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Quantification of Proteins in Blood by Absorptive Microtiter Plate-Based Affinity Purification Coupled to Liquid Chromatography-Mass Spectrometry. Methods Mol Biol 2023; 2628:221-233. [PMID: 36781789 DOI: 10.1007/978-1-0716-2978-9_15] [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: 02/15/2023]
Abstract
Liquid chromatography (LC) coupled to mass spectrometry (MS) is increasingly used for quantification of proteins in blood. This development is prompted by ongoing improvements in detection sensitivities of LC-MS instruments and corresponding sample preparation workflows. The combination of immunoaffinity enrichment and targeted LC-MS detection is a notable analytical platform in this regard as it allows for the quantification of low abundance proteins in biological matrices like plasma and serum. Here, we describe such hybrid methods which are based on the enrichment of proteins with antibodies or affimers coupled to adsorptive microtiter plates, the proteolytic digestion of enriched proteins to release protein-specific peptides, and the detection of these peptides by microflow LC coupled to selected reaction monitoring MS.
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2
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Klont F, Kwiatkowski M, Faiz A, van den Bosch T, Pouwels SD, Dekker FJ, Ten Hacken NHT, Horvatovich P, Bischoff R. Adsorptive Microtiter Plates As Solid Supports in Affinity Purification Workflows. J Proteome Res 2021; 20:5218-5221. [PMID: 34669399 PMCID: PMC8576839 DOI: 10.1021/acs.jproteome.1c00623] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
Affinity ligands
such as antibodies are widely used in (bio)medical
research for purifying proteins from complex biological samples. These
ligands are generally immobilized onto solid supports which facilitate
the separation of a captured protein from the sample matrix. Adsorptive
microtiter plates are commonly used as solid supports prior to immunochemical
detection (e.g., immunoassays) but hardly ever prior to liquid chromatography–mass
spectrometry (LC-MS-)-based detection. Here, we describe the use of
adsorptive microtiter plates for protein enrichment prior to LC-MS
detection, and we discuss opportunities and challenges of corresponding
workflows, based on examples of targeted (i.e., soluble receptor for
advanced glycation end-products (sRAGE) in human serum) and discovery-based
workflows (i.e., transcription factor p65 (NF-κB) in lysed murine
RAW 264.7 macrophages and peptidyl-prolyl cis–trans isomerase
FKBP5 (FKBP5) in lysed human A549 alveolar basal epithelial cells).
Thereby, we aim to highlight the potential usefulness of adsorptive
microtiter plates in affinity purification workflows prior to LC-MS
detection, which could increase their usage in mass spectrometry-based
protein research.
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Affiliation(s)
- Frank Klont
- Department of Analytical Biochemistry, Groningen Research Institute of Pharmacy, University of Groningen, 9700 AB Groningen, The Netherlands
| | - Marcel Kwiatkowski
- Department of Analytical Biochemistry, Groningen Research Institute of Pharmacy, University of Groningen, 9700 AB Groningen, The Netherlands.,Department of Pharmacokinetics, Toxicology and Targeting, Groningen Research Institute of Pharmacy, University of Groningen, 9700 AB Groningen, The Netherlands
| | - Alen Faiz
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, 9700 AB Groningen, The Netherlands
| | - Thea van den Bosch
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, 9700 AB Groningen, The Netherlands
| | - Simon D Pouwels
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, 9700 AB Groningen, The Netherlands
| | - Frank J Dekker
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, 9700 AB Groningen, The Netherlands
| | - Nick H T Ten Hacken
- Department of Pulmonary Diseases, University Medical Center Groningen, University of Groningen, 9700 AB Groningen, The Netherlands
| | - Péter Horvatovich
- Department of Analytical Biochemistry, Groningen Research Institute of Pharmacy, University of Groningen, 9700 AB Groningen, The Netherlands
| | - Rainer Bischoff
- Department of Analytical Biochemistry, Groningen Research Institute of Pharmacy, University of Groningen, 9700 AB Groningen, The Netherlands
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3
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Protein Glycosylation Investigated by Mass Spectrometry: An Overview. Cells 2020; 9:cells9091986. [PMID: 32872358 PMCID: PMC7564411 DOI: 10.3390/cells9091986] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 08/14/2020] [Accepted: 08/24/2020] [Indexed: 12/16/2022] Open
Abstract
The protein glycosylation is a post-translational modification of crucial importance for its involvement in molecular recognition, protein trafficking, regulation, and inflammation. Indeed, abnormalities in protein glycosylation are correlated with several disease states such as cancer, inflammatory diseases, and congenial disorders. The understanding of cellular mechanisms through the elucidation of glycan composition encourages researchers to find analytical solutions for their detection. Actually, the multiplicity and diversity of glycan structures bond to the proteins, the variations in polarity of the individual saccharide residues, and the poor ionization efficiencies make their detection much trickier than other kinds of biopolymers. An overview of the most prominent techniques based on mass spectrometry (MS) for protein glycosylation (glycoproteomics) studies is here presented. The tricks and pre-treatments of samples are discussed as a crucial step prodromal to the MS analysis to improve the glycan ionization efficiency. Therefore, the different instrumental MS mode is also explored for the qualitative and quantitative analysis of glycopeptides and the glycans structural composition, thus contributing to the elucidation of biological mechanisms.
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4
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Sung HJ, Ahn JM, Yoon YH, Na SS, Choi YJ, Kim YI, Lee SY, Lee EB, Cho S, Cho JY. Quiescin Sulfhydryl Oxidase 1 (QSOX1) Secreted by Lung Cancer Cells Promotes Cancer Metastasis. Int J Mol Sci 2018; 19:ijms19103213. [PMID: 30336636 PMCID: PMC6214099 DOI: 10.3390/ijms19103213] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2018] [Revised: 10/12/2018] [Accepted: 10/15/2018] [Indexed: 01/16/2023] Open
Abstract
As lung cancer shows the highest mortality in cancer-related death, serum biomarkers are demanded for lung cancer diagnosis and its treatment. To discover lung cancer protein biomarkers, secreted proteins from primary cultured lung cancer and adjacent normal tissues from patients were subjected to LC/MS⁻MS proteomic analysis. Quiescin sulfhydryl oxidase (QSOX1) was selected as a biomarker candidate from the enriched proteins in the secretion of lung cancer cells. QSOX1 levels were higher in 82% (51 of 62 tissues) of lung cancer tissues compared to adjacent normal tissues. Importantly, QSOX1 serum levels were significantly higher in cancer patients (p < 0.05, Area Under curve (AUC) = 0.89) when measured by multiple reaction monitoring (MRM). Higher levels of QSOX1 were also uniquely detected in lung cancer tissues, among several other solid cancers, by immunohistochemistry. QSOX1-knock-downed Lewis lung cancer (LLC) cells were less viable from oxidative stress and reduced migration and invasion. In addition, LLC mouse models with QSOX1 knock-down also proved that QSOX1 functions in promoting cancer metastasis. In conclusion, QSOX1 might be a lung cancer tissue-derived biomarker and be involved in the promotion of lung cancers, and thus can be a therapeutic target for lung cancers.
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Affiliation(s)
- Hye-Jin Sung
- Department of Biochemistry, BK21 PLUS Program for Creative Veterinary Science Research and Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul 08826, Korea.
| | - Jung-Mo Ahn
- Department of Biochemistry, BK21 PLUS Program for Creative Veterinary Science Research and Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul 08826, Korea.
| | - Yeon-Hee Yoon
- Department of Biochemistry, BK21 PLUS Program for Creative Veterinary Science Research and Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul 08826, Korea.
| | - Sang-Su Na
- Department of Biochemistry, BK21 PLUS Program for Creative Veterinary Science Research and Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul 08826, Korea.
| | - Young-Jin Choi
- Department of Biochemistry, BK21 PLUS Program for Creative Veterinary Science Research and Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul 08826, Korea.
| | - Yong-In Kim
- Department of Biochemistry, BK21 PLUS Program for Creative Veterinary Science Research and Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul 08826, Korea.
| | - Soo-Youn Lee
- Departments of Laboratory Medicine & Genetics and Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06351, Korea.
| | - Eung-Bae Lee
- Department of Thoracic and Cardiovascular Surgery, Kyungpook National University Medical Center, Daegu 41944, Korea.
| | - Sukki Cho
- Department of Thoracic and Cardiovascular Surgery, Seoul National University Bundang Hospital, Seoungnam-si, Gyeonggi-do 13620, Korea.
| | - Je-Yoel Cho
- Department of Biochemistry, BK21 PLUS Program for Creative Veterinary Science Research and Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul 08826, Korea.
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5
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Klont F, Pouwels SD, Hermans J, van de Merbel NC, Horvatovich P, Ten Hacken NHT, Bischoff R. A fully validated liquid chromatography-mass spectrometry method for the quantification of the soluble receptor of advanced glycation end-products (sRAGE) in serum using immunopurification in a 96-well plate format. Talanta 2018; 182:414-421. [PMID: 29501172 DOI: 10.1016/j.talanta.2018.02.015] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Revised: 02/03/2018] [Accepted: 02/05/2018] [Indexed: 12/31/2022]
Abstract
The study of proteins is central to unraveling (patho)physiological processes and has contributed greatly to our understanding of biological systems. Corresponding studies often employ procedures to enrich proteins from their biological matrix using antibodies or other affinity binders coupled to beads with a large surface area and a correspondingly high binding capacity. Striving for maximal binding capacity may, however, not always be required or desirable, for example for proteins of low abundance. Here we describe a simplified immunoprecipitation in 96-well ELISA format (IPE) approach for fast and easy enrichment of proteins. The applicability of this approach for enriching low-abundant proteins was demonstrated by an IPE-based quantitative workflow using liquid chromatography-mass spectrometry (LC-MS) for the soluble Receptor of Advanced Glycation End-products (sRAGE), a promising biomarker in chronic obstructive pulmonary disease (COPD). The method was validated according to U.S. Food and Drug Administration (FDA) and European Medicines Agency (EMA) guidelines and enabled accurate quantitation of sRAGE between 0.1 and 10 ng/mL in 50 µL serum. The assay showed substantial correlation with the two most commonly-used sRAGE immunoassays (ELISAs) (R2-values between 0.7 and 0.8). However, the LC-MS method reported 2-4 times higher sRAGE levels compared to the ELISAs, which is largely due to a suboptimal amount of capturing antibody and/or calibration strategy used by the immunoassays. In conclusion, our simplified IPE approach proved to be an efficient strategy for enriching the low-abundant protein sRAGE from serum and may provide an easy to use platform for enriching other (low-abundant) proteins from complex, biological matrices.
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Affiliation(s)
- Frank Klont
- Department of Analytical Biochemistry, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands; Groningen Research Institute for Asthma and COPD, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands
| | - Simon D Pouwels
- Department of Pulmonary Diseases, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands; Groningen Research Institute for Asthma and COPD, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands
| | - Jos Hermans
- Department of Analytical Biochemistry, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Nico C van de Merbel
- Department of Analytical Biochemistry, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands; Bioanalytical Laboratory, PRA Health Sciences, Early Development Services, Amerikaweg 18, 9407 TK Assen, The Netherlands
| | - Péter Horvatovich
- Department of Analytical Biochemistry, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands; Groningen Research Institute for Asthma and COPD, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands
| | - Nick H T Ten Hacken
- Department of Pulmonary Diseases, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands; Groningen Research Institute for Asthma and COPD, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands
| | - Rainer Bischoff
- Department of Analytical Biochemistry, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands; Groningen Research Institute for Asthma and COPD, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands.
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6
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Halvorsen TG, Reubsaet L. Antibody based affinity capture LC-MS/MS in quantitative determination of proteins in biological matrices. Trends Analyt Chem 2017. [DOI: 10.1016/j.trac.2017.08.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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7
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Ravipaty S, Wu W, Dalvi A, Tanna N, Andreazi J, Friss T, Klotz A, Liao C, Garren J, Schofield S, Diamandis EP, Klein EA, Dobi A, Srivastava S, Tekumalla P, Kiebish MA, Vishnudas V, Sarangarajan RP, Narain NR, Akmaev VR. Clinical Validation of a Serum Protein Panel (FLNA, FLNB and KRT19) for Diagnosis of Prostate Cancer. ACTA ACUST UNITED AC 2017; 8. [PMID: 29682400 PMCID: PMC5909981 DOI: 10.4172/2155-9929.1000323] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
This study reports on the development of a novel serum protein panel of three prostate cancer biomarkers, Filamin A, Filamin B and Keratin-19 (FLNA, FLNB and KRT19) using multivariate models for disease screening and prognosis. ELISA and IPMRM (LC-MS/MS) based assays were developed and analytically validated by quantitative measurements of the biomarkers in serum. Retrospectively collected and clinically annotated serum samples with PSA values and Gleason scores were analyzed from subjects who underwent prostate biopsy, and showed no evidence of cancer with or without indication of prostatic hyperplasia, or had a definitive pathology diagnosis of prostatic adenocarcinoma. Probit linear regression models were used to combine the analytes into score functions to address the following clinical questions: does the biomarker test augment PSA for population screening? Can aggressive disease be differentiated from lower risk disease, and can the panel discriminate between prostate cancer and benign prostate hyperplasia? Modelling of the data showed that the new prostate biomarkers and PSA in combination were better than PSA alone in identifying prostate cancer, improved the prediction of high and low risk disease, and improved prediction of cancer versus benign prostate hyperplasia.
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Affiliation(s)
- Shobha Ravipaty
- Berg, LLC, 500 Old Connecticut Path Framingham, MA 01701, USA
| | - Wenfang Wu
- Berg, LLC, 500 Old Connecticut Path Framingham, MA 01701, USA
| | - Aditee Dalvi
- Berg, LLC, 500 Old Connecticut Path Framingham, MA 01701, USA
| | - Nikunj Tanna
- Berg, LLC, 500 Old Connecticut Path Framingham, MA 01701, USA
| | - Joe Andreazi
- Berg, LLC, 500 Old Connecticut Path Framingham, MA 01701, USA
| | - Tracey Friss
- Berg, LLC, 500 Old Connecticut Path Framingham, MA 01701, USA
| | - Allison Klotz
- Berg, LLC, 500 Old Connecticut Path Framingham, MA 01701, USA
| | - Chenchen Liao
- Berg, LLC, 500 Old Connecticut Path Framingham, MA 01701, USA
| | - Jeonifer Garren
- Berg, LLC, 500 Old Connecticut Path Framingham, MA 01701, USA
| | - Sally Schofield
- Berg, LLC, 500 Old Connecticut Path Framingham, MA 01701, USA
| | - Eleftherios P Diamandis
- Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Eric A Klein
- Glickman Urological and Kidney Institute, Cleveland Clinic, Cleveland, USA
| | - Albert Dobi
- Department of Surgery, Center for Prostate Disease Research, Uniformed Services University of the Health Sciences and the Walter Reed Military Medical Center, Bethesda, Maryland, USA
| | - Shiv Srivastava
- Department of Surgery, Center for Prostate Disease Research, Uniformed Services University of the Health Sciences and the Walter Reed Military Medical Center, Bethesda, Maryland, USA
| | | | | | - Vivek Vishnudas
- Berg, LLC, 500 Old Connecticut Path Framingham, MA 01701, USA
| | | | - Niven R Narain
- Berg, LLC, 500 Old Connecticut Path Framingham, MA 01701, USA
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8
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Florentinus-Mefailoski A, Marshall JG. Linear quantification of a streptavidin–alkaline phosphatase probe for enzyme-linked immuno mass spectrometric assay. Anal Biochem 2016; 503:50-5. [DOI: 10.1016/j.ab.2016.02.014] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Revised: 02/21/2016] [Accepted: 02/22/2016] [Indexed: 02/05/2023]
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9
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Castillo MJ, McShane AJ, Cai M, Shen Y, Wang L, Yao X. Nonisotopic reagents for a cost-effective increase in sample throughput of targeted quantitative proteomics. Anal Chem 2015; 87:9209-16. [PMID: 26291548 DOI: 10.1021/acs.analchem.5b01727] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The new technology of ultrathroughput MS (uMS) transforms the intrinsic capability of analyte multiplexing in mass spectrometry (MS) to sample multiplexing. Core technological advantages of uMS rely on the decoupled use of isotopic quantitation reference and nonisotopic mass coding of samples. These advantages include: (1) high sample-throughput potential, (2) utilization of minimal amounts of expensive stable isotopes for the quantitation reference, and (3) unleashing of the open-source exploration of the chemical structure diversity of nonisotopic reagents to significantly enhance the MS detectability of analytes. A particular uMS method, ultrathroughput multiple reaction monitoring (uMRM), is reported for one-experiment quantitation of a surrogate peptide (SVILLGR) of prostate specific antigen (PSA) in multiple serum samples. Following derivatization of the pair of spiked, isotopic reference (SVILLGR*) and endogenous, native peptide in each sample, all samples were pooled for a step of simultaneous enrichment and cleanup of derivatized peptide pairs using immobilized antibody. The MS analysis of the pooled sample reported the quantity and sample origin of the surrogate peptide. Several analyses with different sample throughput were presented, with the highest being 15-in-1. Screening of nonisotopic reagents used combinatorial libraries of peptidyl compounds, and the reagent selection was based on the derivatization effectiveness and the capability of MS signal enhancement for the peptide. The precision, accuracy, and linearity of the uMRM MS technology were found to be comparable with standard isotope dilution MRM MS.
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Affiliation(s)
- Mary Joan Castillo
- Department of Chemistry and ‡Institute for Systems Genomics, University of Connecticut , Storrs, Connecticut 06269, United States
| | - Adam J McShane
- Department of Chemistry and ‡Institute for Systems Genomics, University of Connecticut , Storrs, Connecticut 06269, United States
| | - Min Cai
- Department of Chemistry and ‡Institute for Systems Genomics, University of Connecticut , Storrs, Connecticut 06269, United States
| | - Yuanyuan Shen
- Department of Chemistry and ‡Institute for Systems Genomics, University of Connecticut , Storrs, Connecticut 06269, United States
| | - Lei Wang
- Department of Chemistry and ‡Institute for Systems Genomics, University of Connecticut , Storrs, Connecticut 06269, United States
| | - Xudong Yao
- Department of Chemistry and ‡Institute for Systems Genomics, University of Connecticut , Storrs, Connecticut 06269, United States
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10
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Rinalducci S, Longo V, Ceci LR, Zolla L. Targeted quantitative phosphoproteomic analysis of erythrocyte membranes during blood bank storage. JOURNAL OF MASS SPECTROMETRY : JMS 2015; 50:326-335. [PMID: 25800014 DOI: 10.1002/jms.3531] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2014] [Revised: 09/29/2014] [Accepted: 10/15/2014] [Indexed: 06/04/2023]
Abstract
One of the hallmarks of blood bank stored red blood cells (RBCs) is the irreversible transition from a discoid to a spherocyte-like morphology with membrane perturbation and cytoskeleton disorders. Therefore, identification of the storage-associated modifications in the protein-protein interactions between the cytoskeleton and the lipid bilayer may contribute to enlighten the molecular mechanisms involved in the alterations of mechanical properties of stored RBCs. Here we report the results obtained analyzing RBCs after 0, 21 and 35 days of storage under standard blood banking conditions by label free mass spectrometry (MS)-based experiments. We could quantitatively measure changes in the phosphorylation level of crucial phosphopeptides belonging to β-spectrin, ankyrin-1, α-adducin, dematin, glycophorin A and glycophorin C proteins. Data have been validated by both western blotting and pseudo-Multiple Reaction Monitoring (MRM). Although each phosphopeptide showed a distinctive trend, a sharp increase in the phosphorylation level during the storage duration was observed. Phosphopeptide mapping and structural modeling analysis indicated that the phosphorylated residues localize in protein functional domains fundamental for the maintenance of membrane structural integrity. Along with previous morphological evidence acquired by electron microscopy, our results seem to indicate that 21-day storage may represent a key point for the molecular processes leading to the erythrocyte deformability reduction observed during blood storage. These findings could therefore be helpful in understanding and preventing the morphology-linked mechanisms responsible for the post-transfusion survival of preserved RBCs.
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Affiliation(s)
- Sara Rinalducci
- Department of Ecological and Biological Sciences, University of Tuscia, Viterbo, Italy
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11
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Sun G, Liu H, Zhang Y, Yu J, Yan M, Song X, He W. Gold nanorods-paper electrode based enzyme-free electrochemical immunoassay for prostate specific antigen using porous zinc oxide spheres–silver nanoparticles nanocomposites as labels. NEW J CHEM 2015. [DOI: 10.1039/c5nj00629e] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Gold nanorods-modified paper electrode and porous zinc oxide spheres–silver nanoparticles nanocomposites were used to construct an enzyme-free immunosensor.
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Affiliation(s)
- Guoqiang Sun
- Key Laboratory of Chemical Sensing & Analysis in Universities of Shandong
- School of Chemistry and Chemical Engineering
- University of Jinan
- Jinan 250022
- China
| | - Haiyun Liu
- Key Laboratory of Chemical Sensing & Analysis in Universities of Shandong
- School of Chemistry and Chemical Engineering
- University of Jinan
- Jinan 250022
- China
| | - Yan Zhang
- Key Laboratory of Chemical Sensing & Analysis in Universities of Shandong
- School of Chemistry and Chemical Engineering
- University of Jinan
- Jinan 250022
- China
| | - Jinghua Yu
- Key Laboratory of Chemical Sensing & Analysis in Universities of Shandong
- School of Chemistry and Chemical Engineering
- University of Jinan
- Jinan 250022
- China
| | - Mei Yan
- Key Laboratory of Chemical Sensing & Analysis in Universities of Shandong
- School of Chemistry and Chemical Engineering
- University of Jinan
- Jinan 250022
- China
| | - Xianrang Song
- Cancer Research Center
- Shandong Tumor Hospital
- Jinan 250117
- China
| | - Wenxing He
- School of Biological Sciences and Technology
- University of Jinan
- Jinan 250022
- China
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12
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Florentinus-Mefailoski A, Soosaipillai A, Dufresne J, Diamandis EP, Marshall JG. An enzyme-linked immuno-mass spectrometric assay with the substrate adenosine monophosphate. Anal Bioanal Chem 2014; 407:1119-30. [PMID: 25519722 DOI: 10.1007/s00216-014-8323-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2014] [Revised: 10/29/2014] [Accepted: 11/05/2014] [Indexed: 01/22/2023]
Abstract
An enzyme-linked immuno-mass spectrometric assay (ELIMSA) with the specific detection probe streptavidin conjugated to alkaline phosphatase catalyzed the production of adenosine from the substrate adenosine monophosphate (AMP) for sensitive quantification of prostate-specific antigen (PSA) by mass spectrometry. Adenosine ionized efficiently and was measured to the femtomole range by dilution and direct analysis with micro-liquid chromatography, electrospray ionization, and mass spectrometry (LC-ESI-MS). The LC-ESI-MS assay for adenosine production was shown to be linear and accurate using internal (13)C(15)N adenosine isotope dilution, internal (13)C(15)N adenosine one-point calibration, and external adenosine standard curves with close agreement. The detection limits of LC-ESI-MS for alkaline phosphatase-streptavidin (AP-SA, ∼190,000 Da) was tested by injecting 0.1 μl of a 1 pg/ml solution, i.e., 100 attograms or 526 yoctomole (5.26E-22) of the alkaline-phosphatase labeled probe on column (about 315 AP-SA molecules). The ELIMSA for PSA was linear and showed strong signals across the picogram per milliliter range and could robustly detect PSA from all of the prostatectomy patients and all of the female plasma samples that ranged as low as 70 pg/ml with strong signals well separated from the background and well within the limit of quantification of the AP-SA probe. The results of the ELIMSA assay for PSA are normal and homogenous when independently replicated with a fresh standard over multiple days, and intra and inter diem assay variation was less than 10 % of the mean. In a blind comparison, ELIMSA showed excellent agreement with, but was more sensitive than, the present gold standard commercial fluorescent ELISA, or ECL-based detection, of PSA from normal and prostatectomy samples, respectively.
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13
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Korbakis D, Prassas I, Brinc D, Batruch I, Krastins B, Lopez MF, Diamandis EP. Delineating monoclonal antibody specificity by mass spectrometry. J Proteomics 2014; 114:115-24. [PMID: 25462431 DOI: 10.1016/j.jprot.2014.11.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2014] [Revised: 11/04/2014] [Accepted: 11/08/2014] [Indexed: 02/05/2023]
Abstract
UNLABELLED Generation of monoclonal antibody (mAb) libraries against antigens in complex matrices can prove a valuable analytical tool. However, delineating the specificity of newly generated antibodies is the limiting step of the procedure. Here, we propose a strategy for mAb production by injecting mice with complex biological fluid and mAb characterization by coupling immunoaffinity techniques with Mass spectrometry (immuno-MS). Mice were immunized against fractionated seminal plasma and mAbs were produced. Different immuno-MS protocols based on four types of solid support (i.e. polystyrene microtiter plates, NHS-activated agarose beads, tosyl-activated magnetic beads and MSIA™ pipette tips) were established. A well-characterized mouse monoclonal anti-KLK3 (PSA) Ab was used as a model to evaluate each protocol's robustness and reproducibility and to establish a set of criteria which would allow antigen characterization of newly developed Abs. Three of the newly generated Abs were analyzed using our optimized protocols. Analysis revealed that all assay configurations used were capable of antibody characterization. Furthermore, low-abundance antigens (e.g. ribonuclease T2) could be identified as efficiently as the high-abundance ones. Our data suggest that complex biological samples can be used for the production of mAbs, which will facilitate the analysis of their proteome, while the established immuno-MS protocols can offer efficient mAb characterization. BIOLOGICAL SIGNIFICANCE The inoculation of animals with complex biological samples is aiming at the discovery of novel disease biomarkers, present in the biological specimens, as well as the production of rare reagents that will facilitate the ultra-sensitive analysis of the biomolecules' native form. In the present study, we initially propose a general workflow concerning the handling of biological samples, as well as the monoclonal antibody production. Furthermore, we established protocols for the reliable and reproducible identification of antibody specificity using various immuno-affinity purification techniques coupled to mass spectrometry. Our data suggest that processed biological fluids can be used for the production of mAbs targeting proteins of varying abundance, and that various immuno-MS protocols can offer great capabilities for the mAb characterization procedure.
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Affiliation(s)
- Dimitrios Korbakis
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada; Department of Clinical Biochemistry, University Health Network, Toronto, Canada
| | - Ioannis Prassas
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada; Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, Canada
| | - Davor Brinc
- Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, Canada
| | - Ihor Batruch
- Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, Canada
| | | | - Mary F Lopez
- Thermo Fisher Scientific BRIMS, Cambridge, MA, USA
| | - Eleftherios P Diamandis
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada; Department of Clinical Biochemistry, University Health Network, Toronto, Canada; Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, Canada.
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14
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Bauer M, Ahrné E, Baron AP, Glatter T, Fava LL, Santamaria A, Nigg EA, Schmidt A. Evaluation of Data-Dependent and -Independent Mass Spectrometric Workflows for Sensitive Quantification of Proteins and Phosphorylation Sites. J Proteome Res 2014; 13:5973-88. [DOI: 10.1021/pr500860c] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Manuel Bauer
- Biozentrum, University of Basel, Klingelbergstrasse 50/70, CH-4056 Basel, Switzerland
| | - Erik Ahrné
- Biozentrum, University of Basel, Klingelbergstrasse 50/70, CH-4056 Basel, Switzerland
| | - Anna P. Baron
- Biozentrum, University of Basel, Klingelbergstrasse 50/70, CH-4056 Basel, Switzerland
| | - Timo Glatter
- Biozentrum, University of Basel, Klingelbergstrasse 50/70, CH-4056 Basel, Switzerland
| | - Luca L. Fava
- Biozentrum, University of Basel, Klingelbergstrasse 50/70, CH-4056 Basel, Switzerland
| | - Anna Santamaria
- Biozentrum, University of Basel, Klingelbergstrasse 50/70, CH-4056 Basel, Switzerland
| | - Erich A. Nigg
- Biozentrum, University of Basel, Klingelbergstrasse 50/70, CH-4056 Basel, Switzerland
| | - Alexander Schmidt
- Biozentrum, University of Basel, Klingelbergstrasse 50/70, CH-4056 Basel, Switzerland
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15
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Florentinus-Mefailoski A, Marshall JG. Pyridoxamine-5-phosphate enzyme-linked immune mass spectrometric assay substrate for linear absolute quantification of alkaline phosphatase to the yoctomole range applied to prostate specific antigen. Anal Chem 2014; 86:10684-91. [PMID: 25259405 DOI: 10.1021/ac502572a] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
There is a need to measure proteins that are present in concentrations below the detection limits of existing colorimetric approaches with enzyme-linked immunoabsorbent assays (ELISA). The powerful enzyme alkaline phosphatase conjugated to the highly specific bacterial protein streptavidin binds to biotinylated macromolecules like proteins, antibodies, or other ligands and receptors with a high affinity. The binding of the biotinylated detection antibody, with resulting amplification of the signal by the catalytic production of reporter molecules, is key to the sensitivity of ELISA. The specificity and amplification of the signal by the enzyme alkaline phosphatase in ELISA together with the sensitivity of liquid chromatography electrospray ionization and mass spectrometry (LC-ESI-MS) to detect femtomole to picomole amounts of reporter molecules results in an ultrasensitive enzyme-linked immune mass spectrometric assay (ELIMSA). The novel ELIMSA substrate pyridoxamine-5-phosphate (PA5P) is cleaved by the enzyme alkaline phosphatase to yield the basic and hydrophilic product pyridoxamine (PA) that elutes rapidly with symmetrical peaks and a flat baseline. Pyridoxamine (PA) and (13)C PA were both observed to show a linear relationship between log ion intensity and quantity from picomole to femtomole amounts by liquid chromatography-electrospray ionization and mass spectrometry. Four independent methods, (i) internal (13)C isotope PA dilution curves, (ii) internal (13)C isotope one-point calibration, (iii) external PA standard curve, and (iv) external (13)C PA standard curve, all agreed within 1 digit in the same order of magnitude on the linear quantification of PA. Hence, a mass spectrometer can be used to robustly detect 526 ymol of the alkaline phosphatase streptavidin probe and accurately quantify zeptomole amounts of PSA against log linear absolute standard by micro electrospray on a simple ion trap.
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16
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Abstract
BACKGROUND Most of newly discovered cancer biomarkers fail in the clinic because they lack sensitivity and/or specificity. The current explosion in knowledge of the mutational spectrum of many cancer types, as a result of whole exome and whole genome sequencing, has revealed a wide spectrum of mutations that appear to be highly specific for various cancer types. DISCUSSION Mass spectrometry (MS) has the ability to monitor tryptic peptides in complex biological mixtures with high sensitivity and specificity. It may be possible in the near future to combine the known spectrum of gene mutations revealed by genomics with the power of MS, in order to quantify mutant peptides that are highly specific for cancer, in a multiplex fashion. Such mutant peptides, quantified in the circulation and other fluids, may represent tumor markers that are suitable for detection and monitoring of cancer. SUMMARY The power of genomic and proteomic technologies can be combined to identify highly specific analytes for biomarker applications.
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17
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Mesri M. Advances in Proteomic Technologies and Its Contribution to the Field of Cancer. Adv Med 2014; 2014:238045. [PMID: 26556407 PMCID: PMC4590950 DOI: 10.1155/2014/238045] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/23/2014] [Accepted: 06/30/2014] [Indexed: 12/12/2022] Open
Abstract
Systematic studies of the cancer genome have generated a wealth of knowledge in recent years. These studies have uncovered a number of new cancer genes not previously known to be causal targets in cancer. Genetic markers can be used to determine predisposition to tumor development, but molecularly targeted treatment strategies are not widely available for most cancers. Precision care plans still must be developed by understanding and implementing basic science research into clinical treatment. Proteomics is continuing to make major strides in the discovery of fundamental biological processes as well as more recent transition into an assay platform capable of measuring hundreds of proteins in any biological system. As such, proteomics can translate basic science discoveries into the clinical practice of precision medicine. The proteomic field has progressed at a fast rate over the past five years in technology, breadth and depth of applications in all areas of the bioscience. Some of the previously experimental technical approaches are considered the gold standard today, and the community is now trying to come to terms with the volume and complexity of the data generated. Here I describe contribution of proteomics in general and biological mass spectrometry in particular to cancer research, as well as related major technical and conceptual developments in the field.
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Affiliation(s)
- Mehdi Mesri
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
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18
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Torsetnes SB, Levernæs MS, Broughton MN, Paus E, Halvorsen TG, Reubsaet L. Multiplexing Determination of Small Cell Lung Cancer Biomarkers and Their Isovariants in Serum by Immunocapture LC-MS/MS. Anal Chem 2014; 86:6983-92. [DOI: 10.1021/ac500986t] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Silje B. Torsetnes
- Department
of Pharmaceutical Chemistry, School of Pharmacy, University of Oslo, Oslo, NO-0316, Norway
| | - Maren S. Levernæs
- Department
of Pharmaceutical Chemistry, School of Pharmacy, University of Oslo, Oslo, NO-0316, Norway
| | - Marianne N. Broughton
- Department
of Medical Biochemistry, Oslo University Hospital, Radiumhospitalet, Oslo, 0310, Norway
| | - Elisabeth Paus
- Department
of Medical Biochemistry, Oslo University Hospital, Radiumhospitalet, Oslo, 0310, Norway
| | - Trine G. Halvorsen
- Department
of Pharmaceutical Chemistry, School of Pharmacy, University of Oslo, Oslo, NO-0316, Norway
| | - Léon Reubsaet
- Department
of Pharmaceutical Chemistry, School of Pharmacy, University of Oslo, Oslo, NO-0316, Norway
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19
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Marshall J, Bowden P, Schmit JC, Betsou F. Creation of a federated database of blood proteins: a powerful new tool for finding and characterizing biomarkers in serum. Clin Proteomics 2014; 11:3. [PMID: 24476026 PMCID: PMC4015845 DOI: 10.1186/1559-0275-11-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2013] [Accepted: 10/22/2013] [Indexed: 12/12/2022] Open
Abstract
Protein biomarkers offer major benefits for diagnosis and monitoring of disease processes. Recent advances in protein mass spectrometry make it feasible to use this very sensitive technology to detect and quantify proteins in blood. To explore the potential of blood biomarkers, we conducted a thorough review to evaluate the reliability of data in the literature and to determine the spectrum of proteins reported to exist in blood with a goal of creating a Federated Database of Blood Proteins (FDBP). A unique feature of our approach is the use of a SQL database for all of the peptide data; the power of the SQL database combined with standard informatic algorithms such as BLAST and the statistical analysis system (SAS) allowed the rapid annotation and analysis of the database without the need to create special programs to manage the data. Our mathematical analysis and review shows that in addition to the usual secreted proteins found in blood, there are many reports of intracellular proteins and good agreement on transcription factors, DNA remodelling factors in addition to cellular receptors and their signal transduction enzymes. Overall, we have catalogued about 12,130 proteins identified by at least one unique peptide, and of these 3858 have 3 or more peptide correlations. The FDBP with annotations should facilitate testing blood for specific disease biomarkers.
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Affiliation(s)
- John Marshall
- Department of Chemistry and Biology, Ryerson University, Toronto, Canada
- Luxembourg Center for Clinical Proteomics, CRP SANTE, 1A-B, rue Thomas Edison L-1445 Strassen, Luxembourg, Luxembourg
| | - Peter Bowden
- Department of Chemistry and Biology, Ryerson University, Toronto, Canada
| | - Jean Claude Schmit
- Luxembourg Center for Clinical Proteomics, CRP SANTE, 1A-B, rue Thomas Edison L-1445 Strassen, Luxembourg, Luxembourg
| | - Fay Betsou
- Integrated Biobank of Luxembourg, 6, rue Nicolas Ernest Barblé, Luxembourg L-1210, Luxembourg
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20
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Garbis SD, Townsend PA. Proteomics of human prostate cancer biospecimens: the global, systems-wide perspective for Protein markers with potential clinical utility. Expert Rev Proteomics 2014; 10:337-54. [DOI: 10.1586/14789450.2013.827408] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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21
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Végvári Á, Sjödin K, Rezeli M, Malm J, Lilja H, Laurell T, Marko-Varga G. Identification of a novel proteoform of prostate specific antigen (SNP-L132I) in clinical samples by multiple reaction monitoring. Mol Cell Proteomics 2013; 12:2761-73. [PMID: 23842001 PMCID: PMC3790289 DOI: 10.1074/mcp.m113.028365] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2013] [Revised: 07/07/2013] [Indexed: 12/12/2022] Open
Abstract
Prostate specific antigen (PSA) is a well-established tumor marker that is frequently employed as model biomarker in the development and evaluation of emerging quantitative proteomics techniques, partially as a result of wide access to commercialized immunoassays serving as "gold standards." We designed a multiple reaction monitoring (MRM) assay to detect PSA proteoforms in clinical samples (n = 72), utilizing the specificity and sensitivity of the method. We report, for the first time, a PSA proteoform coded by SNP-L132I (rs2003783) that was observed in nine samples in both heterozygous (n = 7) and homozygous (n = 2) expression profiles. Other isoforms of PSA, derived from protein databases, were not identified by four unique proteotypic tryptic peptides. We have also utilized our MRM assay for precise quantitative analysis of PSA concentrations in both seminal and blood plasma samples. The analytical performance was evaluated, and close agreement was noted between quantitations based on three selected peptides (LSEPAELTDAVK, IVGGWECEK, and SVILLGR) and a routinely used commercialized immunoassay. Additionally, we disclose that the peptide IVGGWECEK is shared with kallikrein-related peptidase 2 and therefore is not unique for PSA. Thus, we propose the use of another tryptic sequence (SVILLGR) for accurate MRM quantification of PSA in clinical samples.
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Affiliation(s)
- Ákos Végvári
- From ‡Clinical Protein Science & Imaging, Biomedical Center, Dept. of Measurement Technology and Industrial Electrical Engineering, Lund University, BMC C13, 221 84 Lund, Sweden
| | - Karin Sjödin
- From ‡Clinical Protein Science & Imaging, Biomedical Center, Dept. of Measurement Technology and Industrial Electrical Engineering, Lund University, BMC C13, 221 84 Lund, Sweden
| | - Melinda Rezeli
- From ‡Clinical Protein Science & Imaging, Biomedical Center, Dept. of Measurement Technology and Industrial Electrical Engineering, Lund University, BMC C13, 221 84 Lund, Sweden
| | - Johan Malm
- ¶Dept. of Laboratory Medicine, Division of Clinical Chemistry, Lund University, Skåne University Hospital in Malmö, SE-205 02 Malmö, Sweden
| | - Hans Lilja
- ¶Dept. of Laboratory Medicine, Division of Clinical Chemistry, Lund University, Skåne University Hospital in Malmö, SE-205 02 Malmö, Sweden
- ‖Depts. of Laboratory Medicine, Surgery (Urology), and Medicine (GU-Oncology), Memorial Sloan-Kettering Cancer Center, New York, New York 10065
- **Nuffield Dept. of Surgical Sciences, University of Oxford, Oxford, OX3 9DU UK
- ‡‡Institute of Biomedical Technology, University of Tampere, Biokatu 8, 33520 Tampere, Finland
| | - Thomas Laurell
- From ‡Clinical Protein Science & Imaging, Biomedical Center, Dept. of Measurement Technology and Industrial Electrical Engineering, Lund University, BMC C13, 221 84 Lund, Sweden
- §§Dept. of Biomedical Engineering, Dongguk University, Seoul, 100-715, South Korea
| | - György Marko-Varga
- From ‡Clinical Protein Science & Imaging, Biomedical Center, Dept. of Measurement Technology and Industrial Electrical Engineering, Lund University, BMC C13, 221 84 Lund, Sweden
- ¶¶First Department of Surgery, Tokyo Medical University, 6-7-1 Nishishinjiku Shinjiku-ku, Tokyo, 160-0023 Japan
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22
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The proteomic revolution in laboratory medicine. Clin Biochem 2013; 46:397-8. [PMID: 23497914 DOI: 10.1016/j.clinbiochem.2013.02.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2012] [Revised: 01/21/2013] [Accepted: 01/30/2013] [Indexed: 12/17/2022]
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23
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van den Broek I, Niessen WM, van Dongen WD. Bioanalytical LC–MS/MS of protein-based biopharmaceuticals. J Chromatogr B Analyt Technol Biomed Life Sci 2013; 929:161-79. [DOI: 10.1016/j.jchromb.2013.04.030] [Citation(s) in RCA: 152] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2013] [Revised: 04/15/2013] [Accepted: 04/20/2013] [Indexed: 12/18/2022]
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24
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Torsetnes SB, Løvbak SG, Claus C, Lund H, Nordlund MS, Paus E, Halvorsen TG, Reubsaet L. Immunocapture and LC–MS/MS for selective quantification and differentiation of the isozymes of the biomarker neuron-specific enolase in serum. J Chromatogr B Analyt Technol Biomed Life Sci 2013; 929:125-32. [DOI: 10.1016/j.jchromb.2013.04.010] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2013] [Revised: 04/06/2013] [Accepted: 04/12/2013] [Indexed: 11/17/2022]
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25
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Pierce NW, Lee JE, Liu X, Sweredoski MJ, Graham RLJ, Larimore EA, Rome M, Zheng N, Clurman BE, Hess S, Shan SO, Deshaies RJ. Cand1 promotes assembly of new SCF complexes through dynamic exchange of F box proteins. Cell 2013; 153:206-15. [PMID: 23453757 DOI: 10.1016/j.cell.2013.02.024] [Citation(s) in RCA: 198] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2012] [Revised: 01/24/2013] [Accepted: 02/12/2013] [Indexed: 11/29/2022]
Abstract
The modular SCF (Skp1, cullin, and F box) ubiquitin ligases feature a large family of F box protein substrate receptors that enable recognition of diverse targets. However, how the repertoire of SCF complexes is sustained remains unclear. Real-time measurements of formation and disassembly indicate that SCF(Fbxw7) is extraordinarily stable, but, in the Nedd8-deconjugated state, the cullin-binding protein Cand1 augments its dissociation by one-million-fold. Binding and ubiquitylation assays show that Cand1 is a protein exchange factor that accelerates the rate at which Cul1-Rbx1 equilibrates with multiple F box protein-Skp1 modules. Depletion of Cand1 from cells impedes recruitment of new F box proteins to pre-existing Cul1 and profoundly alters the cellular landscape of SCF complexes. We suggest that catalyzed protein exchange may be a general feature of dynamic macromolecular machines and propose a hypothesis for how substrates, Nedd8, and Cand1 collaborate to regulate the cellular repertoire of SCF complexes.
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Affiliation(s)
- Nathan W Pierce
- Division of Biology, MC 156-29, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA
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26
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Kuzmanov U, Kosanam H, Diamandis EP. The sweet and sour of serological glycoprotein tumor biomarker quantification. BMC Med 2013; 11:31. [PMID: 23390961 PMCID: PMC3751898 DOI: 10.1186/1741-7015-11-31] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/04/2012] [Accepted: 02/07/2013] [Indexed: 12/25/2022] Open
Abstract
Aberrant and dysregulated protein glycosylation is a well-established event in the process of oncogenesis and cancer progression. Years of study on the glycobiology of cancer have been focused on the development of clinically viable diagnostic applications of this knowledge. However, for a number of reasons, there has been only sparse and varied success. The causes of this range from technical to biological issues that arise when studying protein glycosylation and attempting to apply it to practical applications. This review focuses on the pitfalls, advances, and future directions to be taken in the development of clinically applicable quantitative assays using glycan moieties from serum-based proteins as analytes. Topics covered include the development and progress of applications of lectins, mass spectrometry, and other technologies towards this purpose. Slowly but surely, novel applications of established and development of new technologies will eventually provide us with the tools to reach the ultimate goal of quantification of the full scope of heterogeneity associated with the glycosylation of biomarker candidate glycoproteins in a clinically applicable fashion.
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Affiliation(s)
- Uros Kuzmanov
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, 6th floor, 60 Murray Street, Box 32, Toronto, ON M5T 3L9, Canada
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27
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Affiliation(s)
- E.P. Diamandis
- Department of Pathology and Laboratory Medicine; Mount Sinai Hospital; Toronto; ON; Canada
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28
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Hewel JA, Phanse S, Liu J, Bousette N, Gramolini A, Emili A. Targeted protein identification, quantification and reporting for high-resolution nanoflow targeted peptide monitoring. J Proteomics 2012; 81:159-72. [PMID: 23124093 DOI: 10.1016/j.jprot.2012.10.020] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2012] [Revised: 10/16/2012] [Accepted: 10/20/2012] [Indexed: 01/29/2023]
Abstract
Mass spectrometry-based targeted proteomic assays are experiencing a surge in awareness due to the diverse possibilities arising from the re-application of traditional LC-SRM technology. The FDA-approved quantitative LC-SRM-pipeline in drug discovery motivates the use to quantitatively validate putative proteomic biomarkers. However, complexity of biological specimens bears a huge challenge to identify, in parallel, specific peptides and proteins of interest from large biomarker candidate lists. Methods have been devised to increase scan speeds, improve detection specificity and verify quantitative SRM-features. In contrast, high-resolution mass spectrometers could be used to improve reliability and precision of targeted proteomics assays. Here, we present a new method for identifying, quantifying and reporting peptides in high-resolution targeted proteomics experiments performed on an orbitrap hybrid instrument using stable isotope-labeled internal reference peptides. This high precision targeted peptide monitoring (TPM) method has unique advantages over existing techniques, including the need to only detect the most abundant product ion of a given target for confident peptide identification using a scoring function that evaluates assay performance based on 1) m/z-mass accuracy, 2) retention time accuracy of observed species relative to prediction, and 3) retention time accuracy relative to internal reference peptides. Further, we show management of multiplexed precision TPM-assays using sentinel peptide standards. This article is part of a Special Issue entitled: From protein structures to clinical applications.
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Affiliation(s)
- Johannes A Hewel
- Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, Canada.
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29
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Lemoine J, Fortin T, Salvador A, Jaffuel A, Charrier JP, Choquet-Kastylevsky G. The current status of clinical proteomics and the use of MRM and MRM(3) for biomarker validation. Expert Rev Mol Diagn 2012; 12:333-42. [PMID: 22616699 DOI: 10.1586/erm.12.32] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The transfer of biomarkers from the discovery field to clinical use is still, despite progress, on a road filled with pitfalls. Since the emergence of proteomics, thousands of putative biomarkers have been published, often with overlapping diagnostic capacities. The strengthening of the robustness of discovery technologies, particularly in mass spectrometry, has been followed by intense discussions on establishing well-defined evaluation procedures for the identified targets to ultimately allow the clinical validation and then the clinical use of some of these biomarkers. Some of the obstacles to the evaluation process have been the lack of the availability of quick and easy-to-develop, easy-to-use, robust, specific and sensitive alternative quantitative methods when immunoaffinity-based tests are unavailable. Multiple reaction monitoring (MRM; also called selected reaction monitoring) is currently proving its capabilities as a complementary or alternative technique to ELISA for large biomarker panel evaluation. Here, we present how MRM(3) can overcome the lack of specificity and sensitivity often encountered by MRM when tracking minor proteins diluted by complex biological matrices.
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Affiliation(s)
- Jérôme Lemoine
- UMR 5280 CNRS Université Lyon 1, Institut des Sciences Analytiques, Université de Lyon, 69622 Villeurbanne cedex, France
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30
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Kuzmanov U, Smith CR, Batruch I, Soosaipillai A, Diamandis A, Diamandis EP. Separation of kallikrein 6 glycoprotein subpopulations in biological fluids by anion-exchange chromatography coupled to ELISA and identification by mass spectrometry. Proteomics 2012; 12:799-809. [PMID: 22539431 DOI: 10.1002/pmic.201100371] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Kallikrein 6 (KLK6) has been shown to be aberrantly glycosylated in ovarian cancer. Here, we report a novel HPLC anion exchange method, coupled to a KLK6-specific ELISA, capable of differentiating KLK6 glycoform subgroups in biological fluids. Biological fluids were fractionated using anion exchange and resulting fractions were analyzed for KLK6 content by ELISA producing a four-peak elution profile. Using this assay, the KLK6 elution profile and distribution across peaks of a set (n = 7) of ovarian cancer patient matched serum and ascites fluid samples was found to be different than the profile of serum and cerebrospinal fluid (CSF) of normal individuals (n = 7). Glycosylation patterns of recombinant KLK6 (rKLK6) were characterized using tandem mass spectrometry (MS/MS), and found to consist of a highly heterogeneous KLK6 population. This protein was found to contain all of the four diagnostic KLK6 peaks present in the previously assayed biological fluids. The rKLK6 glycoform composition of each peak was assessed by lectin affinity and MS/MS based glycopeptide quantification by product ion monitoring. The combined results showed an increase in terminal alpha 2-6 linked sialic acid in the N-glycans found on KLK6 from ovarian cancer serum and ascites, as opposed to CSF and serum of normal individuals.
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Affiliation(s)
- Uros Kuzmanov
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
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31
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Quantification of p-cresol sulphate in human plasma by selected reaction monitoring. Anal Bioanal Chem 2012; 404:2097-104. [DOI: 10.1007/s00216-012-6277-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2012] [Revised: 07/04/2012] [Accepted: 07/16/2012] [Indexed: 10/28/2022]
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32
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Prely LM, Paal K, Hermans J, van der Heide S, van Oosterhout AJ, Bischoff R. Quantification of matrix metalloprotease-9 in bronchoalveolar lavage fluid by selected reaction monitoring with microfluidics nano-liquid-chromatography–mass spectrometry. J Chromatogr A 2012; 1246:103-10. [DOI: 10.1016/j.chroma.2012.02.076] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2011] [Revised: 01/15/2012] [Accepted: 02/20/2012] [Indexed: 12/25/2022]
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Shi T, Su D, Liu T, Tang K, Camp DG, Qian WJ, Smith RD. Advancing the sensitivity of selected reaction monitoring-based targeted quantitative proteomics. Proteomics 2012; 12:1074-92. [PMID: 22577010 PMCID: PMC3375056 DOI: 10.1002/pmic.201100436] [Citation(s) in RCA: 157] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2011] [Accepted: 01/12/2012] [Indexed: 12/13/2022]
Abstract
Selected reaction monitoring (SRM) - also known as multiple reaction monitoring (MRM) - has emerged as a promising high-throughput targeted protein quantification technology for candidate biomarker verification and systems biology applications. A major bottleneck for current SRM technology, however, is insufficient sensitivity for, e.g. detecting low-abundance biomarkers likely present at the low ng/mL to pg/mL range in human blood plasma or serum, or extremely low-abundance signaling proteins in cells or tissues. Herein, we review recent advances in methods and technologies, including front-end immunoaffinity depletion, fractionation, selective enrichment of target proteins/peptides including posttranslational modifications, as well as advances in MS instrumentation which have significantly enhanced the overall sensitivity of SRM assays and enabled the detection of low-abundance proteins at low- to sub-ng/mL level in human blood plasma or serum. General perspectives on the potential of achieving sufficient sensitivity for detection of pg/mL level proteins in plasma are also discussed.
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Affiliation(s)
- Tujin Shi
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99352
| | - Dian Su
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99352
| | - Tao Liu
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99352
| | - Keqi Tang
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99352
| | - David G. Camp
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99352
| | - Wei-Jun Qian
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99352
| | - Richard D. Smith
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99352
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Rodthongkum N, Ramireddy R, Thayumanavan S, Vachet RW. Selective enrichment and sensitive detection of peptide and protein biomarkers in human serum using polymeric reverse micelles and MALDI-MS. Analyst 2012; 137:1024-30. [PMID: 22193368 PMCID: PMC3771100 DOI: 10.1039/c2an16089g] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Reverse-micelle forming amphiphilic homopolymers with carboxylic acid and quaternary amine substituents are used to selectively enrich biomarker peptides and protein fragments from human serum prior to matrix assisted laser desorption/ionization mass spectrometry (MALDI-MS) analysis. After depletion of human serum albumin (HSA) and immunoglobulin G (IgG), low abundance peptide biomarkers can be selectively enriched and detected by MALDI-MS at clinically relevant concentrations by using the appropriate homopolymer(s) and extraction pH value(s). Three breast cancer peptide biomarkers, bradykinin, C4a, and ITIH(4), were chosen to test this new approach, and detection limits of 0.5 ng mL(-1), 0.08 ng mL(-1), and 0.2 ng mL(-1), respectively, were obtained. In addition, the amphiphilic homopolymers were used to detect prostate specific antigen (PSA) at concentrations as low as 0.5 ng mL(-1) by targeting a surrogate peptide fragment of this protein biomarker. Selective enrichment and sensitive MS detection of low abundance peptide/protein biomarkers by these polymeric reverse micelles should be a sensitive and straightforward approach for biomarker screening in human serum.
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Affiliation(s)
- Nadnudda Rodthongkum
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003
| | - Rajasekhar Ramireddy
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003
| | - S. Thayumanavan
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003
| | - Richard W. Vachet
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003
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Rafalko A, Dai S, Hancock WS, Karger BL, Hincapie M. Development of a Chip/Chip/SRM platform using digital chip isoelectric focusing and LC-Chip mass spectrometry for enrichment and quantitation of low abundance protein biomarkers in human plasma. J Proteome Res 2012; 11:808-17. [PMID: 22098410 PMCID: PMC3656385 DOI: 10.1021/pr2006704] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Protein biomarkers are critical for diagnosis, prognosis, and treatment of disease. The transition from protein biomarker discovery to verification can be a rate limiting step in clinical development of new diagnostics. Liquid chromatography-selected reaction monitoring mass spectrometry (LC-SRM MS) is becoming an important tool for biomarker verification studies in highly complex biological samples. Analyte enrichment or sample fractionation is often necessary to reduce sample complexity and improve sensitivity of SRM for quantitation of clinically relevant biomarker candidates present at the low ng/mL range in blood. In this paper, we describe an alternative method for sample preparation for LC-SRM MS, which does not rely on availability of antibodies. This new platform is based on selective enrichment of proteotypic peptides from complex biological peptide mixtures via isoelectric focusing (IEF) on a digital ProteomeChip (dPC) for SRM quantitation using a triple quadrupole (QQQ) instrument with an LC-Chip (Chip/Chip/SRM). To demonstrate the value of this approach, the optimization of the Chip/Chip/SRM platform was performed using prostate specific antigen (PSA) added to female plasma as a model system. The combination of immunodepletion of albumin and IgG with peptide fractionation on the dPC, followed by SRM analysis, resulted in a limit of quantitation of PSA added to female plasma at the level of ∼1-2.5 ng/mL with a CV of ∼13%. The optimized platform was applied to measure levels of PSA in plasma of a small cohort of male patients with prostate cancer (PCa) and healthy matched controls with concentrations ranging from 1.5 to 25 ng/mL. A good correlation (r(2) = 0.9459) was observed between standard clinical ELISA tests and the SRM-based assay. Our data demonstrate that the combination of IEF on the dPC and SRM (Chip/Chip/SRM) can be successfully applied for verification of low abundance protein biomarkers in complex samples.
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Affiliation(s)
- Agnes Rafalko
- Barnett Institute of Chemical and Biological Analysis and Department of Chemistry and Chemical Biology Northeastern University, 360 Huntington Avenue, Boston, MA 02115
| | - Shujia Dai
- Barnett Institute of Chemical and Biological Analysis and Department of Chemistry and Chemical Biology Northeastern University, 360 Huntington Avenue, Boston, MA 02115
| | - William S. Hancock
- Barnett Institute of Chemical and Biological Analysis and Department of Chemistry and Chemical Biology Northeastern University, 360 Huntington Avenue, Boston, MA 02115
| | - Barry L. Karger
- Barnett Institute of Chemical and Biological Analysis and Department of Chemistry and Chemical Biology Northeastern University, 360 Huntington Avenue, Boston, MA 02115
| | - Marina Hincapie
- Barnett Institute of Chemical and Biological Analysis and Department of Chemistry and Chemical Biology Northeastern University, 360 Huntington Avenue, Boston, MA 02115
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Sung HJ, Jeon SA, Ahn JM, Seul KJ, Kim JY, Lee JY, Yoo JS, Lee SY, Kim H, Cho JY. Large-scale isotype-specific quantification of Serum amyloid A 1/2 by multiple reaction monitoring in crude sera. J Proteomics 2012; 75:2170-80. [PMID: 22300576 DOI: 10.1016/j.jprot.2012.01.018] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2011] [Revised: 01/09/2012] [Accepted: 01/14/2012] [Indexed: 12/19/2022]
Abstract
Quantification is an essential step in biomarker development. Multiple reaction monitoring (MRM) is a new modified mass spectrometry-based quantification technology that does not require antibody development. Serum amyloid A (SAA) is a positive acute-phase protein identified as a lung cancer biomarker in our previous study. Acute SAA exists in two isoforms with highly similar (92%) amino acid sequences. Until now, studies of SAA have been unable to distinguish between SAA1 and SAA2. To overcome the unavailability of a SAA2-specific antibody, we developed MRM methodology for the verification of SAA1 and SAA2 in clinical crude serum samples from 99 healthy controls and 100 lung adenocarcinoma patients. Differential measurement of SAA1 and SAA2 was made possible for the first time with the developed isotype-specific MRM method. Most healthy control samples had small or no MS/MS peaks of the targeted peptides otherwise, higher peak areas with 10- to 34-fold increase over controls were detected in lung cancer samples. In addition, our SAA1 MRM data demonstrated good agreement with the SAA1 enzyme-linked immunosorbent assay (ELISA) data. Finally, successful quantification of SAA2 in crude serum by MRM, for the first time, shows that SAA2 can be a good biomarker for the detection of lung cancers.
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Affiliation(s)
- Hye-Jin Sung
- Department of Biochemistry, BK21 and Research Institute for Veterinary Science College of veterinary Medicine, Seoul National University, Seoul and ProtAnBio, Daegu, Republic of Korea
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MRM assay for quantitation of complement components in human blood plasma — a feasibility study on multiple sclerosis. J Proteomics 2011; 75:211-20. [DOI: 10.1016/j.jprot.2011.05.042] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2011] [Revised: 04/28/2011] [Accepted: 05/17/2011] [Indexed: 11/17/2022]
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Enjalbert Q, Simon R, Salvador A, Antoine R, Redon S, Ayhan MM, Darbour F, Chambert S, Bretonnière Y, Dugourd P, Lemoine J. Photo-SRM: laser-induced dissociation improves detection selectivity of Selected Reaction Monitoring mode. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2011; 25:3375-3381. [PMID: 22002689 DOI: 10.1002/rcm.5232] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Selected Reaction Monitoring (SRM) carried out on triple-quadrupole mass spectrometers coupled to liquid chromatography has been a reference method to develop quantitative analysis of small molecules in biological or environmental matrices for years and is currently emerging as a promising tool in clinical proteomic. However, sensitive assays in complex matrices are often hampered by the presence of co-eluted compounds that share redundant transitions with the target species. On-the-fly better selection of the precursor ion by high-field asymmetric waveform ion mobility spectrometry (FAIMS) or increased quadrupole resolution is one way to escape from interferences. In the present work we document the potential interest of substituting classical gas-collision activation mode by laser-induced dissociation in the visible wavelength range to improve the specificity of the fragmentation step. Optimization of the laser beam pathway across the different quadrupoles to ensure high photo-dissociation yield in Q2 without detectable fragmentation in Q1 was assessed with sucrose tagged with a push-pull chromophore. Next, the proof of concept that photo-SRM ensures more specific detection than does conventional collision-induced dissociation (CID)-based SRM was carried out with oxytocin peptide. Oxytocin was derivatized by the thiol-reactive QSY® 7 C(5)-maleimide quencher on cysteine residues to shift its absorption property into the visible range. Photo-SRM chromatograms of tagged oxytocin spiked in whole human plasma digest showed better detection specificity and sensitivity than CID, that resulted in extended calibration curve linearity. We anticipate that photo-SRM might significantly improve the limit of quantification of classical SRM-based assays targeting cysteine-containing peptides.
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39
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Florentinus AK, Bowden P, Sardana G, Diamandis EP, Marshall JG. Identification and quantification of peptides and proteins secreted from prostate epithelial cells by unbiased liquid chromatography tandem mass spectrometry using goodness of fit and analysis of variance. J Proteomics 2011; 75:1303-17. [PMID: 22120120 DOI: 10.1016/j.jprot.2011.11.002] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2011] [Revised: 10/29/2011] [Accepted: 11/05/2011] [Indexed: 10/15/2022]
Abstract
The proteins secreted by prostate cancer cells (PC3(AR)6) were separated by strong anion exchange chromatography, digested with trypsin and analyzed by unbiased liquid chromatography tandem mass spectrometry with an ion trap. The spectra were matched to peptides within proteins using a goodness of fit algorithm that showed a low false positive rate. The parent ions for MS/MS were randomly and independently sampled from a log-normal population and therefore could be analyzed by ANOVA. Normal distribution analysis confirmed that the parent and fragment ion intensity distributions were sampled over 99.9% of their range that was above the background noise. Arranging the ion intensity data with the identified peptide and protein sequences in structured query language (SQL) permitted the quantification of ion intensity across treatments, proteins and peptides. The intensity of 101,905 fragment ions from 1421 peptide precursors of 583 peptides from 233 proteins separated over 11 sample treatments were computed together in one ANOVA model using the statistical analysis system (SAS) prior to Tukey-Kramer honestly significant difference (HSD) testing. Thus complex mixtures of proteins were identified and quantified with a high degree of confidence using an ion trap without isotopic labels, multivariate analysis or comparing chromatographic retention times.
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40
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Zhu P, Bowden P, Zhang D, Marshall JG. Mass spectrometry of peptides and proteins from human blood. MASS SPECTROMETRY REVIEWS 2011; 30:685-732. [PMID: 24737629 DOI: 10.1002/mas.20291] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2008] [Revised: 12/09/2009] [Accepted: 01/19/2010] [Indexed: 06/03/2023]
Abstract
It is difficult to convey the accelerating rate and growing importance of mass spectrometry applications to human blood proteins and peptides. Mass spectrometry can rapidly detect and identify the ionizable peptides from the proteins in a simple mixture and reveal many of their post-translational modifications. However, blood is a complex mixture that may contain many proteins first expressed in cells and tissues. The complete analysis of blood proteins is a daunting task that will rely on a wide range of disciplines from physics, chemistry, biochemistry, genetics, electromagnetic instrumentation, mathematics and computation. Therefore the comprehensive discovery and analysis of blood proteins will rank among the great technical challenges and require the cumulative sum of many of mankind's scientific achievements together. A variety of methods have been used to fractionate, analyze and identify proteins from blood, each yielding a small piece of the whole and throwing the great size of the task into sharp relief. The approaches attempted to date clearly indicate that enumerating the proteins and peptides of blood can be accomplished. There is no doubt that the mass spectrometry of blood will be crucial to the discovery and analysis of proteins, enzyme activities, and post-translational processes that underlay the mechanisms of disease. At present both discovery and quantification of proteins from blood are commonly reaching sensitivities of ∼1 ng/mL.
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Affiliation(s)
- Peihong Zhu
- Department of Chemistry and Biology, Ryerson University, 350 Victoria Street, Toronto, Ontario, Canada M5B 2K3
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41
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Abstract
Mass spectrometry is emerging as one of the most promising analytical techniques to examine simultaneously hundreds of analytes quickly, precisely, and accurately, using minute sample volumes. Currently, a major bottleneck in the verification phase of putative biomarkers is the lack of methods/reagents to quantify low levels of analytes in biological fluids. A major objective is to establish a high-throughput multiple reaction monitoring (MRM) assay capable of quantifying low-abundance proteins or peptides in biological fluids (low μg/L range) using mass spectrometry. The experimental procedure we propose, called immuno-mass spectrometry, consists of immuno-capturing analytes of interest from relevant biological fluids in 96-well microtiter plates and performing in-well tryptic digestion, with subsequent MRM of digested peptides on a triple quadrupole mass spectrometer. With such a strategy, limits of detection of 0.1-1 μg/L proteins in serum with a coefficient of variation of <20% can be obtained. This methodology could be adapted quickly and easily to potential candidates of interest, thus providing a much needed technology to bridge the gap between discovery and validation platforms.
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42
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Yuri M, Hiramoto M, Naito M, Matsumoto M, Matsumoto SI, Morita S, Mori K, Yokota H, Teramura T. Identification and relative quantitation of an orphan G-protein coupled receptor SREB2 (GPR85) protein in tissue using a linear ion trap mass spectrometer. J Proteome Res 2011; 10:2658-63. [PMID: 21395347 DOI: 10.1021/pr101252p] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
SREB2 (GPR85) is an orphan G-protein coupled receptor (GPCR) whose function is unknown. We previously prepared a SREB2-overexpressing transgenic mouse for functional analysis but were unable to confirm SREB2 protein expression level by immunochemical or biochemical methods. In this article, we report mass spectrometric identification and relative quantitative analysis of SREB2 in the forebrains of transgenic and wild type mice using nanoliquid chromatography coupled with a linear ion-trap mass spectrometer. By analyzing Chinese hamster ovary (CHO) cells overexpressing the SREB2 gene, we identified a proteotypic SREB2 peptide, GPTPPTLLGIR. Using a stable isotope-labeled analog as an authentic peptide for protein identification and as an internal control for relative quantitation, SREB2 was directly identified from the membrane fraction of forebrains from wild type and SREB2 transgenic mice. SREB2 protein expression level in the transgenic mouse was estimated to be 3-fold higher than that in the wild type littermate.
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Affiliation(s)
- Masatoshi Yuri
- Astellas Pharma Inc., 21 Miyukigaoka, Tsukuba, Ibaraki 305-8585, Japan
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43
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McGrath SC, Schieltz DM, McWilliams LG, Pirkle JL, Barr JR. Detection and Quantification of Ricin in Beverages Using Isotope Dilution Tandem Mass Spectrometry. Anal Chem 2011; 83:2897-905. [DOI: 10.1021/ac102571f] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Sara C. McGrath
- Division of Laboratory Sciences, National Center for Environmental Health, Centers for Disease Control and Prevention, 4770 Buford Highway, Atlanta, Georgia 30341, United States
| | - David M. Schieltz
- Division of Laboratory Sciences, National Center for Environmental Health, Centers for Disease Control and Prevention, 4770 Buford Highway, Atlanta, Georgia 30341, United States
| | - Lisa G. McWilliams
- Battelle (on Contract with the Division of Laboratory Sciences), 4770 Buford Highway, Atlanta, Georgia 30341, United States
| | - James L. Pirkle
- Division of Laboratory Sciences, National Center for Environmental Health, Centers for Disease Control and Prevention, 4770 Buford Highway, Atlanta, Georgia 30341, United States
| | - John R. Barr
- Division of Laboratory Sciences, National Center for Environmental Health, Centers for Disease Control and Prevention, 4770 Buford Highway, Atlanta, Georgia 30341, United States
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44
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Prakash A, Rezai T, Krastins B, Sarracino D, Athanas M, Russo P, Ross MM, Zhang H, Tian Y, Kulasingam V, Drabovich AP, Smith C, Batruch I, Liotta L, Petricoin E, Diamandis EP, Chan DW, Lopez MF. Platform for establishing interlaboratory reproducibility of selected reaction monitoring-based mass spectrometry peptide assays. J Proteome Res 2010; 9:6678-88. [PMID: 20945832 DOI: 10.1021/pr100821m] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Mass spectrometry (MS) is an attractive alternative to quantification of proteins by immunoassays, particularly for protein biomarkers of clinical relevance. Reliable quantification requires that the MS-based assays are robust, selective, and reproducible. Thus, the development of standardized protocols is essential to introduce MS into clinical research laboratories. The aim of this study was to establish a complete workflow for assessing the transferability and reproducibility of selected reaction monitoring (SRM) assays between clinical research laboratories. Four independent laboratories in North America, using identical triple-quadrupole mass spectrometers (Quantum Ultra, Thermo), were provided with standard protocols and instrumentation settings to analyze unknown samples and internal standards in a digested plasma matrix to quantify 51 peptides from 39 human proteins using a multiplexed SRM assay. The interlaboratory coefficient of variation (CV) was less than 10% for 25 of 39 peptides quantified (12 peptides were not quantified based upon hydrophobicity) and exhibited CVs less than 20% for the remaining peptides. In this report, we demonstrate that previously developed research platforms for SRM assays can be improved and optimized for deployment in clinical research environments.
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Affiliation(s)
- A Prakash
- Thermo Fisher Scientific, Biomarker research in Mass Spectrometry, Cambridge, Massachusettes, United States
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45
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Chi-square comparison of tryptic peptide-to-protein distributions of tandem mass spectrometry from blood with those of random expectation. Anal Biochem 2010; 409:189-94. [PMID: 20977879 DOI: 10.1016/j.ab.2010.10.027] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2010] [Revised: 09/19/2010] [Accepted: 10/18/2010] [Indexed: 11/23/2022]
Abstract
Proteomics uses tandem mass spectrometers and correlation algorithms to match peptides and their fragment spectra to amino acid sequences. The replication of multiple liquid chromatography experiments with electrospray ionization of peptides and tandem mass spectrometry (LC-ESI-MS/MS) produces large sets of MS/MS spectra. There is a need to assess the quality of large sets of experimental results by statistical comparison with that of random expectation. Classical frequency-based statistics such as goodness-of-fit tests for peptide-to-protein distributions could be used to calculate the probability that an entire set of experimental results has arisen by random chance. The frequency distributions of authentic MS/MS spectra from human blood were compared with those of false positive MS/MS spectra generated by a computer, or instrument noise, using the chi-square test. Here the mechanics of the chi-square test to compare the results in toto from a set of LC-ESI-MS/MS experiments with those of random expectation is detailed. The chi-square analysis of authentic spectra demonstrates unambiguously that the analysis of blood proteins separated by partition chromatography prior to tryptic digestions has a low probability that the cumulative peptide-to-protein distribution is the same as that of random or noise false positive spectra.
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46
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Hewel JA, Liu J, Onishi K, Fong V, Chandran S, Olsen JB, Pogoutse O, Schutkowski M, Wenschuh H, Winkler DFH, Eckler L, Zandstra PW, Emili A. Synthetic peptide arrays for pathway-level protein monitoring by liquid chromatography-tandem mass spectrometry. Mol Cell Proteomics 2010; 9:2460-73. [PMID: 20467045 DOI: 10.1074/mcp.m900456-mcp200] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Effective methods to detect and quantify functionally linked regulatory proteins in complex biological samples are essential for investigating mammalian signaling pathways. Traditional immunoassays depend on proprietary reagents that are difficult to generate and multiplex, whereas global proteomic profiling can be tedious and can miss low abundance proteins. Here, we report a target-driven liquid chromatography-tandem mass spectrometry (LC-MS/MS) strategy for selectively examining the levels of multiple low abundance components of signaling pathways which are refractory to standard shotgun screening procedures and hence appear limited in current MS/MS repositories. Our stepwise approach consists of: (i) synthesizing microscale peptide arrays, including heavy isotope-labeled internal standards, for use as high quality references to (ii) build empirically validated high density LC-MS/MS detection assays with a retention time scheduling system that can be used to (iii) identify and quantify endogenous low abundance protein targets in complex biological mixtures with high accuracy by correlation to a spectral database using new software tools. The method offers a flexible, rapid, and cost-effective means for routine proteomic exploration of biological systems including "label-free" quantification, while minimizing spurious interferences. As proof-of-concept, we have examined the abundance of transcription factors and protein kinases mediating pluripotency and self-renewal in embryonic stem cell populations.
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Affiliation(s)
- Johannes A Hewel
- Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, Canada
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47
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Proteomics in clinical chemistry: will it be long? Trends Biotechnol 2010; 28:225-9. [DOI: 10.1016/j.tibtech.2010.02.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2009] [Revised: 02/11/2010] [Accepted: 02/23/2010] [Indexed: 12/11/2022]
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Ban K, Kim KH, Cho CK, Sauvé M, Diamandis EP, Backx PH, Drucker DJ, Husain M. Glucagon-like peptide (GLP)-1(9-36)amide-mediated cytoprotection is blocked by exendin(9-39) yet does not require the known GLP-1 receptor. Endocrinology 2010; 151:1520-31. [PMID: 20172966 DOI: 10.1210/en.2009-1197] [Citation(s) in RCA: 174] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The widely expressed dipeptidyl peptidase-4 enzyme rapidly cleaves the gut hormone glucagon-like peptide-1 [GLP-1(7-36)amide] at the N terminus to generate GLP-1(9-36)amide. Both intact GLP-1(7-36)amide and GLP-1(9-36)amide exert cardioprotective actions in rodent hearts; however, the mechanisms underlying the actions of GLP-1(9-36)amide remain poorly understood. We used mass spectrometry of coronary effluents to demonstrate that isolated mouse hearts rapidly convert infused GLP-1(7-36)amide to GLP-1(9-36)amide. After ischemia-reperfusion (I/R) injury of isolated mouse hearts, administration of GLP-1(9-36)amide or exendin-4 improved functional recovery and reduced infarct size. The direct actions of these peptides were studied in cultured neonatal mouse cardiomyocytes. Both GLP-1(9-36)amide and exendin-4 increased levels of cAMP and phosphorylation of ERK1/2 and the phosphoinositide 3-kinase target protein kinase B/Akt. In I/R injury models in vitro, both peptides improved mouse cardiomyocyte viability and reduced lactate dehydrogenase release and caspase-3 activation. These effects were attenuated by inhibitors of ERK1/2 and phosphoinositide 3-kinase. Unexpectedly, the cardioprotective actions of GLP-1(9-36)amide were blocked by exendin(9-39) yet preserved in Glp1r(-/-) cardiomyocytes. Furthermore, GLP-1(9-36)amide, but not exendin-4, improved the survival of human aortic endothelial cells undergoing I/R injury, actions sensitive to the nitric oxide synthase inhibitor, N(G)-nitro-l-arginine methyl ester (L-NAME). In summary, our findings demonstrate separate actions for GLP-1(9-36)amide vs. the GLP-1R agonist exendin-4 and reveal the existence of a GLP-1(9-36)amide-responsive, exendin(9-39)-sensitive, cardioprotective signaling pathway distinct from that associated with the classical GLP-1 receptor.
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Affiliation(s)
- Kiwon Ban
- TMDT 3-904, 200 Elizabeth Street, Toronto, Ontario, Canada M5G 2C4
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49
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Bowden P, Pendrak V, Zhu P, Marshall JG. Meta sequence analysis of human blood peptides and their parent proteins. J Proteomics 2010; 73:1163-75. [PMID: 20170764 DOI: 10.1016/j.jprot.2010.02.007] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2009] [Revised: 01/23/2010] [Accepted: 02/09/2010] [Indexed: 11/19/2022]
Abstract
Sequence analysis of the blood peptides and their qualities will be key to understanding the mechanisms that contribute to error in LC-ESI-MS/MS. Analysis of peptides and their proteins at the level of sequences is much more direct and informative than the comparison of disparate accession numbers. A portable database of all blood peptide and protein sequences with descriptor fields and gene ontology terms might be useful for designing immunological or MRM assays from human blood. The results of twelve studies of human blood peptides and/or proteins identified by LC-MS/MS and correlated against a disparate array of genetic libraries were parsed and matched to proteins from the human ENSEMBL, SwissProt and RefSeq databases by SQL. The reported peptide and protein sequences were organized into an SQL database with full protein sequences and up to five unique peptides in order of prevalence along with the peptide count for each protein. Structured query language or BLAST was used to acquire descriptive information in current databases. Sampling error at the level of peptides is the largest source of disparity between groups. Chi Square analysis of peptide to protein distributions confirmed the significant agreement between groups on identified proteins.
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Affiliation(s)
- Peter Bowden
- Department of Chemistry and Biology, Ryerson University, Toronto, Canada
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Kumar V, Barnidge DR, Chen LS, Twentyman JM, Cradic KW, Grebe SK, Singh RJ. Quantification of Serum 1–84 Parathyroid Hormone in Patients with Hyperparathyroidism by Immunocapture In Situ Digestion Liquid Chromatography–Tandem Mass Spectrometry. Clin Chem 2010; 56:306-13. [DOI: 10.1373/clinchem.2009.134643] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Abstract
Background: Immunoassays specific for 1–84 parathyroid hormone (PTH) reportedly reflect the bioactivity of PTH; however, PTH immunoassays can be susceptible to interference by cross-reacting PTH fragments. In addition, these assays currently lack standardization. A methodology using immunocapture purification with liquid chromatography–tandem mass spectrometry (LC-MS/MS) detection, along with a stable isotope–labeled internal standard, may help address these issues.
Methods: We isolated 1–84 PTH from 1 mL serum by immunocapture on a 6.5-mm polystyrene bead. The immobilized PTH was digested in situ and analyzed by LC-MS/MS. For quantification, we used the selected reaction monitoring response from the N-terminal tryptic peptide 1–13 PTH (1SVSEIQLMHNLGK13).
Results: The linear range of the assay was 39.1–4560 ng/L, and the limit of detection and limit of quantification were 14.5 ng/L and 39.1 ng/L, respectively. The intraassay CVs ranged from 6% to 11%, and the interassay CVs ranged from 7% to 17%. Interference by PTH fragments 1–44 PTH, 7–84 PTH, 43–68 PTH, 52–84 PTH, 64–84 PTH, and PTH-related protein (PTHrP) was ≤1% to ≤0.001%. Method comparison of LC-MS/MS vs the Roche Cobas® immunoassay yielded Deming fit of LC-MS/MS = 1.01x immunoassay – 13.21. The mean bias by Bland–Altman plot was −9.4%.
Conclusions: In patients with hyperparathyroidism, the immunocapture in situ digestion LC-MS/MS method can provide accurate and precise PTH results compared with immunoassay.
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Affiliation(s)
- Vivek Kumar
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
| | - David R Barnidge
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
| | - Li-Sheng Chen
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
| | | | - Kendall W Cradic
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
| | - Stefan K Grebe
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
| | - Ravinder J Singh
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
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