1
|
Chen YT, Liao WR, Wang HT, Chen HW, Chen SF. Targeted protein quantitation in human body fluids by mass spectrometry. MASS SPECTROMETRY REVIEWS 2023; 42:2379-2403. [PMID: 35702881 DOI: 10.1002/mas.21788] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 01/11/2022] [Accepted: 04/08/2022] [Indexed: 06/15/2023]
Abstract
Human body fluids (biofluids) contain various proteins, some of which reflect individuals' physiological conditions or predict diseases. Therefore, the analysis of biofluids can provide substantial information on novel biomarkers for clinical diagnosis and prognosis. In the past decades, mass spectrometry (MS)-based technologies have been developed as proteomic strategies not only for the identification of protein biomarkers but also for biomarker verification/validation in body fluids for clinical applications. The main advantage of targeted MS-based methodologies is the accurate and specific simultaneous quantitation of multiple biomarkers with high sensitivity. Here, we review MS-based methodologies that are currently used for the targeted quantitation of protein components in human body fluids, especially in plasma, urine, cerebrospinal fluid, and saliva. In addition, the currently used MS-based methodologies are summarized with a specific focus on applicable clinical sample types, MS configurations, and acquisition modes.
Collapse
Affiliation(s)
- Yi-Ting Chen
- Department of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- Department of Nephrology, Kidney Research Center, Linkou Medical Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan
- Molecular and Medicine Research Center, Chang Gung University, Taoyuan, Taiwan
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Wan-Rou Liao
- Department of Chemistry, National Taiwan Normal University, Taipei, Taiwan
| | - Hsueh-Ting Wang
- Instrumentation Center, National Taiwan Normal University, Taipei, Taiwan
| | - Hsiao-Wei Chen
- Molecular and Medicine Research Center, Chang Gung University, Taoyuan, Taiwan
| | - Sung-Fang Chen
- Department of Chemistry, National Taiwan Normal University, Taipei, Taiwan
- Instrumentation Center, National Taiwan Normal University, Taipei, Taiwan
| |
Collapse
|
2
|
Meehan SD, Bhattacharya S. Retinal Ganglion Cell Axon Fractionation. Methods Mol Biol 2023; 2636:43-53. [PMID: 36881294 DOI: 10.1007/978-1-0716-3012-9_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2023]
Abstract
Retinal ganglion cell (RGC) axon regeneration in mammals can be stimulated through gene knockouts, pharmacological agents, and biophysical stimulation. Here we present a fractionation method to isolate regenerating RGC axons for downstream analysis using immunomagnetic separation of cholera toxin subunit B (CTB)-bound RGC axons. After optic nerve tissue dissection and dissociation, conjugated CTB is used to bind preferentially to regenerated RGC axons. Anti-CTB antibodies crosslinked to magnetic sepharose beads are used to isolate CTB-bound axons from a nonbound fraction of extracellular matrix and neuroglia. We provide a method of verifying fractionation by immunodetection of conjugated CTB and the RGC marker, Tuj1 (β-tubulin III). These fractions can be further analyzed with lipidomic methods, such as LC-MS/MS to gather fraction-specific enrichments.
Collapse
Affiliation(s)
- Sean D Meehan
- Bascom Palmer Eye Institute, Miller School of Medicine at University of Miami, Miami, FL, USA.,Miami Integrative Metabolomics Research Center, Miami, FL, USA.,Molecular Cellular Pharmacology Graduate Program, University of Miami, Miami, FL, USA
| | - Sanjoy Bhattacharya
- Bascom Palmer Eye Institute, Miller School of Medicine at University of Miami, Miami, FL, USA. .,Miami Integrative Metabolomics Research Center, Miami, FL, USA. .,Molecular Cellular Pharmacology Graduate Program, University of Miami, Miami, FL, USA.
| |
Collapse
|
3
|
Wheeler JX, Thelwell C, Rigsby P, Whiting G. Quantitation of thrombin-activatable fibrinolysis inhibitor in human plasma by isotope dilution mass spectrometry. Anal Biochem 2021; 638:114413. [PMID: 34644544 DOI: 10.1016/j.ab.2021.114413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 10/07/2021] [Accepted: 10/08/2021] [Indexed: 11/17/2022]
Abstract
Measurement of Thrombin-activatable fibrinolysis inhibitor (TAFI) in human plasma is dependent on reproducible assays. To date, standards for measuring TAFI are frequently calibrated relative to pooled normal human plasma and arbitrarily assigned a potency of 100% TAFI, despite variation in TAFI concentrations between plasma pools. Alternatively, TAFI calibrators can be assigned a value in SI units but the approach used for value assignment is not consistent and furthermore, if purified TAFI is used to determine TAFI concentration in plasma, may be adversely affected by matrix effects. A TAFI plasma standard in mass units with traceability to the SI unit of mass is desirable. We report here the establishment of a quantitative mass spectrometry method for TAFI in plasma. Traceability is obtained by reference to calibrators that consist of blank plasma spiked with a defined amount of purified TAFI, value assigned by amino acid analysis. The calibrators are run alongside the samples, using the same preparation steps and conditions; an acetonitrile assisted tryptic digestion and multi-dimensional liquid chromatography (LC) separation followed by SRM-MS analysis. We measured the TAFI quantitatively in human plasma with reproducibility, reliability and precision, and demonstrated the applicability of this approach for value assigning a common reference standard.
Collapse
Affiliation(s)
- Jun X Wheeler
- National Institute for Biological Standards and Control, South Mimms, Potters Bar, EN6 3QG, UK
| | - Craig Thelwell
- National Institute for Biological Standards and Control, South Mimms, Potters Bar, EN6 3QG, UK
| | - Peter Rigsby
- National Institute for Biological Standards and Control, South Mimms, Potters Bar, EN6 3QG, UK
| | - Gail Whiting
- National Institute for Biological Standards and Control, South Mimms, Potters Bar, EN6 3QG, UK.
| |
Collapse
|
4
|
Ignjatovic V, Geyer PE, Palaniappan KK, Chaaban JE, Omenn GS, Baker MS, Deutsch EW, Schwenk JM. Mass Spectrometry-Based Plasma Proteomics: Considerations from Sample Collection to Achieving Translational Data. J Proteome Res 2019; 18:4085-4097. [PMID: 31573204 DOI: 10.1021/acs.jproteome.9b00503] [Citation(s) in RCA: 104] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The proteomic analysis of human blood and blood-derived products (e.g., plasma) offers an attractive avenue to translate research progress from the laboratory into the clinic. However, due to its unique protein composition, performing proteomics assays with plasma is challenging. Plasma proteomics has regained interest due to recent technological advances, but challenges imposed by both complications inherent to studying human biology (e.g., interindividual variability) and analysis of biospecimens (e.g., sample variability), as well as technological limitations remain. As part of the Human Proteome Project (HPP), the Human Plasma Proteome Project (HPPP) brings together key aspects of the plasma proteomics pipeline. Here, we provide considerations and recommendations concerning study design, plasma collection, quality metrics, plasma processing workflows, mass spectrometry (MS) data acquisition, data processing, and bioinformatic analysis. With exciting opportunities in studying human health and disease though this plasma proteomics pipeline, a more informed analysis of human plasma will accelerate interest while enhancing possibilities for the incorporation of proteomics-scaled assays into clinical practice.
Collapse
Affiliation(s)
- Vera Ignjatovic
- Haematology Research , Murdoch Children's Research Institute , Parkville , VIC 3052 , Australia.,Department of Paediatrics , The University of Melbourne , Parkville , VIC 3052 , Australia
| | - Philipp E Geyer
- NNF Center for Protein Research, Faculty of Health Sciences , University of Copenhagen , 2200 Copenhagen , Denmark.,Department of Proteomics and Signal Transduction , Max Planck Institute of Biochemistry , 82152 Martinsried , Germany
| | - Krishnan K Palaniappan
- Freenome , 259 East Grand Avenue , South San Francisco , California 94080 , United States
| | - Jessica E Chaaban
- Haematology Research , Murdoch Children's Research Institute , Parkville , VIC 3052 , Australia
| | - Gilbert S Omenn
- Departments of Computational Medicine & Bioinformatics, Human Genetics, and Internal Medicine and School of Public Health , University of Michigan , 100 Washtenaw Avenue , Ann Arbor , Michigan 48109-2218 , United States
| | - Mark S Baker
- Department of Biomedical Sciences, Faculty of Medicine & Health Sciences , Macquarie University , 75 Talavera Road , North Ryde , NSW 2109 , Australia
| | - Eric W Deutsch
- Institute for Systems Biology , 401 Terry Avenue North , Seattle , Washington 98109 , United States
| | - Jochen M Schwenk
- Affinity Proteomics, SciLifeLab , KTH Royal Institute of Technology , 171 65 Stockholm , Sweden
| |
Collapse
|
5
|
Abstract
The limitations commonly observed in data-dependent acquisition (DDA) mass spectrometric investigation of non-depleted human plasma are mainly due to the large dynamic concentration range of protein expression. Less abundant proteins are usually masked by highly abundant proteins and are therefore difficult to reliably detect. Sequential window acquisition of all theoretical fragment-ion spectra (SWATH) mass spectrometry (MS), as a representative of data-independent acquisition (DIA) approaches, provides an opportunity to improve plasma-based biomarker discovery studies because this approach does not rely on precursor intensity for fragmentation selection but rather analyzes all precursors in specified mass ranges. Here, we describe a workflow for SWATH-MS-based analysis of non-depleted plasma including sample preparation, data acquisition, and statistical analysis.
Collapse
|
6
|
A Method for Simplification of Complex Group Causal Loop Diagrams Based on Endogenisation, Encapsulation and Order-Oriented Reduction. SYSTEMS 2017. [DOI: 10.3390/systems5030046] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
|
7
|
Becher F, Ciccolini J, Imbs DC, Marin C, Fournel C, Dupuis C, Fakhry N, Pourroy B, Ghettas A, Pruvost A, Junot C, Duffaud F, Lacarelle B, Salas S. A simple and rapid LC-MS/MS method for therapeutic drug monitoring of cetuximab: a GPCO-UNICANCER proof of concept study in head-and-neck cancer patients. Sci Rep 2017; 7:2714. [PMID: 28578404 PMCID: PMC5457398 DOI: 10.1038/s41598-017-02821-x] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2016] [Accepted: 04/19/2017] [Indexed: 01/01/2023] Open
Abstract
Administration of first-in-class anti-EGFR monoclonal antibody cetuximab is contingent upon extensive pharmacogenomic testing. However in addition to tumor genomics, drug exposure levels could play a critical, yet largely underestimated role, because several reports have demonstrated that cetuximab pharmacokinetic parameters, in particular clearance values, were associated with survival in patients. Here, we have developed an original bioanalytical method based upon the use of LC-MS/MS technology and a simplified sample preparation procedure to assay cetuximab in plasma samples from patients, thus meeting the requirements of standard Therapeutic Drug Monitoring in routine clinical practice. When tested prospectively in a pilot study in 25 head-and-neck cancer patients, this method showed that patients with clinical benefit had cetixumab residual concentrations higher than non-responding patients (i.e., 49 ± 16.3 µg/ml VS. 25.8 ± 17 µg/ml, p < 0.01 t test). Further ROC analysis showed that 33.8 µg/ml was the Cmin threshold predictive of response with an acceptable sensitivity (87%) and specificity (78%). Mass spectrometry-based therapeutic drug monitoring of cetuximab in head-and-neck cancer patients could therefore help to rapidly predict cetuximab efficacy and to adapt dosing if required.
Collapse
Affiliation(s)
- François Becher
- Service de Pharmacologie et d'Immunoanalyse (SPI), CEA, INRA, Université Paris-Saclay, 91191, Gif sur Yvette, France.,Groupe de Pharmacologie Clinique & Oncologique (GPCO)-Unicancer, 101 rue de Tolbiac, 75013, Paris, France
| | - Joseph Ciccolini
- Groupe de Pharmacologie Clinique & Oncologique (GPCO)-Unicancer, 101 rue de Tolbiac, 75013, Paris, France. .,Clinical Pharmacokinetics Laboratory, SMARTc unit, Inserm S_911 CRO2, Aix Marseille Univ and La Timone University Hospital of Marseille, Marseille, France.
| | - Diane-Charlotte Imbs
- Groupe de Pharmacologie Clinique & Oncologique (GPCO)-Unicancer, 101 rue de Tolbiac, 75013, Paris, France.,Clinical Pharmacokinetics Laboratory, SMARTc unit, Inserm S_911 CRO2, Aix Marseille Univ and La Timone University Hospital of Marseille, Marseille, France
| | - Clémence Marin
- Groupe de Pharmacologie Clinique & Oncologique (GPCO)-Unicancer, 101 rue de Tolbiac, 75013, Paris, France.,Clinical Pharmacokinetics Laboratory, SMARTc unit, Inserm S_911 CRO2, Aix Marseille Univ and La Timone University Hospital of Marseille, Marseille, France
| | - Claire Fournel
- Medical Oncology Unit, La Timone University Hospital of Marseille, Marseille, France
| | - Charlotte Dupuis
- Medical Oncology Unit, La Timone University Hospital of Marseille, Marseille, France
| | - Nicolas Fakhry
- Department of Head & Neck Surgery, La Conception University Hospital of Marseille, Marseille, France
| | - Bertrand Pourroy
- Onco-Pharma, La Timone University Hospital of Marseille, Marseille, France
| | - Aurélie Ghettas
- Service de Pharmacologie et d'Immunoanalyse (SPI), CEA, INRA, Université Paris-Saclay, 91191, Gif sur Yvette, France
| | - Alain Pruvost
- Service de Pharmacologie et d'Immunoanalyse (SPI), CEA, INRA, Université Paris-Saclay, 91191, Gif sur Yvette, France
| | - Christophe Junot
- Service de Pharmacologie et d'Immunoanalyse (SPI), CEA, INRA, Université Paris-Saclay, 91191, Gif sur Yvette, France
| | - Florence Duffaud
- Medical Oncology Unit, La Timone University Hospital of Marseille, Marseille, France
| | - Bruno Lacarelle
- Groupe de Pharmacologie Clinique & Oncologique (GPCO)-Unicancer, 101 rue de Tolbiac, 75013, Paris, France.,Clinical Pharmacokinetics Laboratory, SMARTc unit, Inserm S_911 CRO2, Aix Marseille Univ and La Timone University Hospital of Marseille, Marseille, France
| | - Sebastien Salas
- Medical Oncology Unit, La Timone University Hospital of Marseille, Marseille, France
| |
Collapse
|
8
|
Chutipongtanate S, Chatchen S, Svasti J. Plasma prefractionation methods for proteomic analysis and perspectives in clinical applications. Proteomics Clin Appl 2017; 11. [DOI: 10.1002/prca.201600135] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Revised: 01/24/2017] [Accepted: 02/10/2017] [Indexed: 12/16/2022]
Affiliation(s)
- Somchai Chutipongtanate
- Pediatric Translational Research Unit, Department of Pediatrics, Faculty of Medicine Ramathibodi Hospital; Mahidol University; Salaya Thailand
| | - Supawat Chatchen
- Department of Tropical Pediatrics, Faculty of Tropical Medicine; Mahidol University; Salaya Thailand
| | - Jisnuson Svasti
- Laboratory of Biochemistry; Chulabhorn Research Institute, Krung Thep Maha Nakhon; Thailand
- Applied Biological Sciences Program; Chulabhorn Graduate Institute; Thailand
| |
Collapse
|
9
|
Lee HJ, Kim HJ, Liebler DC. Efficient Microscale Basic Reverse Phase Peptide Fractionation for Global and Targeted Proteomics. J Proteome Res 2016; 15:2346-54. [PMID: 27255222 DOI: 10.1021/acs.jproteome.6b00102] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Analysis of small biological samples would benefit from an efficient microscale fractionation strategy that minimizes sample handling, transfer steps, and accompanying losses. Here we describe a microscale basic reverse phase liquid chromatographic (bRPLC) fractionation method that offers high reproducibility and efficiency for peptide mixtures from small (5-20 μg) samples. We applied our platform to detect differentially expressed proteins from lung tumor cell lines that are sensitive (11-18) and resistant (11-18R) to the tyrosine kinase inhibitor erlotinib. Label-free analyses of 5-20 μg samples yielded identifications of approximately 3,200 to 4,000 proteins with coefficients of variation of 1.9-8.9% in replicate analyses. iTRAQ analyses produced similar protein inventories. Label-free and iTRAQ analyses displayed high concordance in identifications of proteins differentially expressed in 11-18 and 11-18R cells. Micro-bRPLC fractionation of cell proteomes increased sensitivity by an average of 4.5-fold in targeted quantitation using parallel reaction monitoring for three representative receptor tyrosine kinases (EGFR, PDGFRA, and BMX), which are present at low abundance in 11-18 and 11-18R cells. These data illustrate the broad utility of micro-bRPLC fractionation for global and targeted proteomic analyses. Data are available through Proteome eXchange Accession PXD003604.
Collapse
Affiliation(s)
- Hyoung-Joo Lee
- Department of Biochemistry, Vanderbilt University School of Medicine , 607 Light Hall, 2215 Garland Avenue, Nashville, Tennessee 37232-0146, United States
| | - Hye-Jung Kim
- Department of Biochemistry, Vanderbilt University School of Medicine , 607 Light Hall, 2215 Garland Avenue, Nashville, Tennessee 37232-0146, United States
| | - Daniel C Liebler
- Department of Biochemistry, Vanderbilt University School of Medicine , 607 Light Hall, 2215 Garland Avenue, Nashville, Tennessee 37232-0146, United States
| |
Collapse
|