 11/21/2022]
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39
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Kramer G, Woolerton Y, van Straalen JP, Vissers JPC, Dekker N, Langridge JI, Beynon RJ, Speijer D, Sturk A, Aerts JMFG. Accuracy and Reproducibility in Quantification of Plasma Protein Concentrations by Mass Spectrometry without the Use of Isotopic Standards. PLoS One 2015; 10:e0140097. [PMID: 26474480 PMCID: PMC4608811 DOI: 10.1371/journal.pone.0140097] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Accepted: 09/22/2015] [Indexed: 12/28/2022] Open
Abstract
Background Quantitative proteomic analysis with mass spectrometry holds great promise for simultaneously quantifying proteins in various biosamples, such as human plasma. Thus far, studies addressing the reproducible measurement of endogenous protein concentrations in human plasma have focussed on targeted analyses employing isotopically labelled standards. Non-targeted proteomics, on the other hand, has been less employed to this end, even though it has been instrumental in discovery proteomics, generating large datasets in multiple fields of research. Results Using a non-targeted mass spectrometric assay (LCMSE), we quantified abundant plasma proteins (43 mg/mL—40 ug/mL range) in human blood plasma specimens from 30 healthy volunteers and one blood serum sample (ProteomeXchange: PXD000347). Quantitative results were obtained by label-free mass spectrometry using a single internal standard to estimate protein concentrations. This approach resulted in quantitative results for 59 proteins (cut off ≥11 samples quantified) of which 41 proteins were quantified in all 31 samples and 23 of these with an inter-assay variability of ≤ 20%. Results for 7 apolipoproteins were compared with those obtained using isotope-labelled standards, while 12 proteins were compared to routine immunoassays. Comparison of quantitative data obtained by LCMSE and immunoassays showed good to excellent correlations in relative protein abundance (r = 0.72–0.96) and comparable median concentrations for 8 out of 12 proteins tested. Plasma concentrations of 56 proteins determined by LCMSE were of similar accuracy as those reported by targeted studies and 7 apolipoproteins quantified by isotope-labelled standards, when compared to reference concentrations from literature. Conclusions This study shows that LCMSE offers good quantification of relative abundance as well as reasonable estimations of concentrations of abundant plasma proteins.
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Affiliation(s)
- Gertjan Kramer
- Department of Medical Biochemistry, Academic Medical Centre, University of Amsterdam, Amsterdam, the Netherlands
- * E-mail:
| | - Yvonne Woolerton
- Centre for Proteome Research, Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Jan P. van Straalen
- Department of Clinical Chemistry, Academic Medical Centre, University of Amsterdam, Amsterdam, the Netherlands
| | | | - Nick Dekker
- Department of Medical Biochemistry, Academic Medical Centre, University of Amsterdam, Amsterdam, the Netherlands
| | | | - Robert J. Beynon
- Centre for Proteome Research, Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Dave Speijer
- Department of Medical Biochemistry, Academic Medical Centre, University of Amsterdam, Amsterdam, the Netherlands
| | - Auguste Sturk
- Department of Clinical Chemistry, Academic Medical Centre, University of Amsterdam, Amsterdam, the Netherlands
| | - Johannes M. F. G. Aerts
- Department of Medical Biochemistry, Academic Medical Centre, University of Amsterdam, Amsterdam, the Netherlands
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40
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Abstract
Necrotizing enterocolitis (NEC) remains a significant cause of morbidity and mortality in premature neonates. Despite decades of investigation, treating clinicians are still not able to determine which premature infants are at greatest risk of developing NEC and which of the affected infants will develop severe NEC requiring operation. A biomarker is a specific molecular indicator that can be used to identify or measure the progress of a disease. Many potential biomarkers have been studied for their potential relevance to NEC. Those showing promise include C-reactive protein, intestinal fatty acid-binding protein, platelet-activating factor and many others. None to date have achieved sufficient predictive value to be clinically useful. Distinguishing between the specific changes in NEC and the non-specific inflammation of sepsis has proven challenging. Urine is a particularly attractive site for potential biomarkers. It can be collected readily and non-invasively, and it is a rich source of both proteins and peptides. Preliminary work has revealed some promising biomarkers of NEC in urine. Combined with clinical data, they have been shown to be highly predictive in small series of patients. Advances in high-throughput molecular analysis have opened the door to finding biomarkers that may meaningfully improve the outcome of infants at risk for NEC.
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Affiliation(s)
- Karl G Sylvester
- Department of Surgery, Stanford University School of Medicine, Stanford, CA, USA
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41
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Webb-Robertson BJM, Wiberg HK, Matzke MM, Brown JN, Wang J, McDermott JE, Smith RD, Rodland KD, Metz TO, Pounds JG, Waters KM. Review, evaluation, and discussion of the challenges of missing value imputation for mass spectrometry-based label-free global proteomics. J Proteome Res 2015; 14:1993-2001. [PMID: 25855118 DOI: 10.1021/pr501138h] [Citation(s) in RCA: 167] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
In this review, we apply selected imputation strategies to label-free liquid chromatography-mass spectrometry (LC-MS) proteomics datasets to evaluate the accuracy with respect to metrics of variance and classification. We evaluate several commonly used imputation approaches for individual merits and discuss the caveats of each approach with respect to the example LC-MS proteomics data. In general, local similarity-based approaches, such as the regularized expectation maximization and least-squares adaptive algorithms, yield the best overall performances with respect to metrics of accuracy and robustness. However, no single algorithm consistently outperforms the remaining approaches, and in some cases, performing classification without imputation sometimes yielded the most accurate classification. Thus, because of the complex mechanisms of missing data in proteomics, which also vary from peptide to protein, no individual method is a single solution for imputation. On the basis of the observations in this review, the goal for imputation in the field of computational proteomics should be to develop new approaches that work generically for this data type and new strategies to guide users in the selection of the best imputation for their dataset and analysis objectives.
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Affiliation(s)
| | - Holli K Wiberg
- Pacific Northwest National Laboratory, PO BOX 999, K7-20, Richland, Washington 99352, United States
| | - Melissa M Matzke
- Pacific Northwest National Laboratory, PO BOX 999, K7-20, Richland, Washington 99352, United States
| | - Joseph N Brown
- Pacific Northwest National Laboratory, PO BOX 999, K7-20, Richland, Washington 99352, United States
| | - Jing Wang
- Pacific Northwest National Laboratory, PO BOX 999, K7-20, Richland, Washington 99352, United States
| | - Jason E McDermott
- Pacific Northwest National Laboratory, PO BOX 999, K7-20, Richland, Washington 99352, United States
| | - Richard D Smith
- Pacific Northwest National Laboratory, PO BOX 999, K7-20, Richland, Washington 99352, United States
| | - Karin D Rodland
- Pacific Northwest National Laboratory, PO BOX 999, K7-20, Richland, Washington 99352, United States
| | - Thomas O Metz
- Pacific Northwest National Laboratory, PO BOX 999, K7-20, Richland, Washington 99352, United States
| | - Joel G Pounds
- Pacific Northwest National Laboratory, PO BOX 999, K7-20, Richland, Washington 99352, United States
| | - Katrina M Waters
- Pacific Northwest National Laboratory, PO BOX 999, K7-20, Richland, Washington 99352, United States
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42
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Sajic T, Liu Y, Aebersold R. Using data-independent, high-resolution mass spectrometry in protein biomarker research: perspectives and clinical applications. Proteomics Clin Appl 2015; 9:307-21. [PMID: 25504613 DOI: 10.1002/prca.201400117] [Citation(s) in RCA: 148] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2014] [Revised: 11/13/2014] [Accepted: 12/10/2014] [Indexed: 12/17/2022]
Abstract
In medicine, there is an urgent need for protein biomarkers in a range of applications that includes diagnostics, disease stratification, and therapeutic decisions. One of the main technologies to address this need is MS, used for protein biomarker discovery and, increasingly, also for protein biomarker validation. Currently, data-dependent analysis (also referred to as shotgun proteomics) and targeted MS, exemplified by SRM, are the most frequently used mass spectrometric methods. Recently developed data-independent acquisition techniques combine the strength of shotgun and targeted proteomics, while avoiding some of the limitations of the respective methods. They provide high-throughput, accurate quantification, and reproducible measurements within a single experimental setup. Here, we describe and review data-independent acquisition strategies and their recent use in clinically oriented studies. In addition, we also provide a detailed guide for the implementation of SWATH-MS (where SWATH is sequential window acquisition of all theoretical mass spectra)-one of the data-independent strategies that have gained wide application of late.
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Affiliation(s)
- Tatjana Sajic
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
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43
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Cho YT, Su H, Wu WJ, Wu DC, Hou MF, Kuo CH, Shiea J. Biomarker Characterization by MALDI-TOF/MS. Adv Clin Chem 2015; 69:209-54. [PMID: 25934363 DOI: 10.1016/bs.acc.2015.01.001] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Mass spectrometric techniques frequently used in clinical diagnosis, such as gas chromatography-mass spectrometry, liquid chromatography-mass spectrometry, ambient ionization mass spectrometry, and matrix-assisted laser desorption ionization/time-of-flight mass spectrometry (MALDI-TOF/MS), are discussed. Due to its ability to rapidly detect large biomolecules in trace amounts, MALDI-TOF/MS is an ideal tool for characterizing disease biomarkers in biologic samples. Clinical applications of MS for the identification and characterization of microorganisms, DNA fragments, tissues, and biofluids are introduced. Approaches for using MALDI-TOF/MS to detect various disease biomarkers including peptides, proteins, and lipids in biological fluids are further discussed. Finally, various sample pretreatment methods which improve the detection efficiency of disease biomarkers are introduced.
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Affiliation(s)
- Yi-Tzu Cho
- Department of Cosmetic Applications and Management, Yuh-Ing Junior College of Health Care & Management, Kaohsiung, Taiwan
| | - Hung Su
- Department of Chemistry, National Sun Yat-sen University, Kaohsiung, Taiwan
| | - Wen-Jeng Wu
- Department of Urology, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
| | - Deng-Chyang Wu
- Division of Gastroenterology, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan; Center for Stem Cell Research, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Ming-Feng Hou
- Department of Surgery, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan; Cancer Center, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
| | - Chao-Hung Kuo
- Division of Gastroenterology, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan; Center for Stem Cell Research, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Jentaie Shiea
- Department of Chemistry, National Sun Yat-sen University, Kaohsiung, Taiwan; Center for Stem Cell Research, Kaohsiung Medical University, Kaohsiung, Taiwan; Cancer Center, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan; Department of Medicinal and Applied Chemistry, Kaohsiung Medical University, Kaohsiung, Taiwan.
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44
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Sauer S, Luge T. Nutriproteomics: Facts, concepts, and perspectives. Proteomics 2015; 15:997-1013. [DOI: 10.1002/pmic.201400383] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Revised: 11/03/2014] [Accepted: 11/27/2014] [Indexed: 12/19/2022]
Affiliation(s)
- Sascha Sauer
- Otto Warburg Laboratory; Max Planck Institute for Molecular Genetics; Berlin Germany
| | - Toni Luge
- Otto Warburg Laboratory; Max Planck Institute for Molecular Genetics; Berlin Germany
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45
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Schneck NA, Lowenthal M, Phinney K, Lee SB. Current trends in magnetic particle enrichment for mass spectrometry-based analysis of cardiovascular protein biomarkers. Nanomedicine (Lond) 2015; 10:433-46. [DOI: 10.2217/nnm.14.188] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Magnetic particles have traditionally been utilized to isolate and enrich various cardiovascular protein biomarkers for mass spectrometry-based proteomic analysis. The application of functionalized magnetic particles for immunocapture is attractive due to their easy manipulation, large surface area-to-volume ratios for maximal antibody binding, good recovery and high magnetic saturation. Magnetic particle enrichment coupled with mass spectrometry can act as a complementary tool for clinical sandwich-immunoassay development since it can provide improved target specificity and true metrological traceability. The purpose of this review is to summarize current separation methods and technologies that use magnetic particles to enrich protein biomarkers from complex matrices, specifically focusing on cardiovascular disease-related proteins and the advantages of magnetic particles over existing techniques.
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Affiliation(s)
- Nicole A Schneck
- Department of Chemistry & Biochemistry, University of Maryland, College Park, MD 20742, USA
- Biomolecular Measurement Division, National Institute of Standards & Technology, Gaithersburg, MD 20899, USA
| | - Mark Lowenthal
- Biomolecular Measurement Division, National Institute of Standards & Technology, Gaithersburg, MD 20899, USA
| | - Karen Phinney
- Biomolecular Measurement Division, National Institute of Standards & Technology, Gaithersburg, MD 20899, USA
| | - Sang Bok Lee
- Department of Chemistry & Biochemistry, University of Maryland, College Park, MD 20742, USA
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46
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Targeted mass spectrometry analysis of the proteins IGF1, IGF2, IBP2, IBP3 and A2GL by blood protein precipitation. J Proteomics 2015; 113:29-37. [DOI: 10.1016/j.jprot.2014.09.013] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2014] [Revised: 09/11/2014] [Accepted: 09/23/2014] [Indexed: 11/18/2022]
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47
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Stenken JA, Poschenrieder AJ. Bioanalytical chemistry of cytokines--a review. Anal Chim Acta 2015; 853:95-115. [PMID: 25467452 PMCID: PMC4717841 DOI: 10.1016/j.aca.2014.10.009] [Citation(s) in RCA: 194] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2014] [Revised: 09/30/2014] [Accepted: 10/08/2014] [Indexed: 02/06/2023]
Abstract
Cytokines are bioactive proteins produced by many different cells of the immune system. Due to their role in different inflammatory disease states and maintaining homeostasis, there is enormous clinical interest in the quantitation of cytokines. The typical standard methods for quantitation of cytokines are immunoassay-based techniques including enzyme-linked immusorbent assays (ELISA) and bead-based immunoassays read by either standard or modified flow cytometers. A review of recent developments in analytical methods for measurements of cytokine proteins is provided. This review briefly covers cytokine biology and the analysis challenges associated with measurement of these biomarker proteins for understanding both health and disease. New techniques applied to immunoassay-based assays are presented along with the uses of aptamers, electrochemistry, mass spectrometry, optical resonator-based methods. Methods used for elucidating the release of cytokines from single cells as well as in vivo collection methods are described.
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Affiliation(s)
- Julie A Stenken
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, USA.
| | - Andreas J Poschenrieder
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, USA; Pharmaceutical Radiochemistry, Technische Universität München, Walther-Meißner-Street 3, D-85748 Garching, Germany
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48
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Li J, Zhou L, Wang H, Yan H, Li N, Zhai R, Jiao F, Hao F, Jin Z, Tian F, Peng B, Zhang Y, Qian X. A new sample preparation method for the absolute quantitation of a target proteome using 18O labeling combined with multiple reaction monitoring mass spectrometry. Analyst 2015; 140:1281-90. [DOI: 10.1039/c4an02092h] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
A new sample preparation method for target proteome absolute quantitation using 18O labeling-MRM MS.
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49
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Rossetti C, Abdel Qader A, Halvorsen TG, Sellergren B, Reubsaet L. Antibody-Free Biomarker Determination: Exploring Molecularly Imprinted Polymers for Pro-Gastrin Releasing Peptide. Anal Chem 2014; 86:12291-8. [DOI: 10.1021/ac503559c] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Cecilia Rossetti
- Department
of Pharmaceutical Chemistry, School of Pharmacy, University of Oslo, NO-0316 Oslo, Norway
| | - Abed Abdel Qader
- Department
of Environmental Chemistry and Analytical Chemistry,
Institute for Environmental Research (INFU), Technical University of Dortmund, D-44221 Dortmund, Germany
| | - Trine Grønhaug Halvorsen
- Department
of Pharmaceutical Chemistry, School of Pharmacy, University of Oslo, NO-0316 Oslo, Norway
| | - Börje Sellergren
- Department
of Environmental Chemistry and Analytical Chemistry,
Institute for Environmental Research (INFU), Technical University of Dortmund, D-44221 Dortmund, Germany
- Department
of Biomedical Sciences, Faculty of Health and Society, University of Malmö, 205 06 Malmö, Sweden
| | - Léon Reubsaet
- Department
of Pharmaceutical Chemistry, School of Pharmacy, University of Oslo, NO-0316 Oslo, Norway
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50
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Pan C, Zhou Y, Dator R, Ginghina C, Zhao Y, Movius J, Peskind E, Zabetian CP, Quinn J, Galasko D, Stewart T, Shi M, Zhang J. Targeted discovery and validation of plasma biomarkers of Parkinson's disease. J Proteome Res 2014; 13:4535-45. [PMID: 24853996 PMCID: PMC4224986 DOI: 10.1021/pr500421v] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Despite extensive research, an unmet need remains for protein biomarkers of Parkinson's disease (PD) in peripheral body fluids, especially blood, which is easily accessible clinically. The discovery of such biomarkers is challenging, however, due to the enormous complexity and huge dynamic range of human blood proteins, which are derived from nearly all organ systems, with those originating specifically from the central nervous system (CNS) being exceptionally low in abundance. In this investigation of a relatively large cohort (∼300 subjects), selected reaction monitoring (SRM) assays (a targeted approach) were used to probe plasma peptides derived from glycoproteins previously found to be altered in the CNS based on PD diagnosis or severity. Next, the detected peptides were interrogated for their diagnostic sensitivity and specificity as well as the correlation with PD severity, as determined by the Unified Parkinson's Disease Rating Scale (UPDRS). The results revealed that 12 of the 50 candidate glycopeptides were reliably and consistently identified in plasma samples, with three of them displaying significant differences among diagnostic groups. A combination of four peptides (derived from PRNP, HSPG2, MEGF8, and NCAM1) provided an overall area under curve (AUC) of 0.753 (sensitivity: 90.4%; specificity: 50.0%). Additionally, combining two peptides (derived from MEGF8 and ICAM1) yielded significant correlation with PD severity, that is, UPDRS (r = 0.293, p = 0.004). The significance of these results is at least two-fold: (1) it is possible to use a targeted approach to identify otherwise very difficult to detect CNS related biomarkers in peripheral blood and (2) the novel biomarkers, if validated in independent cohorts, can be employed to assist with clinical diagnosis of PD as well as monitoring disease progression.
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Affiliation(s)
- Catherine Pan
- Department of Pathology, University of Washington School of Medicine , 325 9th Avenue, HMC 359635, Seattle, Washington 98104, United States
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