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Nie S, O'Brien Johnson R, Livson Y, Greer T, Zheng X, Li N. Maximizing hydrophobic peptide recovery in proteomics and antibody development using a mass spectrometry compatible surfactant. Anal Biochem 2022; 658:114924. [PMID: 36162445 DOI: 10.1016/j.ab.2022.114924] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 09/18/2022] [Indexed: 11/01/2022]
Abstract
Peptide loss due to surface absorption can happen at any step in a protein analysis workflow and is sometimes especially deleterious for hydrophobic peptides. In this study, we found the LC-MS compatible surfactant, n-Dodecyl-β-D-maltoside (DDM), can maximize hydrophobic peptide recovery in various samples including single cell digests, mAb clinical PK samples, and mAb peptide mapping samples. In HeLa single cell proteomics analysis, more than half of all unique peptides identified were found only in DDM prepared samples, most of which had significantly higher hydrophobicities compared to peptides in control samples. In clinical PK studies, DDM enhanced hydrophobic complementarity-determining region (CDR) peptide signals significantly. The fold change of CDR peptides' intensity enhancement in DDM added samples compared to controls correlate with peptide retention time and hydrophobicity, providing guidance for surrogate peptide selection and peptide standard handling in PK studies. For peptide mapping analysis of mAbs, DDM can improve hydrophobic peptide signal and solution stability over 48 h in an autosampler at 4 °C, which can aid method qualification and transfer during drug development. Lastly, maximizing hydrophobic peptide recovery from samples dried in vacuo was achieved by DDM reconstitution, which provided higher signal for later eluting peaks and higher proteome coverage overall.
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Affiliation(s)
- Song Nie
- Analytical Chemistry, Regeneron Pharmaceuticals Inc., 777 Old Saw Mill River Road, Tarrytown, NY, 10591-6707, United States.
| | - Reid O'Brien Johnson
- Analytical Chemistry, Regeneron Pharmaceuticals Inc., 777 Old Saw Mill River Road, Tarrytown, NY, 10591-6707, United States
| | - Yuliya Livson
- Analytical Chemistry, Regeneron Pharmaceuticals Inc., 777 Old Saw Mill River Road, Tarrytown, NY, 10591-6707, United States
| | - Tyler Greer
- Analytical Chemistry, Regeneron Pharmaceuticals Inc., 777 Old Saw Mill River Road, Tarrytown, NY, 10591-6707, United States
| | - Xiaojing Zheng
- Analytical Chemistry, Regeneron Pharmaceuticals Inc., 777 Old Saw Mill River Road, Tarrytown, NY, 10591-6707, United States.
| | - Ning Li
- Analytical Chemistry, Regeneron Pharmaceuticals Inc., 777 Old Saw Mill River Road, Tarrytown, NY, 10591-6707, United States
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2
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Mendoza-Porras O, Pires PRL, Goswami H, Meirelles FV, Colgrave ML, Wijffels G. Cytokines in the grass, a lesson learnt: Measuring cytokines in plasma using multiple reaction monitoring mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2020; 34:e8723. [PMID: 31922636 DOI: 10.1002/rcm.8723] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 01/08/2020] [Accepted: 01/09/2020] [Indexed: 06/10/2023]
Abstract
RATIONALE Cytokines are cell regulatory molecules of high importance as indicators for homeostasis and pathology in many species. The current method to measure cytokines in body fluids is reagent dependent, requiring highly specific paired antibodies. METHODS A liquid chromatography/multiple reaction monitoring mass spectrometry (LC/MRM-MS)-based approach was developed to simultaneously establish the limits of detection (LODs) and quantification (LOQs) for recombinant cytokines IL-1β, IL-6, IFNγ and TNFα as pure standards and in bovine sera. All experimental LC/MRM-MS data are available at CSIRO Data Access Portal repository under identifier doi.org/10.25919/5de8a0232a862. RESULTS The present method enabled LODs and LOQs as low as 1.05 and 1.12 fmol/μL in the experiment comprised of pure standards. Comparable results were obtained in the experiment where digested cytokines were mixed with pre-digested sera proteins. The intrinsic matrix effects were evident when intact cytokines were co-digested within undiluted and undigested sera decreasing the ability to detect and quantify cytokines by 10,000-fold compared with pure standards and pre-digested sera. CONCLUSIONS The developed LC/MRM-MS method provided insights into the difficulties in detecting the target peptides when embedded in complex matrices. Nonetheless, the method may potentially be readily applied in biomarker-focused research interrogating fluids of lesser complexity such as synovial fluid, cerebrospinal fluid and tissue culture media.
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Affiliation(s)
- Omar Mendoza-Porras
- CSIRO Agriculture and Food, 306 Carmody Rd, St Lucia, Queensland, 4067, Australia
| | - Pedro R L Pires
- CSIRO Agriculture and Food, 306 Carmody Rd, St Lucia, Queensland, 4067, Australia
- University of São Paulo, Av Duque de Caxais Morte 225, Jardim Elite, São Paulo, Brazil
| | - Hareshwar Goswami
- CSIRO Agriculture and Food, 306 Carmody Rd, St Lucia, Queensland, 4067, Australia
| | - Flavio V Meirelles
- University of São Paulo, Av Duque de Caxais Morte 225, Jardim Elite, São Paulo, Brazil
| | - Michelle L Colgrave
- CSIRO Agriculture and Food, 306 Carmody Rd, St Lucia, Queensland, 4067, Australia
| | - Gene Wijffels
- CSIRO Agriculture and Food, 306 Carmody Rd, St Lucia, Queensland, 4067, Australia
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Hata K, Izumi Y, Hara T, Matsumoto M, Bamba T. In-Line Sample Processing System with an Immobilized Trypsin-Packed Fused-Silica Capillary Tube for the Proteomic Analysis of a Small Number of Mammalian Cells. Anal Chem 2020; 92:2997-3005. [PMID: 31961143 DOI: 10.1021/acs.analchem.9b03993] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Omics analysis at single-cell resolution has helped to demonstrate the shaping of cellular heterogeneity on the basis of the expression of various molecules. However, in-depth proteomic analysis of low-quantity samples has remained challenging because of difficulties associated with the measurement of large numbers of proteins by shotgun proteomics using nanoflow liquid chromatography tandem mass spectrometry (nano-LC/MS/MS). To meet such a demand, we developed a method called in-line sample preparation for efficient cellular proteomics (ISPEC) in which cells were captured, directly lysed, and digested with immobilized trypsin within fused-silica capillaries. ISPEC minimized sample loss during the sample preparation processes with a relatively small number of mammalian cells (<1000 cells) and improved the stability and efficiency of digestion by immobilized trypsin, compared to a conventional preparation method. Using our optimized ISPEC method with nano-LC/MS/MS analysis, we identified 1351, 351, and 60 proteins from 100 cells, 10 cells, and single cells, respectively. The linear response of the signal intensity of each peptide to the introduced cell number indicates the quantitative recovery of the proteome from a very small number of cells. Thus, our ISPEC strategy facilitates quantitative proteomic analysis of small cell populations.
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Affiliation(s)
| | | | | | - Masaki Matsumoto
- Department of Omics and Systems Biology, Graduate School of Medical and Dental Sciences , Niigata University , 1-757, Asahimachi-dori , Niigata , 951-8510 , Japan
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4
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Wu R, Xing S, Badv M, Didar TF, Lu Y. Step-Wise Assessment and Optimization of Sample Handling Recovery Yield for Nanoproteomic Analysis of 1000 Mammalian Cells. Anal Chem 2019; 91:10395-10400. [DOI: 10.1021/acs.analchem.9b02092] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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5
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Ranade AV, Mukhtarov R, An Liu KJ, Behrner MA, Sun B. Characterization of Sample Loss Caused by Competitive Adsorption of Proteins in Vials Using Sodium Dodecyl Sulfate-Polyacrylamide Gel Electrophoresis. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2019; 35:4224-4232. [PMID: 30813715 DOI: 10.1021/acs.langmuir.8b04281] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Sample loss caused by competitive protein adsorption on solid surfaces from complex samples remains to be a major hurdle in sensitive analyses of proteins. No label-free techniques can easily quantify individual proteins adsorbed on irregular surfaces of Eppendorf vials or Falcon tubes, which are commonly used to contain complex biological samples. Multiplexed characterization of such adsorption by different proteins is technically challenging. Herein, we developed a direct protein analysis based on sodium dodecyl sulfate-polyacrylamide gel electrophoresis for the characterization of sample loss occurred on the curved surface with limited area. Using this simple and easily accessible method, we discovered the effect of ethylenediaminetetraacetic acid on surface adsorption of different milk proteins, specifically an augmented loss of milk proteins in low-binding sample vials. In this study, we also identified severe biases of silver staining and established proteomics-based mapping of protein distribution in biological samples for absolute quantification of competitive protein adsorption on irregular surfaces.
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Bittremieux W, Tabb DL, Impens F, Staes A, Timmerman E, Martens L, Laukens K. Quality control in mass spectrometry-based proteomics. MASS SPECTROMETRY REVIEWS 2018; 37:697-711. [PMID: 28802010 DOI: 10.1002/mas.21544] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2017] [Revised: 07/24/2017] [Accepted: 07/24/2017] [Indexed: 05/21/2023]
Abstract
Mass spectrometry is a highly complex analytical technique and mass spectrometry-based proteomics experiments can be subject to a large variability, which forms an obstacle to obtaining accurate and reproducible results. Therefore, a comprehensive and systematic approach to quality control is an essential requirement to inspire confidence in the generated results. A typical mass spectrometry experiment consists of multiple different phases including the sample preparation, liquid chromatography, mass spectrometry, and bioinformatics stages. We review potential sources of variability that can impact the results of a mass spectrometry experiment occurring in all of these steps, and we discuss how to monitor and remedy the negative influences on the experimental results. Furthermore, we describe how specialized quality control samples of varying sample complexity can be incorporated into the experimental workflow and how they can be used to rigorously assess detailed aspects of the instrument performance.
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Affiliation(s)
- Wout Bittremieux
- Department of Mathematics and Computer Science, University of Antwerp, Antwerp, Belgium
- Biomedical Informatics Research Center Antwerp (Biomina), University of Antwerp/Antwerp University Hospital, Edegem, Belgium
| | - David L Tabb
- Division of Molecular Biology and Human Genetics, Stellenbosch University Faculty of Medicine and Health Sciences, Tygerberg Hospital, Cape Town, South Africa
| | - Francis Impens
- VIB Proteomics Core, Ghent, Belgium
- VIB-UGent Center for Medical Biotechnology, Ghent, Belgium
- Faculty of Medicine and Health Sciences, Department of Biochemistry, Ghent University, Ghent, Belgium
| | - An Staes
- VIB Proteomics Core, Ghent, Belgium
- VIB-UGent Center for Medical Biotechnology, Ghent, Belgium
- Faculty of Medicine and Health Sciences, Department of Biochemistry, Ghent University, Ghent, Belgium
| | - Evy Timmerman
- VIB Proteomics Core, Ghent, Belgium
- VIB-UGent Center for Medical Biotechnology, Ghent, Belgium
- Faculty of Medicine and Health Sciences, Department of Biochemistry, Ghent University, Ghent, Belgium
| | - Lennart Martens
- VIB-UGent Center for Medical Biotechnology, Ghent, Belgium
- Faculty of Medicine and Health Sciences, Department of Biochemistry, Ghent University, Ghent, Belgium
- Bioinformatics Institute Ghent, Ghent University, Zwijnaarde, Belgium
| | - Kris Laukens
- Department of Mathematics and Computer Science, University of Antwerp, Antwerp, Belgium
- Biomedical Informatics Research Center Antwerp (Biomina), University of Antwerp/Antwerp University Hospital, Edegem, Belgium
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7
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Lee MCG, Sun B. Quantitation of nonspecific protein adsorption at solid–liquid interfaces for single-cell proteomics. CAN J CHEM 2018. [DOI: 10.1139/cjc-2017-0304] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Protein nonspecific adsorption that occurred at the solid–liquid interface has been subjected to intense physical and chemical characterizations due to its crucial role in a wide range of applications, including food and pharmaceutical industries, medical implants, biosensing, and so on. Protein-adsorption caused sample loss has largely hindered the studies of single-cell proteomics; the prevention of such loss requires the understanding of protein–surface adsorption at the proteome level, in which the competitive adsorption of thousands and millions of proteins with vast dynamic range occurs. To this end, we feel the necessity to review current methodologies on their potentials to characterize — more specifically to quantify — the proteome-wide adsorption. We hope this effort can help advancing single-cell proteomics and trace proteomics.
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Affiliation(s)
| | - Bingyun Sun
- Department of Chemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
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Clair G, Piehowski PD, Nicola T, Kitzmiller JA, Huang EL, Zink EM, Sontag RL, Orton DJ, Moore RJ, Carson JP, Smith RD, Whitsett JA, Corley RA, Ambalavanan N, Ansong C. Spatially-Resolved Proteomics: Rapid Quantitative Analysis of Laser Capture Microdissected Alveolar Tissue Samples. Sci Rep 2016; 6:39223. [PMID: 28004771 PMCID: PMC5177886 DOI: 10.1038/srep39223] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Accepted: 11/16/2016] [Indexed: 01/12/2023] Open
Abstract
Laser capture microdissection (LCM)-enabled region-specific tissue analyses are critical to better understand complex multicellular processes. However, current proteomics workflows entail several manual sample preparation steps and are challenged by the microscopic mass-limited samples generated by LCM, impacting measurement robustness, quantification and throughput. Here, we coupled LCM with a proteomics workflow that provides fully automated analysis of proteomes from microdissected tissues. Benchmarking against the current state-of-the-art in ultrasensitive global proteomics (FASP workflow), our approach demonstrated significant improvements in quantification (~2-fold lower variance) and throughput (>5 times faster). Using our approach we for the first time characterized, to a depth of >3,400 proteins, the ontogeny of protein changes during normal lung development in microdissected alveolar tissue containing only 4,000 cells. Our analysis revealed seven defined modules of coordinated transcription factor-signaling molecule expression patterns, suggesting a complex network of temporal regulatory control directs normal lung development with epigenetic regulation fine-tuning pre-natal developmental processes.
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Affiliation(s)
- Geremy Clair
- Biological Science Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Paul D Piehowski
- Biological Science Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Teodora Nicola
- Department of Pediatrics, University of Alabama at Birmingham, Birmingham, AL 35249, USA
| | - Joseph A Kitzmiller
- Division of Pulmonary Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Eric L Huang
- Biological Science Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Erika M Zink
- Biological Science Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Ryan L Sontag
- Biological Science Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Daniel J Orton
- Biological Science Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Ronald J Moore
- Biological Science Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - James P Carson
- Texas Advanced Computing Center, University of Texas at Austin, Austin, TX 78712, USA
| | - Richard D Smith
- Biological Science Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Jeffrey A Whitsett
- Division of Pulmonary Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Richard A Corley
- Biological Science Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | | | - Charles Ansong
- Biological Science Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
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9
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Hoofnagle AN, Whiteaker JR, Carr SA, Kuhn E, Liu T, Massoni SA, Thomas SN, Townsend RR, Zimmerman LJ, Boja E, Chen J, Crimmins DL, Davies SR, Gao Y, Hiltke TR, Ketchum KA, Kinsinger CR, Mesri M, Meyer MR, Qian WJ, Schoenherr RM, Scott MG, Shi T, Whiteley GR, Wrobel JA, Wu C, Ackermann BL, Aebersold R, Barnidge DR, Bunk DM, Clarke N, Fishman JB, Grant RP, Kusebauch U, Kushnir MM, Lowenthal MS, Moritz RL, Neubert H, Patterson SD, Rockwood AL, Rogers J, Singh RJ, Van Eyk JE, Wong SH, Zhang S, Chan DW, Chen X, Ellis MJ, Liebler DC, Rodland KD, Rodriguez H, Smith RD, Zhang Z, Zhang H, Paulovich AG. Recommendations for the Generation, Quantification, Storage, and Handling of Peptides Used for Mass Spectrometry-Based Assays. Clin Chem 2016; 62:48-69. [PMID: 26719571 DOI: 10.1373/clinchem.2015.250563] [Citation(s) in RCA: 154] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
BACKGROUND For many years, basic and clinical researchers have taken advantage of the analytical sensitivity and specificity afforded by mass spectrometry in the measurement of proteins. Clinical laboratories are now beginning to deploy these work flows as well. For assays that use proteolysis to generate peptides for protein quantification and characterization, synthetic stable isotope-labeled internal standard peptides are of central importance. No general recommendations are currently available surrounding the use of peptides in protein mass spectrometric assays. CONTENT The Clinical Proteomic Tumor Analysis Consortium of the National Cancer Institute has collaborated with clinical laboratorians, peptide manufacturers, metrologists, representatives of the pharmaceutical industry, and other professionals to develop a consensus set of recommendations for peptide procurement, characterization, storage, and handling, as well as approaches to the interpretation of the data generated by mass spectrometric protein assays. Additionally, the importance of carefully characterized reference materials-in particular, peptide standards for the improved concordance of amino acid analysis methods across the industry-is highlighted. The alignment of practices around the use of peptides and the transparency of sample preparation protocols should allow for the harmonization of peptide and protein quantification in research and clinical care.
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Affiliation(s)
| | | | | | | | - Tao Liu
- Pacific Northwest National Laboratory, Richland, WA
| | | | | | | | | | | | - Jing Chen
- Johns Hopkins University, Baltimore, MD
| | | | | | - Yuqian Gao
- Pacific Northwest National Laboratory, Richland, WA
| | | | | | | | | | | | - Wei-Jun Qian
- Pacific Northwest National Laboratory, Richland, WA
| | | | | | - Tujin Shi
- Pacific Northwest National Laboratory, Richland, WA
| | | | - John A Wrobel
- University of North Carolina School of Medicine, Chapel Hill, NC
| | - Chaochao Wu
- Pacific Northwest National Laboratory, Richland, WA
| | | | - Ruedi Aebersold
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | | | | | | | | | - Russ P Grant
- Laboratory Corporation of America Holdings, Inc., Burlington, NC
| | | | - Mark M Kushnir
- University of Utah and ARUP Laboratories, Salt Lake City, UT
| | | | | | | | | | - Alan L Rockwood
- University of Utah and ARUP Laboratories, Salt Lake City, UT
| | | | | | | | | | | | | | - Xian Chen
- University of North Carolina School of Medicine, Chapel Hill, NC
| | | | | | | | | | | | | | - Hui Zhang
- Johns Hopkins University, Baltimore, MD
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Adsorption of cationic peptides to solid surfaces of glass and plastic. PLoS One 2015; 10:e0122419. [PMID: 25932639 PMCID: PMC4416745 DOI: 10.1371/journal.pone.0122419] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2014] [Accepted: 02/20/2015] [Indexed: 01/12/2023] Open
Abstract
Cationic membrane-active peptides have been studied for years in the hope of developing them into novel types of therapeutics. In this article, we investigate an effect that might have significant experimental implications for investigators who wish to study these peptides, namely, that the peptides adsorb to solid surfaces of glass and plastic. Specifically, we use analytical HPLC to systematically quantify the adsorption of the three cationic membrane-active peptides mastoparan X, melittin, and magainin 2 to the walls of commonly used glass and plastic sample containers. Our results show that, at typical experimental peptide concentrations, 90% or more of the peptides might be lost from solution due to rapid adsorption to the walls of the sample containers. Thus, our results emphasize that investigators should always keep these adsorption effects in mind when designing and interpreting experiments on cationic membrane-active peptides. We conclude the article by discussing different strategies for reducing the experimental impact of these adsorption effects.
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Wohlgemuth I, Lenz C, Urlaub H. Studying macromolecular complex stoichiometries by peptide-based mass spectrometry. Proteomics 2015; 15:862-79. [PMID: 25546807 PMCID: PMC5024058 DOI: 10.1002/pmic.201400466] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Revised: 11/24/2014] [Accepted: 12/22/2014] [Indexed: 11/11/2022]
Abstract
A majority of cellular functions are carried out by macromolecular complexes. A host of biochemical and spectroscopic methods exists to characterize especially protein/protein complexes, however there has been a lack of a universal method to determine protein stoichiometries. Peptide‐based MS, especially as a complementary method to the MS analysis of intact protein complexes, has now been developed to a point where it can be employed to assay protein stoichiometries in a routine manner. While the experimental demands are still significant, peptide‐based MS has been successfully applied to analyze stoichiometries for a variety of protein complexes from very different biological backgrounds. In this review, we discuss the requirements especially for targeted MS acquisition strategies to be used in this context, with a special focus on the interconnected experimental aspects of sample preparation, protein digestion, and peptide stability. In addition, different strategies for the introduction of quantitative peptide standards and their suitability for different scenarios are compared.
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Affiliation(s)
- Ingo Wohlgemuth
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Goettingen, Germany
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12
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Cho HR, Park JS, Wood TD, Choi YS. Longitudinal Assessment of Peptide Recoveries from a Sample Solution in an Autosampler Vial for Proteomics. B KOREAN CHEM SOC 2015. [DOI: 10.1002/bkcs.10082] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Ha Ra Cho
- College of Pharmacy; Dankook University; Chungnam 330-714 South Korea
| | - Jun Seo Park
- College of Pharmacy; Dankook University; Chungnam 330-714 South Korea
| | - Troy D. Wood
- Department of Chemistry; State University of New York at Buffalo; Buffalo NY 14260-3000 USA
| | - Yong Seok Choi
- College of Pharmacy; Dankook University; Chungnam 330-714 South Korea
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13
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Improved sensitivity of the nano ultra-high performance liquid chromatography-tandem mass spectrometric analysis of low-concentrated neuropeptides by reducing aspecific adsorption and optimizing the injection solvent. J Chromatogr A 2014; 1360:217-28. [DOI: 10.1016/j.chroma.2014.07.086] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Revised: 07/15/2014] [Accepted: 07/27/2014] [Indexed: 11/18/2022]
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Maes K, Smolders I, Michotte Y, Van Eeckhaut A. Strategies to reduce aspecific adsorption of peptides and proteins in liquid chromatography-mass spectrometry based bioanalyses: an overview. J Chromatogr A 2014; 1358:1-13. [PMID: 25022477 DOI: 10.1016/j.chroma.2014.06.072] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2014] [Revised: 06/11/2014] [Accepted: 06/22/2014] [Indexed: 12/20/2022]
Abstract
In the drug-discovery setting, the development of new peptide and protein-based biopharmaceuticals attracts increased attention from the pharmaceutical industry and consequently demands the development of high-throughput LC-MS methods. Regulatory guidelines require bioanalytical methods to be validated not only in terms of linearity, sensitivity, accuracy, precision, selectivity and stability, but also in terms of carryover. Carryover results from the aspecific adsorption of analyte(s) to parts of the analytical system and thus introduces bias in both identification and quantification assays. Moreover, nonspecific binding occurs at the surface of materials used during sample preparation, such as pipette tips, sample tubes and LC-vials. Hence, linearity, sensitivity and repeatability of the analyses are negatively affected. Due to the great diversity in physicochemical properties of biomolecules, there is no general approach available to minimize adsorption phenomena. Therefore, we aim to present different strategies which can be generically applied to reduce nonspecific binding of peptides and proteins. In the first part of this review, a systematic approach is proposed to guide the reader through the different solvents which can be used to dissolve the analyte of interest. Indeed, proper solubilization is one of the most important factors for a successful analysis. In addition, alternative approaches are described to improve analyte recovery from the sample vial. The second part focuses on strategies to efficiently reduce adsorption at components of the autosampler, column and mass spectrometer. Thereby carryover is reduced while maintaining a sufficiently wide dynamic range of the assay.
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Affiliation(s)
- Katrien Maes
- Department of Pharmaceutical Chemistry and Drug Analysis, Center for Neurosciences (C4N), Vrije Universiteit Brussel, Laarbeeklaan 103, 1090 Brussels, Belgium
| | - Ilse Smolders
- Department of Pharmaceutical Chemistry and Drug Analysis, Center for Neurosciences (C4N), Vrije Universiteit Brussel, Laarbeeklaan 103, 1090 Brussels, Belgium
| | - Yvette Michotte
- Department of Pharmaceutical Chemistry and Drug Analysis, Center for Neurosciences (C4N), Vrije Universiteit Brussel, Laarbeeklaan 103, 1090 Brussels, Belgium
| | - Ann Van Eeckhaut
- Department of Pharmaceutical Chemistry and Drug Analysis, Center for Neurosciences (C4N), Vrije Universiteit Brussel, Laarbeeklaan 103, 1090 Brussels, Belgium.
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Zeng T, Wilson CJ, Mitch WA. Effect of chemical oxidation on the sorption tendency of dissolved organic matter to a model hydrophobic surface. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2014; 48:5118-5126. [PMID: 24697505 DOI: 10.1021/es405257b] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
The application of chemical oxidants may alter the sorption properties of dissolved organic matter (DOM), such as humic and fulvic acids, proteins, polysaccharides, and lipids, affecting their fate in water treatment processes, including attachment to other organic components, activated carbon, and membranes (e.g., organic fouling). Similar reactions with chlorine (HOCl) and bromine (HOBr) produced at inflammatory sites in vivo affect the fate of biomolecules (e.g., protein aggregation). In this study, quartz crystal microbalance with dissipation monitoring (QCM-D) was used to evaluate changes in the noncovalent interactions of proteins, polysaccharides, fatty acids, and humic and fulvic acids with a model hydrophobic surface as a function of increasing doses of HOCl, HOBr, and ozone (O3). All three oxidants enhanced the sorption tendency of proteins to the hydrophobic surface at low doses but reduced their sorption tendency at high doses. All three oxidants reduced the sorption tendency of polysaccharides and fatty acids to the hydrophobic surface. HOCl and HOBr increased the sorption tendency of humic and fulvic acids to the hydrophobic surface with maxima at moderate doses, while O3 decreased their sorption tendency. The behavior observed with two water samples was similar to that observed with humic and fulvic acids, pointing to the importance of these constituents. For chlorination, the highest sorption tendency to the hydrophobic surface was observed within the range of doses typically applied during water treatment. These results suggest that ozone pretreatment would minimize membrane fouling by DOM, while chlorine pretreatment would promote DOM removal by activated carbon.
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Affiliation(s)
- Teng Zeng
- Department of Chemical and Environmental Engineering, Yale University , 9 Hillhouse Avenue, New Haven, Connecticut 06520, United States
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Mateos J, Pintor-Iglesias A, Fernández-Puente P, García-Camba M, Ruiz-Romero C, Doménech N, Blanco FJ. Cryoconservation of peptide extracts from trypsin digestion of proteins for proteomic analysis in a hospital biobank facility. J Proteome Res 2014; 13:1930-7. [PMID: 24521361 DOI: 10.1021/pr401046u] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
We tested a semiautomated protocol for the proper storage and conservation in a hospital biobank of tryptic peptide extracts coming from samples with low and high protein complexity for subsequent mass spectrometry analysis. Low-complexity samples (serum albumin, serotransferrin. and alpha-S1-casein) were loaded in replicates in SDS-PAGE and subjected to standard in-gel trypsin digestion. For LC-MALDI-TOF/TOF analysis, purified β-galactosidase and human serum samples were in-solution digested following standard procedures and desalted with C18 stage-tips. In both cases, peptides extracts were aliquoted in individually 2D coded tubes, vacuum-dried, barcode-read, and stored in an automated -20 °C freezer in the Biobank facility. Samples were kept dried at -20 °C until the corresponding time-point of analysis, then reconstituted in the proper buffer and analyzed by either MALDI-TOF/TOF (peptide fingerprinting and MS/MS) or LC-MALDI-TOF/TOF following a highly reproducible pattern to ensure the reproducibility of the results. Protein identification was done with either Mascot or Protein Pilot as search engines using constant parameters. Over a period of 1 year we checked six different time points at days 0, 7, 30, 90, 180, and 365. We compared MS and MS/MS protein score, number of identified peptides, and coverage of the identified proteins. In the low complexity samples, the number of peptides detected gradually decreased over time, especially affecting the MS score. However, two of the three proteins - serum albumin and serotransferrin - were identified by both PMF and MS/MS at day 90. By day 180, only MS/MS identification in some replicates was possible. By LC-MS/MS, β-galactosidase and the most abundant serum proteins were identified with good scores at all time points even by day 365, with no detectable peptide loss or decrease in the fragmentation efficiency, although a progressive decrease in peptide intensity indicates that detection of low abundant proteins could not be optimal after very long periods of time. Our results encourage us to use the biobank facility in the future for long-term storage - up to 3 months - of dried peptide extracts.
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Affiliation(s)
- Jesús Mateos
- Rheumatology Division, Proteomics Unit-ProteoRed/ISCIII, INIBIC-Hospital Universitario A Coruña , As Xubias 84, 15006 A Coruña, Spain
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17
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Hioki Y, Kuyama H, Hamana C, Takeyama K, Tanaka K. An improved sample preparation method for the sensitive detection of peptides by MALDI-MS. JOURNAL OF MASS SPECTROMETRY : JMS 2013; 48:1217-1223. [PMID: 24259210 DOI: 10.1002/jms.3283] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2013] [Revised: 08/20/2013] [Accepted: 09/09/2013] [Indexed: 06/02/2023]
Abstract
We describe here an optimization study of the sample preparation conditions for sensitive detection of peptides by matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS). Among many factors in the conditions, we varied the percent acetonitrile in the peptide solution, the percent acetonitrile in the matrix solution and the α-cyano-4-hydroxycinnamic acid (CHCA) concentration in the matrix solution. CHCA was chosen because it is the most frequently used matrix for analyzing peptides. The well-established dried-droplet method was employed for sample deposition. The examined range of the concentration of CHCA was from 0.01 to 10 mg/ml, and the MeCN content of the solvent for matrix/analyte was 10% to 50%. The indicator for the detection sensitivity was the S/N ratio of the peaks of peptides used. Highly increased sensitivity (100- to 1000-fold) was observed for the optimal CHCA concentration of 0.1 mg/ml in 20% MeCN/0.1% aq. trifluoroacetic acid (TFA), as compared with the conventional concentration (10 mg/ml) in 50% MeCN/0.1% aq. TFA. For example, the limit of detection of human ACTH 18-39 was 10 amol/well for the optimal condition but 10 fmol/well for the conventional condition. The optimal condition (0.1 mg/ml CHCA in 20% MeCN/0.1% aq. TFA) was verified with five model peptides and provided significant improvement in sensitivity (by two to three orders of magnitude) compared with the conventional conditions. Optimizing the CHCA concentration and solvent composition significantly improved the detection sensitivity in the analysis of peptides by MALDI-MS.
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Affiliation(s)
- Yusaku Hioki
- Koichi Tanaka Laboratory of Advanced Science and Technology (KTLAST), Shimadzu Corporation, Nishinokyo-Kuwabaracho Nakagyo-ku, Kyoto, 604-8511, Japan
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18
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Stejskal K, Potěšil D, Zdráhal Z. Suppression of Peptide Sample Losses in Autosampler Vials. J Proteome Res 2013; 12:3057-62. [DOI: 10.1021/pr400183v] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Karel Stejskal
- Research
Group Proteomics, Central European Institute of Technology and ‡National Centre
for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech
Republic
| | - David Potěšil
- Research
Group Proteomics, Central European Institute of Technology and ‡National Centre
for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech
Republic
| | - Zbyněk Zdráhal
- Research
Group Proteomics, Central European Institute of Technology and ‡National Centre
for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech
Republic
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19
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Bark SJ, Wegrzyn J, Taupenot L, Ziegler M, O'Connor DT, Ma Q, Smoot M, Ideker T, Hook V. The protein architecture of human secretory vesicles reveals differential regulation of signaling molecule secretion by protein kinases. PLoS One 2012; 7:e41134. [PMID: 22916103 PMCID: PMC3420874 DOI: 10.1371/journal.pone.0041134] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2012] [Accepted: 06/17/2012] [Indexed: 12/25/2022] Open
Abstract
Secretory vesicles are required for release of chemical messengers to mediate intercellular signaling among human biological systems. It is necessary to define the organization of the protein architecture of the ‘human’ dense core secretory vesicles (DCSV) to understand mechanisms for secretion of signaling molecules essential for cellular regulatory processes. This study, therefore, conducted extensive quantitative proteomics and systems biology analyses of human DCSV purified from human pheochromocytoma. Over 600 human DCSV proteins were identified with quantitative evaluation of over 300 proteins, revealing that most proteins participate in producing peptide hormones and neurotransmitters, enzymes, and the secretory machinery. Systems biology analyses provided a model of interacting DCSV proteins, generating hypotheses for differential intracellular protein kinases A and C signaling pathways. Activation of cellular PKA and PKC pathways resulted in differential secretion of neuropeptides, catecholamines, and β-amyloid of Alzheimer's disease for mediating cell-cell communication. This is the first study to define a model of the protein architecture of human DCSV for human disease and health.
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Affiliation(s)
- Steven J. Bark
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California, United States of America
- * E-mail: (SJB) ; or (VH)
| | - Jill Wegrzyn
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California, United States of America
| | - Laurent Taupenot
- Department of Medicine, University of California San Diego, La Jolla, California, United States of America
| | - Michael Ziegler
- Department of Medicine, University of California San Diego, La Jolla, California, United States of America
| | - Daniel T. O'Connor
- Department of Medicine, University of California San Diego, La Jolla, California, United States of America
| | - Qi Ma
- Graduate Program in Bioinformatics and Systems Biology, University of California San Diego, La Jolla, California, United States of America
| | - Michael Smoot
- Department of Medicine, University of California San Diego, La Jolla, California, United States of America
| | - Trey Ideker
- Department of Medicine, University of California San Diego, La Jolla, California, United States of America
| | - Vivian Hook
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California, United States of America
- Departments of Neurosciences and Pharmacology, University of California San Diego, La Jolla, California, United States of America
- * E-mail: (SJB) ; or (VH)
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20
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The absolute quantification of endogenous levels of brain neuropeptides in vivo using LC-MS/MS. Bioanalysis 2011; 3:1271-85. [PMID: 21649502 DOI: 10.4155/bio.11.91] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Neuropeptides seem to play an important role when the CNS is challenged. In order to obtain better insights into the central peptidergic effects, it is essential to monitor their concentration in the brain. Quantification of neuropeptides in dialysates is challenging due to their low extracellular concentrations (low pM range), their low microdialysis efficiencies, the need for acceptable temporal resolution, the small sample volumes, the complexity of the matrix and the tendency of peptides to stick to glass and polymeric materials. The quantification of neuropeptides in dialysates therefore necessitates the use of very sensitive nano-LC-MS/MS methods. A number of LC-MS/MS and microdialysis parameters need to be optimized to achieve maximal sensitivity. The optimized and validated methods can be used to investigate the in vivo neuropeptide release during pathological conditions, in this way initiating new and immense challenges for the development of new drugs.
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21
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Dixit CK, Vashist SK, MacCraith BD, O'Kennedy R. Evaluation of apparent non-specific protein loss due to adsorption on sample tube surfaces and/or altered immunogenicity. Analyst 2011; 136:1406-11. [DOI: 10.1039/c0an00689k] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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22
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Paulo JA, Lee LS, Wu B, Repas K, Banks PA, Conwell DL, Steen H. Optimized sample preparation of endoscopic collected pancreatic fluid for SDS-PAGE analysis. Electrophoresis 2010; 31:2377-87. [PMID: 20589857 DOI: 10.1002/elps.200900762] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The standardization of methods for human body fluid protein isolation is a critical initial step for proteomic analyses aimed to discover clinically relevant biomarkers. Several caveats have hindered pancreatic fluid proteomics, including the heterogeneity of samples and protein degradation. We aim to optimize sample handling of pancreatic fluid that has been collected using a safe and effective endoscopic collection method (endoscopic pancreatic function test). Using SDS-PAGE protein profiling, we investigate (i) precipitation techniques to maximize protein extraction, (ii) auto-digestion of pancreatic fluid following prolonged exposure to a range of temperatures, (iii) effects of multiple freeze-thaw cycles on protein stability, and (iv) the utility of protease inhibitors. Our experiments revealed that TCA precipitation resulted in the most efficient extraction of protein from pancreatic fluid of the eight methods we investigated. In addition, our data reveal that although auto-digestion of proteins is prevalent at 23 and 37 degrees C, incubation on ice significantly slows such degradation. Similarly, when the sample is maintained on ice, proteolysis is minimal during multiple freeze-thaw cycles. We have also determined the addition of protease inhibitors to be assay-dependent. Our optimized sample preparation strategy can be applied to future proteomic analyses of pancreatic fluid.
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Affiliation(s)
- Joao A Paulo
- Department of Pathology, Children's Hospital Boston and Harvard Medical School, Boston, MA 02115, USA
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23
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Comparison between a linear ion trap and a triple quadruple MS in the sensitive detection of large peptides at femtomole amounts on column. J Sep Sci 2010; 33:2478-88. [DOI: 10.1002/jssc.201000157] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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24
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Lortie M, Bark S, Blantz R, Hook V. Detecting low-abundance vasoactive peptides in plasma: progress toward absolute quantitation using nano liquid chromatography-mass spectrometry. Anal Biochem 2009; 394:164-70. [PMID: 19615967 PMCID: PMC2745394 DOI: 10.1016/j.ab.2009.07.021] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2009] [Revised: 07/10/2009] [Accepted: 07/14/2009] [Indexed: 11/19/2022]
Abstract
Profiling changes in the concentration of functionally related peptide hormones is critical to understanding the etiology of many diseases and therapies. We present novel data using nano liquid chromatography-mass spectrometry (LC-MS) to simultaneously measure a select group of vasoactive peptides (angiotensin, bradykinin, and related hormones) in 50-microl plasma samples, enabling repeated sampling in rodent models. By chromatographically resolving target peptides and using multiple reaction monitoring to enhance MS sensitivity, linear responses down to 10(-17) mol were achieved. Purification of plasma peptides by either methanol precipitation or off-line high-performance liquid chromatography (HPLC) fractionation enabled the detection of endogenous peptides and revealed approaches for enhancing recovery. As proof of principle, seven vasoactive peptides were profiled before, during, and after acute angiotensin-converting enzyme (ACE) inhibition in an anesthetized rat. Of note was an apparent 10-fold increase in vasodilatory bradykinin that reversed after drug infusion but relatively minor changes in angiotensin II levels. Targeted MS analysis used to profile functionally related peptides or other analytes will greatly enhance our ability to define the sequence of events regulating complex and dynamic physiological processes.
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Affiliation(s)
- Mark Lortie
- Division of Nephrology and Hypertension, VA San Diego Healthcare System, Biomarker and Diagnotics Discovery Center, Department of Pathology, UCSD School of Medicine, San Diego, CA 92093-0612, USA.
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25
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Cantone JL, Xu-Lin A, Toyn JH, Drexler DM. Application of quantitative LC–MS surrogate peptide methodology in the analysis of the amyloid beta peptide (Aβ) biosynthetic intermediate protein APP–βCTF. J Neurosci Methods 2009; 180:255-60. [DOI: 10.1016/j.jneumeth.2009.03.018] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2008] [Revised: 03/09/2009] [Accepted: 03/21/2009] [Indexed: 10/20/2022]
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26
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Kraut A, Marcellin M, Adrait A, Kuhn L, Louwagie M, Kieffer-Jaquinod S, Lebert D, Masselon CD, Dupuis A, Bruley C, Jaquinod M, Garin J, Gallagher-Gambarelli M. Peptide Storage: Are You Getting the Best Return on Your Investment? Defining Optimal Storage Conditions for Proteomics Samples. J Proteome Res 2009; 8:3778-85. [DOI: 10.1021/pr900095u] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Alexandra Kraut
- CEA, DSV, iRTSV, Laboratoire d’Etude de la Dynamique des Protéomes, Grenoble, F-38054, France, INSERM, U880, Grenoble, F-38054, France, and Université Joseph Fourier, Grenoble, F-38054, France
| | - Marlène Marcellin
- CEA, DSV, iRTSV, Laboratoire d’Etude de la Dynamique des Protéomes, Grenoble, F-38054, France, INSERM, U880, Grenoble, F-38054, France, and Université Joseph Fourier, Grenoble, F-38054, France
| | - Annie Adrait
- CEA, DSV, iRTSV, Laboratoire d’Etude de la Dynamique des Protéomes, Grenoble, F-38054, France, INSERM, U880, Grenoble, F-38054, France, and Université Joseph Fourier, Grenoble, F-38054, France
| | - Lauriane Kuhn
- CEA, DSV, iRTSV, Laboratoire d’Etude de la Dynamique des Protéomes, Grenoble, F-38054, France, INSERM, U880, Grenoble, F-38054, France, and Université Joseph Fourier, Grenoble, F-38054, France
| | - Mathilde Louwagie
- CEA, DSV, iRTSV, Laboratoire d’Etude de la Dynamique des Protéomes, Grenoble, F-38054, France, INSERM, U880, Grenoble, F-38054, France, and Université Joseph Fourier, Grenoble, F-38054, France
| | - Sylvie Kieffer-Jaquinod
- CEA, DSV, iRTSV, Laboratoire d’Etude de la Dynamique des Protéomes, Grenoble, F-38054, France, INSERM, U880, Grenoble, F-38054, France, and Université Joseph Fourier, Grenoble, F-38054, France
| | - Dorothée Lebert
- CEA, DSV, iRTSV, Laboratoire d’Etude de la Dynamique des Protéomes, Grenoble, F-38054, France, INSERM, U880, Grenoble, F-38054, France, and Université Joseph Fourier, Grenoble, F-38054, France
| | - Christophe D. Masselon
- CEA, DSV, iRTSV, Laboratoire d’Etude de la Dynamique des Protéomes, Grenoble, F-38054, France, INSERM, U880, Grenoble, F-38054, France, and Université Joseph Fourier, Grenoble, F-38054, France
| | - Alain Dupuis
- CEA, DSV, iRTSV, Laboratoire d’Etude de la Dynamique des Protéomes, Grenoble, F-38054, France, INSERM, U880, Grenoble, F-38054, France, and Université Joseph Fourier, Grenoble, F-38054, France
| | - Christophe Bruley
- CEA, DSV, iRTSV, Laboratoire d’Etude de la Dynamique des Protéomes, Grenoble, F-38054, France, INSERM, U880, Grenoble, F-38054, France, and Université Joseph Fourier, Grenoble, F-38054, France
| | - Michel Jaquinod
- CEA, DSV, iRTSV, Laboratoire d’Etude de la Dynamique des Protéomes, Grenoble, F-38054, France, INSERM, U880, Grenoble, F-38054, France, and Université Joseph Fourier, Grenoble, F-38054, France
| | - Jérôme Garin
- CEA, DSV, iRTSV, Laboratoire d’Etude de la Dynamique des Protéomes, Grenoble, F-38054, France, INSERM, U880, Grenoble, F-38054, France, and Université Joseph Fourier, Grenoble, F-38054, France
| | - Maighread Gallagher-Gambarelli
- CEA, DSV, iRTSV, Laboratoire d’Etude de la Dynamique des Protéomes, Grenoble, F-38054, France, INSERM, U880, Grenoble, F-38054, France, and Université Joseph Fourier, Grenoble, F-38054, France
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27
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Pezeshki A, Vergote V, Van Dorpe S, Baert B, Burvenich C, Popkov A, De Spiegeleer B. Adsorption of peptides at the sample drying step: Influence of solvent evaporation technique, vial material and solution additive. J Pharm Biomed Anal 2009; 49:607-12. [DOI: 10.1016/j.jpba.2008.12.003] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2008] [Revised: 12/02/2008] [Accepted: 12/03/2008] [Indexed: 10/21/2022]
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28
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Optimizing the performance of tin dioxide microspheres for phosphopeptide enrichment. Anal Chim Acta 2009; 638:51-7. [DOI: 10.1016/j.aca.2009.01.063] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2008] [Revised: 01/29/2009] [Accepted: 01/30/2009] [Indexed: 01/10/2023]
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29
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Cavaliere C, Cucci F, Guarino C, Gubbiotti R, Samperi R, Laganà A. Absolute quantification of cardiac troponin T by means of liquid chromatography/triple quadrupole tandem mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2008; 22:1159-1167. [PMID: 18338372 DOI: 10.1002/rcm.3495] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
A liquid chromatography/tandem mass spectrometric method for absolute quantification of cardiac troponin T (cTnT) in mouse heart tissue is presented. Even in such a complex biological sample, the multiple reaction monitoring acquisition mode allowed the selective and sensitive determination of a specific peptide, obtained by cTnT enzymatic digestion. The concentration of this cTnT-specific peptide was considered as a representation of the concentration of its parent protein. Quantification was carried out by means of the matrix-matched calibration curve, constructed by adding the synthetic standard of the target peptide and another synthetic structurally analogous peptide as internal standard. Method identification limit and method quantification limit were estimated as 60 and 110 ng of cTnT per mg of total extracted proteins, respectively. The developed label-free approach has been applied for the absolute quantitation of cTnT because of its diagnostic and prognostic value as cardiac disease marker. However, the method could be of general application, since it requires only the synthesis of two suitable peptides, a protein tryptic cleavage product and an internal standard.
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Affiliation(s)
- Chiara Cavaliere
- Department of Chemistry, Sapienza University of Rome, Piazzale Aldo Moro 5, Rome, Italy
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