1
|
Rosenblatt KP, Zhang Z, Doss R, Gurnani PP, Grobman WA, Silver RM, Parry S, Reddy UM, Cao S, Haas DM. A multisite study to develop and validate first trimester, circulating microparticle biomarkers for tiered risk stratification of spontaneous preterm birth in nulliparas. Am J Obstet Gynecol 2024:S0002-9378(24)00614-8. [PMID: 38789072 DOI: 10.1016/j.ajog.2024.05.032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 04/19/2024] [Accepted: 05/17/2024] [Indexed: 05/26/2024]
Abstract
BACKGROUND Despite much research, advances in early prediction of spontaneous preterm birth (sPTB) has been slow. The evolving field of circulating microparticle (CMP) biology may identify novel blood-based, and clinically useful, biomarkers. OBJECTIVE To test the ability of a previously identified, 7-marker set of CMP-derived proteins from the first trimester of pregnancy, in the form of an in vitro diagnostic multivariate index assay (IVDMIA), to stratify pregnant patients according to their risk for sPTB. STUDY DESIGN We employed a previously validated set of CMP protein biomarkers, utilizing mass spectrometry assays and a nested case-control design in a subset of participants from the Nulliparous Pregnancy Outcomes Study: monitoring mothers-to-be (nuMoM2b). We evaluated these biomarkers in the form of an IVDMIA to predict risk for sPTB at different gestational ages. Plasma samples collected at 9- to 13-weeks' gestation were analyzed. The IVDMIA assigned subjects to 1 of 3 sPTB risk categories: low risk (LR), moderate risk (MR), or high risk (HR). Independent validation on a set-aside set confirmed the IVDMIA's performance in risk stratification. RESULTS Samples from 400 participants from the nuMoM2b cohort were used for the study; of these, 160 delivered<37 weeks and 240 delivered at term. Through Monte Carlo simulation in which the validation results were adjusted based on actual weekly sPTB incidence rates in the nuMoM2b cohort, the IVDMIA stratifications demonstrated statistically significant differences among the risk groups in time-to-event (birth) analysis (P<.0001). The incidence-rate adjusted cumulative risks of sPTB at ≤32 weeks' gestation were 0.4%, 1.6%, and 7.5%, respectively for the LR, MR, and HR groups, respectively. Compared to the LR group, the corresponding risk ratios of the IVDMIA assigned MR and HR group were 4.25 (95% confidence interval [CI] 2.2-7.9) and 19.92 (95% CI 10.4-37.4), respectively. CONCLUSION A first trimester CMP protein biomarker panel can be used to stratify risk for sPTB at different gestational ages. Such a multitiered stratification tool could be used to assess risk early in pregnancy to enable timely clinical management and interventions, and, ultimately, to enable the development of tailored care pathways for sPTB prevention.
Collapse
Affiliation(s)
| | - Zhen Zhang
- Departments of Pathology and Oncology, Center for Biomarker Discovery and Translation, Johns Hopkins University School of Medicine, Baltimore, MD
| | | | | | - William A Grobman
- Department of Obstetrics and Gynecology, The Ohio State University School of Medicine, Columbus, OH
| | - Robert M Silver
- Department of Obstetrics and Gynecology, University of Utah School of Medicine, Salt Lake City, UT
| | - Samuel Parry
- Department of Obstetrics and Gynecology, University of Pennsylvania School of Medicine, Philadelphia, PA
| | - Uma M Reddy
- Department of Obstetrics and Gynecology, Columbia University School of Medicine, New York, NY
| | - Sha Cao
- Department of Biostatistics, Indiana University School of Medicine, Indianapolis, IN
| | - David M Haas
- Department of Obstetrics and Gynecology, Indiana University School of Medicine, Indianapolis, IN.
| |
Collapse
|
2
|
Taylor AH, Konje JC, Ayakannu T. Identification of Potentially Novel Molecular Targets of Endometrial Cancer Using a Non-Biased Proteomic Approach. Cancers (Basel) 2023; 15:4665. [PMID: 37760635 PMCID: PMC10527058 DOI: 10.3390/cancers15184665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 08/29/2023] [Accepted: 09/04/2023] [Indexed: 09/29/2023] Open
Abstract
The present study was aimed at identifying novel proteins in endometrial cancer (EC), employing proteomic analysis of tissues obtained after surgery. A differential MS-based proteomic analysis was conducted from whole tissues dissected from biopsies from post-menopausal women, histologically confirmed as endometrial cancer (two endometrioid and two serous; n = 4) or normal atrophic endometrium (n = 4), providing 888 differentially expressed proteins with 246 of these previously documented elsewhere as expressed in EC and 372 proteins not previously demonstrated to be expressed in EC but associated with other types of cancer. Additionally, 33 proteins not recorded previously in PubMed as being expressed in any forms of cancer were also identified, with only 26 of these proteins having a publication associated with their expression patterns or putative functions. The putative functions of the 26 proteins (GRN, APP, HEXA, CST3, CAD, QARS, SIAE, WARS, MYH8, CLTB, GOLIM4, SCARB2, BOD1L1, C14orf142, C9orf142, CCDC13, CNPY4, FAM169A, HN1L, PIGT, PLCL1, PMFBP1, SARS2, SCPEP1, SLC25A24 and ZC3H4) in other tissues point towards and provide a basis for further investigation of these previously unrecognised novel EC proteins. The developmental biology, disease, extracellular matrix, homeostatic, immune, metabolic (both RNA and protein), programmed cell death, signal transduction, molecular transport, transcriptional networks and as yet uncharacterised pathways indicate that these proteins are potentially involved in endometrial carcinogenesis and thus may be important in EC diagnosis, prognostication and treatment and thus are worthy of further investigation.
Collapse
Affiliation(s)
- Anthony H. Taylor
- Reproductive Sciences Section, Department of Cancer Studies & Molecular Medicine, University of Leicester, Leicester LE1 7RH, UK; (A.H.T.); (J.C.K.)
- Department of Molecular and Cell Biology, University of Leicester, Leicester LE1 7RH, UK
| | - Justin C. Konje
- Reproductive Sciences Section, Department of Cancer Studies & Molecular Medicine, University of Leicester, Leicester LE1 7RH, UK; (A.H.T.); (J.C.K.)
- Department of Health Sciences, University of Leicester, Leicester LE1 7RH, UK
- Weill Cornell Medicine-Qatar, Al Rayyan, Doha P.O. Box 24144, Qatar
| | - Thangesweran Ayakannu
- Reproductive Sciences Section, Department of Cancer Studies & Molecular Medicine, University of Leicester, Leicester LE1 7RH, UK; (A.H.T.); (J.C.K.)
- Department of Obstetrics & Gynaecology, Taylor’s University, Subang Jaya 47500, Selangor, Malaysia
- Sunway Medical Centre, Bandar Sunway, Subang Jaya 47500, Selangor, Malaysia
| |
Collapse
|
3
|
Sajid MS, Jabeen F, Hussain D, Gardner QA, Ashiq MN, Najam‐ul‐Haq M. Boronic acid functionalized fibrous cellulose for the selective enrichment of glycopeptides. J Sep Sci 2020; 43:1348-1355. [DOI: 10.1002/jssc.201900983] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 01/19/2020] [Accepted: 01/19/2020] [Indexed: 12/29/2022]
Affiliation(s)
- Muhammad Salman Sajid
- Division of Analytical ChemistryInstitute of Chemical SciencesBahauddin Zakariya University Multan Pakistan
| | - Fahmida Jabeen
- Division of Analytical ChemistryInstitute of Chemical SciencesBahauddin Zakariya University Multan Pakistan
| | - Dilshad Hussain
- Division of Analytical ChemistryInstitute of Chemical SciencesBahauddin Zakariya University Multan Pakistan
| | | | - Muhammad Naeem Ashiq
- Division of Analytical ChemistryInstitute of Chemical SciencesBahauddin Zakariya University Multan Pakistan
| | - Muhammad Najam‐ul‐Haq
- Division of Analytical ChemistryInstitute of Chemical SciencesBahauddin Zakariya University Multan Pakistan
| |
Collapse
|
4
|
Ar-gas cluster ion beam in ToF-SIMS for peptide and protein analysis. Biointerphases 2020; 15:021011. [DOI: 10.1116/6.0000105] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
|
5
|
A simple and rapid pipeline for identification of receptor-binding sites on the surface proteins of pathogens. Sci Rep 2020; 10:1163. [PMID: 31980725 PMCID: PMC6981161 DOI: 10.1038/s41598-020-58305-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 01/14/2020] [Indexed: 12/02/2022] Open
Abstract
Ligand-receptor interactions play a crucial role in the plethora of biological processes. Several methods have been established to reveal ligand-receptor interface, however, the majority of methods are time-consuming, laborious and expensive. Here we present a straightforward and simple pipeline to identify putative receptor-binding sites on the pathogen ligands. Two model ligands (bait proteins), domain III of protein E of West Nile virus and NadA of Neisseria meningitidis, were incubated with the proteins of human brain microvascular endothelial cells immobilized on nitrocellulose or PVDF membrane, the complex was trypsinized on-membrane, bound peptides of the bait proteins were recovered and detected on MALDI-TOF. Two peptides of DIII (~916 Da and ~2003 Da) and four peptides of NadA (~1453 Da, ~1810 Da, ~2051 Da and ~2433 Da) were identified as plausible receptor-binders. Further, binding of the identified peptides to the proteins of endothelial cells was corroborated using biotinylated synthetic analogues in ELISA and immunocytochemistry. Experimental pipeline presented here can be upscaled easily to map receptor-binding sites on several ligands simultaneously. The approach is rapid, cost-effective and less laborious. The proposed experimental pipeline could be a simpler alternative or complementary method to the existing techniques used to reveal amino-acids involved in the ligand-receptor interface.
Collapse
|
6
|
Loraine J, Alhumaidan O, Bottrill AR, Mistry SC, Andrew P, Mukamolova GV, Turapov O. Efficient Protein Digestion at Elevated Temperature in the Presence of Sodium Dodecyl Sulfate and Calcium Ions for Membrane Proteomics. Anal Chem 2019; 91:9516-9521. [PMID: 31259536 DOI: 10.1021/acs.analchem.9b00484] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The growing significance of membrane proteins inspires continuous development and improvement of methods for robust membrane proteomics. Here, we developed a very simple and efficient method for membrane protein digestion using an ionic detergent, sodium dodecyl sulfate (SDS), at high temperature, conditions where trypsin is normally inactivated. Our results suggest that trypsin can be stabilized by a combination of calcium ions and sodium chloride, which enables protein digestion at elevated temperature in the presence of strong ionic detergents such as SDS. Finding the conditions for stabilization of trypsin offers novel opportunities for the application of detergents for the investigation of membrane proteins.
Collapse
Affiliation(s)
- Jessica Loraine
- Department of Infection, Immunity and Inflammation , University of Leicester , Leicester LE1 9HN , United Kingdom
| | - Ohoud Alhumaidan
- Department of Infection, Immunity and Inflammation , University of Leicester , Leicester LE1 9HN , United Kingdom.,Department of Respiratory Sciences , University of Leicester , Leicester LE1 9HN , United Kingdom.,Department of Clinical Laboratory Sciences , King Saud University , Riyadh 11433 , Saudi Arabia
| | - Andrew R Bottrill
- Protein Nucleic Acid Chemistry Laboratory , University of Leicester , Leicester LE1 7RH , United Kingdom
| | - Sharad C Mistry
- Protein Nucleic Acid Chemistry Laboratory , University of Leicester , Leicester LE1 7RH , United Kingdom
| | - Peter Andrew
- Department of Infection, Immunity and Inflammation , University of Leicester , Leicester LE1 9HN , United Kingdom.,Department of Respiratory Sciences , University of Leicester , Leicester LE1 9HN , United Kingdom
| | - Galina V Mukamolova
- Department of Infection, Immunity and Inflammation , University of Leicester , Leicester LE1 9HN , United Kingdom.,Department of Respiratory Sciences , University of Leicester , Leicester LE1 9HN , United Kingdom
| | - Obolbek Turapov
- Department of Infection, Immunity and Inflammation , University of Leicester , Leicester LE1 9HN , United Kingdom.,Department of Respiratory Sciences , University of Leicester , Leicester LE1 9HN , United Kingdom
| |
Collapse
|
7
|
Zhang P, Gaffrey MJ, Zhu Y, Chrisler WB, Fillmore TL, Yi L, Nicora CD, Zhang T, Wu H, Jacobs J, Tang K, Kagan J, Srivastava S, Rodland KD, Qian WJ, Smith RD, Liu T, Wiley HS, Shi T. Carrier-Assisted Single-Tube Processing Approach for Targeted Proteomics Analysis of Low Numbers of Mammalian Cells. Anal Chem 2019; 91:1441-1451. [PMID: 30557009 PMCID: PMC6555634 DOI: 10.1021/acs.analchem.8b04258] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Heterogeneity in composition is inherent in all cell populations, even those containing a single cell type. Single-cell proteomics characterization of cell heterogeneity is currently achieved by antibody-based technologies, which are limited by the availability of high-quality antibodies. Herein we report a simple, easily implemented, mass spectrometry (MS)-based targeted proteomics approach, termed cLC-SRM (carrier-assisted liquid chromatography coupled to selected reaction monitoring), for reliable multiplexed quantification of proteins in low numbers of mammalian cells. We combine a new single-tube digestion protocol to process low numbers of cells with minimal loss together with sensitive LC-SRM for protein quantification. This single-tube protocol builds upon trifluoroethanol digestion and further minimizes sample losses by tube pretreatment and the addition of carrier proteins. We also optimized the denaturing temperature and trypsin concentration to significantly improve digestion efficiency. cLC-SRM was demonstrated to have sufficient sensitivity for reproducible detection of most epidermal growth factor receptor (EGFR) pathway proteins expressed at levels ≥30 000 and ≥3000 copies per cell for 10 and 100 mammalian cells, respectively. Thus, cLC-SRM enables reliable quantification of low to moderately abundant proteins in less than 100 cells and could be broadly useful for multiplexed quantification of important proteins in small subpopulations of cells or in size-limited clinical samples. Further improvements of this method could eventually enable targeted single-cell proteomics when combined with either SRM or other emerging ultrasensitive MS detection.
Collapse
Affiliation(s)
- Pengfei Zhang
- Key Laboratory of Cancer Proteomics of Chinese Ministry of Health, Xiangya Hospital, Central South University, Changsha, Hunan 410008, People’s Republic of China
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Matthew J. Gaffrey
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Ying Zhu
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - William B. Chrisler
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Thomas L. Fillmore
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Lian Yi
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Carrie D. Nicora
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Tong Zhang
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Huanming Wu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Jon Jacobs
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Keqi Tang
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Jacob Kagan
- Cancer Biomarkers Research Group, Division of Cancer Prevention, National Cancer Institute, Bethesda, Maryland 20892, United States
| | - Sudhir Srivastava
- Cancer Biomarkers Research Group, Division of Cancer Prevention, National Cancer Institute, Bethesda, Maryland 20892, United States
| | - Karin D. Rodland
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Wei-Jun Qian
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Richard D. Smith
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Tao Liu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - H. Steven Wiley
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Tujin Shi
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| |
Collapse
|
8
|
Serum Albumin and Ca2+ Are Natural Competence Inducers in the Human Pathogen Acinetobacter baumannii. Antimicrob Agents Chemother 2016; 60:4920-9. [PMID: 27270286 DOI: 10.1128/aac.00529-16] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Accepted: 05/28/2016] [Indexed: 01/07/2023] Open
Abstract
The increasing frequency of bacteria showing antimicrobial resistance (AMR) raises the menace of entering into a postantibiotic era. Horizontal gene transfer (HGT) is one of the prime reasons for AMR acquisition. Acinetobacter baumannii is a nosocomial pathogen with outstanding abilities to survive in the hospital environment and to acquire resistance determinants. Its capacity to incorporate exogenous DNA is a major source of AMR genes; however, few studies have addressed this subject. The transformation machinery as well as the factors that induce natural competence in A. baumannii are unknown. In this study, we demonstrate that naturally competent strain A118 increases its natural transformation frequency upon the addition of Ca(2+)or albumin. We show that comEA and pilQ are involved in this process since their expression levels are increased upon the addition of these compounds. An unspecific protein, like casein, does not reproduce this effect, showing that albumin's effect is specific. Our work describes the first specific inducers of natural competence in A. baumannii Overall, our results suggest that the main protein in blood enhances HGT in A. baumannii, contributing to the increase of AMR in this threatening human pathogen.
Collapse
|
9
|
Deng J, Lazar IM. Proteolytic Digestion and TiO2 Phosphopeptide Enrichment Microreactor for Fast MS Identification of Proteins. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2016; 27:686-698. [PMID: 26883530 DOI: 10.1007/s13361-015-1332-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Revised: 12/20/2015] [Accepted: 12/27/2015] [Indexed: 06/05/2023]
Abstract
The characterization of phosphorylation state(s) of a protein is best accomplished by using isolated or enriched phosphoprotein samples or their corresponding phosphopeptides. The process is typically time-consuming as, often, a combination of analytical approaches must be used. To facilitate throughput in the study of phosphoproteins, a microreactor that enables a novel strategy for performing fast proteolytic digestion and selective phosphopeptide enrichment was developed. The microreactor was fabricated using 100 μm i.d. fused-silica capillaries packed with 1-2 mm beds of C18 and/or TiO2 particles. Proteolytic digestion-only, phosphopeptide enrichment-only, and sequential proteolytic digestion/phosphopeptide enrichment microreactors were developed and tested with standard protein mixtures. The protein samples were adsorbed on the C18 particles, quickly digested with a proteolytic enzyme infused over the adsorbed proteins, and further eluted onto the TiO2 microreactor for enrichment in phosphopeptides. A number of parameters were optimized to speed up the digestion and enrichments processes, including microreactor dimensions, sample concentrations, digestion time, flow rates, buffer compositions, and pH. The effective time for the steps of proteolytic digestion and enrichment was less than 5 min. For simple samples, such as standard protein mixtures, this approach provided equivalent or better results than conventional bench-top methods, in terms of both enzymatic digestion and selectivity. Analysis times and reagent costs were reduced ~10- to 15-fold. Preliminary analysis of cell extracts and recombinant proteins indicated the feasibility of integration of these microreactors in more advanced workflows amenable for handling real-world biological samples. Graphical Abstract ᅟ.
Collapse
Affiliation(s)
- Jingren Deng
- Department of Biological Sciences, Virginia Tech, 1981 Kraft Drive, Blacksburg, VA, 24061, USA
| | - Iulia M Lazar
- Department of Biological Sciences, Virginia Tech, 1981 Kraft Drive, Blacksburg, VA, 24061, USA.
| |
Collapse
|
10
|
Identification and LC–MS/MS-based analyses of technical enzymes in wheat flour and baked products. Eur Food Res Technol 2016. [DOI: 10.1007/s00217-015-2536-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
11
|
Last D, Müller J, Dawood AWH, Moldenhauer EJ, Pavlidis IV, Bornscheuer UT. Highly efficient and easy protease-mediated protein purification. Appl Microbiol Biotechnol 2015; 100:1945-1953. [DOI: 10.1007/s00253-015-7206-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Revised: 11/25/2015] [Accepted: 11/28/2015] [Indexed: 11/29/2022]
|
12
|
Abstract
Sample preparation has lagged far behind the evolution of instrumentation used in mass-linked protein analysis. Trypsin digestion, for example, still takes a day, as it did 50 years ago, while mass spectral analyses are achieved in seconds. Higher order structure of proteins is frequently modified by varying digestion conditions: shifting the initial points of trypsin cleavage, changing digestion pathways, accelerating peptide bond demasking and altering the distribution of miscleaved products at the completion of proteolysis. Reduction and alkylation are even circumvented in many cases. This review focuses on immobilized enzyme reactor technology as a means to achieve accelerated trypsin digestion by exploiting these phenomena.
Collapse
|
13
|
Recent developments in nanoparticle-based MALDI mass spectrometric analysis of phosphoproteomes. Mikrochim Acta 2014. [DOI: 10.1007/s00604-014-1191-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
|
14
|
Kailasa SK, Wu HF. Rapid enrichment of phosphopeptides by BaTiO3 nanoparticles after microwave-assisted tryptic digest of phosphoproteins, and their identification by MALDI-MS. Mikrochim Acta 2012. [DOI: 10.1007/s00604-012-0854-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
15
|
Kailasa SK, Wu HF. Functionalized quantum dots with dopamine dithiocarbamate as the matrix for the quantification of efavirenz in human plasma and as affinity probes for rapid identification of microwave tryptic digested proteins in MALDI-TOF-MS. J Proteomics 2011; 75:2924-33. [PMID: 22202183 DOI: 10.1016/j.jprot.2011.12.008] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2011] [Revised: 12/09/2011] [Accepted: 12/10/2011] [Indexed: 01/01/2023]
Abstract
Functionalized quantum dots with dopamine dithiocarbamate (QDs-DDTC) were utilized for the first time as an efficient material for the quantification of efavirenz in human plasma of HIV infected patients and rapid identification of microwave tryptic digest proteins (cytochrome c, lysozyme and BSA) by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS). The synthesized QDs-DDTC was characterized by using spectroscopic (UV-visible, FT-IR and (1)H NMR) and microscopic (SEM and TEM) techniques. Functionalized QDs-DDTC exhibited a high desorption/ionization efficiency for the rapid quantification of small molecules (efavirenz, tobramycin and aspartame) at low-mass region. QDs-DDTC has well ability to trap target species, and capable to transfer laser energy for efficient desorption/ionization of analytes with background-free detection. The use of QDs-DDTC as a matrix provided good linearity for the quantification of small molecules (R(2)=~0.9983), with good reproducibility (RSD<10%), in the analysis of efavirenz in the plasma of HIV infected patients by the standard addition method. We also demonstrated that the use of functionalized QDs-DDTC as affinity probes for the rapid identification of microwave tryptic digested proteins (cytochrome c, lysozyme and BSA) by MALDI-TOF-MS. QDs-DDTC-based MALDI-TOF-MS approach provides simplicity, rapidity, accuracy, and precision for the determination of efavirenz in human plasma of HIV infected patients and rapid identification of microwave tryptic digested proteins. This new material presents a marked advance in the development of matrix-free mass spectrometric methods for the rapid and precise quantitative determination of a variety of molecules. This article is part of a Special Issue entitled: Proteomics: The clinical link.
Collapse
Affiliation(s)
- Suresh Kumar Kailasa
- Department of Chemistry, National Sun Yat-Sen University, Kaohsiung, 80424, Taiwan
| | | |
Collapse
|
16
|
Terilli RR, Moura H, Woolfitt AR, Rees J, Schieltz DM, Barr JR. A historical and proteomic analysis of botulinum neurotoxin type/G. BMC Microbiol 2011; 11:232. [PMID: 22008244 PMCID: PMC3215672 DOI: 10.1186/1471-2180-11-232] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2010] [Accepted: 10/18/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Clostridium botulinum is the taxonomic designation for at least six diverse species that produce botulinum neurotoxins (BoNTs). There are seven known serotypes of BoNTs (/A through/G), all of which are potent toxins classified as category A bioterrorism agents. BoNT/G is the least studied of the seven serotypes. In an effort to further characterize the holotoxin and neurotoxin-associated proteins (NAPs), we conducted an in silico and proteomic analysis of commercial BoNT/G complex. We describe the relative quantification of the proteins present in the/G complex and confirm our ability to detect the toxin activity in vitro. In addition, we review previous literature to provide a complete description of the BoNT/G complex. RESULTS An in-depth comparison of protein sequences indicated that BoNT/G shares the most sequence similarity with the/B serotype. A temperature-modified Endopep-MS activity assay was successful in the detection of BoNT/G activity. Gel electrophoresis and in gel digestions, followed by MS/MS analysis of/G complex, revealed the presence of four proteins in the complexes: neurotoxin (BoNT) and three NAPs--nontoxic-nonhemagglutinin (NTNH) and two hemagglutinins (HA70 and HA17). Rapid high-temperature in-solution tryptic digestions, coupled with MS/MS analysis, generated higher than previously reported sequence coverages for all proteins associated with the complex: BoNT 66%, NTNH 57%, HA70 91%, and HA17 99%. Label-free relative quantification determined that the complex contains 30% BoNT, 38% NTNH, 28% HA70, and 4% HA17 by weight comparison and 17% BoNT, 23% NTNH, 42% HA70, and 17% HA17 by molecular comparison. CONCLUSIONS The in silico protein sequence comparisons established that the/G complex is phenetically related to the other six serotypes of C. botulinum. Proteomic analyses and Endopep-MS confirmed the presence of BoNT and NAPs, along with the activity of the commercial/G complex. The use of data-independent MS(E) data analysis, coupled to label-free quantification software, suggested that the weight ratio BoNT:NAPs is 1:3, whereas the molar ratio of BoNT:NTNH:HA70:HA17 is 1:1:2:1, within the BoNT/G progenitor toxin.
Collapse
Affiliation(s)
- Rebecca R Terilli
- Centers for Disease Control and Prevention, National Center for Environmental Health, Division of Laboratory Sciences, Atlanta, GA 30341, USA
| | | | | | | | | | | |
Collapse
|
17
|
Pierce CL, Rees JC, Fernández FM, Barr JR. Viable Staphylococcus aureus quantitation using ¹⁵N metabolically labeled bacteriophage amplification coupled with a multiple reaction monitoring proteomic workflow. Mol Cell Proteomics 2011; 11:M111.012849. [PMID: 21972246 DOI: 10.1074/mcp.m111.012849] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
A multiple reaction monitoring liquid chromatography method with tandem mass spectrometric detection for quantitation of Staphylococcus aureus via phage amplification detection is described. This phage amplification detection method enables rapid and accurate quantitation of viable S. aureus by detecting an amplified capsid protein from a specific phage. A known amount of metabolically labeled (15)N reference bacteriophage, utilized as the input phage and as the internal standard for quantitation, was spiked into S. aureus samples. Following a 2-h incubation, the sample was subjected to a 3-min rapid trypsin digest and analyzed by high-throughput liquid chromatography tandem mass spectrometric detection targeting peptides unique to both the (15)N (input phage) and (14)N (progeny phage) capsid proteins. Quantitation was achieved by comparing peak areas of target peptides from the metabolically labeled (15)N bacteriophage peptide internal standard with that of the wild-type (14)N peptides that were produced by phage amplification and subsequent digestion when the host bacteria was present. This approach is based on the fact that a labeled species differs from the unlabeled one in terms of its mass but exhibits almost identical chemical properties such as ion yields and retention times. A 6-point calibration curve for S. aureus concentration was constructed with standards ranging from 5.0 × 10(4) colony forming units (CFU) ml(-1) to 2.0 × 10(6) CFU ml(-1), with the (15)N reference phage spiked at a concentration of 1.0 × 10(9) plaque forming units (PFU) ml(-1). Amplification with (15)N bacteriophage coupled with LC-MS/MS detection offers speed (3 h total analysis time), sensitivity (LOD: < 5.0 × 10(4) CFU ml(-1)), accuracy, and precision for quantitation of S. aureus.
Collapse
Affiliation(s)
- Carrie L Pierce
- National Center for Environmental Health, Centers for Disease Control and Prevention, 4770 Buford Highway, MS F-50, Atlanta, GA 30341; School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332
| | - Jon C Rees
- National Center for Environmental Health, Centers for Disease Control and Prevention, 4770 Buford Highway, MS F-50, Atlanta, GA 30341
| | - Facundo M Fernández
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332
| | - John R Barr
- National Center for Environmental Health, Centers for Disease Control and Prevention, 4770 Buford Highway, MS F-50, Atlanta, GA 30341.
| |
Collapse
|
18
|
Urea free and more efficient sample preparation method for mass spectrometry based protein identification via combining the formic acid-assisted chemical cleavage and trypsin digestion. Talanta 2011; 86:429-35. [DOI: 10.1016/j.talanta.2011.08.052] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2011] [Revised: 08/20/2011] [Accepted: 08/26/2011] [Indexed: 11/20/2022]
|
19
|
Vale G, Santos HM, Carreira RJ, Fonseca L, Miró M, Cerdà V, Reboiro-Jato M, Capelo JL. An assessment of the ultrasonic probe-based enhancement of protein cleavage with immobilized trypsin. Proteomics 2011; 11:3866-76. [PMID: 21805637 DOI: 10.1002/pmic.201100200] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2011] [Revised: 04/17/2011] [Accepted: 07/11/2011] [Indexed: 11/07/2022]
Abstract
The use of ultrasonic probe, in conjunction with immobilized trypsin, has been explored in this work for potential enhancement of protein digestion. Several solid supports commonly used to immobilize trypsin were subjected to different ultrasonication amplitudes and time in order to investigate their mechanical resistance to ultrasonic energy when provided by the ultrasonic probe. Glass beads and magnetic particles were found to remain intact in most conditions studied. It was found that immobilized trypsin cannot be reused after ultrasonication since the enzymatic activity was greatly diminished. For comparative purposes, vortex shaking was also explored for protein cleavage. Four standard proteins--bovine serum albumin, α-lactalbumin, carbonic anhydrase and ovalbumin--were successfully identified using peptide mass fingerprint, or peptide fragment fingerprint. In addition, the performance of the classical protein cleavage (overnight, 12 h) and the ultrasonic methods was found to be similar when the digestion of a complex proteome, human plasma, was assessed through 18-O quantification. The digestion yields found were 90-117% for the ultrasonic and 5-21% for the vortex when those methods were compared with the classical overnight digestion.
Collapse
Affiliation(s)
- Gonçalo Vale
- REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia da Universidade Nova de Lisboa, Monte da Caparica, Portugal
| | | | | | | | | | | | | | | |
Collapse
|
20
|
Turiák L, Ozohanics O, Marino F, Drahos L, Vékey K. Digestion protocol for small protein amounts for nano-HPLC-MS(MS) analysis. J Proteomics 2011; 74:942-7. [DOI: 10.1016/j.jprot.2011.01.007] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2010] [Revised: 11/28/2010] [Accepted: 01/13/2011] [Indexed: 11/30/2022]
|
21
|
Moura H, Terilli RR, Woolfitt AR, Gallegos-Candela M, McWilliams LG, Solano MI, Pirkle JL, Barr JR. Studies on botulinum neurotoxins type /C1 and mosaic/DC using Endopep-MS and proteomics. ACTA ACUST UNITED AC 2011; 61:288-300. [PMID: 21205003 DOI: 10.1111/j.1574-695x.2010.00774.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Botulinum neurotoxins (BoNTs) are very potent toxins and category A biological threat agents. BoNT serotypes /C1 and /D affect birds and mammals and can be potentially lethal to humans. We have previously described the usefulness of the Endopep-MS method to detect the activity of BoNT A through G. This report was followed by the application of the method to clinical samples. The activity of the BoNT serotypes associated with human disease (/A, /B, /E, and /F) was successfully detected. However, BoNT/C and /D require different conditions for fast substrate cleavage, and a comprehensive description of a method to study BoNT/C and /D has not yet been reported. This work describes a new, optimized version of the Endopep-MS method to detect BoNTs /C1 and /DC either spiked directly in 20 μL of reaction buffer or spiked in a larger volume of buffer and further extracted using antibody-coated magnetic beads. It was found that the incubation temperature at 42 °C was more effective for both toxin serotypes, but each toxin serotype has an optimum cleavage pH. Additionally, we describe for the first time a proteomics study using a fast trypsin digestion method and label-free quantification of these toxin serotypes.
Collapse
Affiliation(s)
- Hercules Moura
- Division of Laboratory Sciences, National Center for Environmental Health, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | | | | | | | | | | | | | | |
Collapse
|
22
|
Multilayer gold nanoparticle-assisted protein tryptic digestion in solution and in gel under photothermal heating. Anal Bioanal Chem 2010; 399:377-85. [DOI: 10.1007/s00216-010-4375-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2010] [Revised: 10/20/2010] [Accepted: 10/24/2010] [Indexed: 11/26/2022]
|
23
|
Nelson WC, Peng I, Lee GA, Loo JA, Garrell RL, Kim CJCJ. Incubated protein reduction and digestion on an electrowetting-on-dielectric digital microfluidic chip for MALDI-MS. Anal Chem 2010; 82:9932-7. [PMID: 21058643 DOI: 10.1021/ac101833b] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Localized heating of droplets on an electrowetting-on-dielectric (EWOD) chip has been implemented and shown to accelerate trypsin digestion reaction rates, sample drying, and matrix crystallization for matrix-assisted laser desorption ionization mass spectrometry (MALDI-MS). Achieving this involved extending the functionality of previous EWOD droplet-based techniques by developing a multifunctional electrode with closed-loop temperature control, while minimizing overall system complexity and addressing challenges associated with rapid evaporation. For the EWOD chip design, we discuss the performance of multifunctional surface electrodes for actuation, localized Joule heating, and thermistic temperature sensing. Furthermore, a hydrophilic pattern is formed in the multifunctional electrode to control the location of an evaporating droplet on the electrode. To demonstrate the capabilities and limitations of this technique, we performed three experiments and measured the results using MALDI-MS: (i) insulin disulfide reductions in dithiothreitol (DTT) over a range of heater temperatures (22-70 °C) to show how reaction rates can be affected by thermal control, (ii) insulin disulfide reductions at 130 °C in dimethyl sulfoxide (DMSO) to demonstrate a reaction in a high boiling point solvent, and (iii) tryptic digestions of cytochrome c at 22 and 40 °C to show that heated droplets can yield reasonably higher peptide sequence coverage than unheated droplets. Although they do not decouple the effects of changing temperatures and concentrations, these experiments verified that thermal cycling by EWOD electrodes accelerates reaction rates in liquid droplets in air.
Collapse
Affiliation(s)
- Wyatt C Nelson
- Mechanical and Aerospace Engineering Department, 420 Westwood Plaza, Engineering IV Room 37-129, University of California, Los Angeles (UCLA), Los Angeles, California 90095, USA
| | | | | | | | | | | |
Collapse
|
24
|
Overview on modern approaches to speed up protein identification workflows relying on enzymatic cleavage and mass spectrometry-based techniques. Anal Chim Acta 2009; 650:151-9. [DOI: 10.1016/j.aca.2009.07.034] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2009] [Revised: 07/14/2009] [Accepted: 07/15/2009] [Indexed: 11/19/2022]
|
25
|
Ma J, Liu J, Sun L, Gao L, Liang Z, Zhang L, Zhang Y. Online Integration of Multiple Sample Pretreatment Steps Involving Denaturation, Reduction, and Digestion with Microflow Reversed-Phase Liquid Chromatography−Electrospray Ionization Tandem Mass Spectrometry for High-Throughput Proteome Profiling. Anal Chem 2009; 81:6534-40. [DOI: 10.1021/ac900971w] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Junfeng Ma
- Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China and Graduate School of Chinese Academy of Sciences, Beijing 100039, China
| | - Jinxiang Liu
- Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China and Graduate School of Chinese Academy of Sciences, Beijing 100039, China
| | - Liangliang Sun
- Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China and Graduate School of Chinese Academy of Sciences, Beijing 100039, China
| | - Liang Gao
- Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China and Graduate School of Chinese Academy of Sciences, Beijing 100039, China
| | - Zhen Liang
- Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China and Graduate School of Chinese Academy of Sciences, Beijing 100039, China
| | - Lihua Zhang
- Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China and Graduate School of Chinese Academy of Sciences, Beijing 100039, China
| | - Yukui Zhang
- Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China and Graduate School of Chinese Academy of Sciences, Beijing 100039, China
| |
Collapse
|
26
|
Kim SJ, Wang F, Burns MA, Kurabayashi K. Temperature-programmed natural convection for micromixing and biochemical reaction in a single microfluidic chamber. Anal Chem 2009; 81:4510-6. [PMID: 19419189 PMCID: PMC2727855 DOI: 10.1021/ac900512x] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Micromixing is a crucial step for biochemical reactions in microfluidic networks. A critical challenge is that the system containing micromixers needs numerous pumps, chambers, and channels not only for the micromixing but also for the biochemical reactions and detections. Thus, a simple and compatible design of the micromixer element for the system is essential. Here, we propose a simple, yet effective, scheme that enables micromixing and a biochemical reaction in a single microfluidic chamber without using any pumps. We accomplish this process by using natural convection in conjunction with alternating heating of two heaters for efficient micromixing, and by regulating capillarity for sample transport. As a model application, we demonstrate micromixing and subsequent polymerase chain reaction (PCR) for an influenza viral DNA fragment. This process is achieved in a platform of a microfluidic cartridge and a microfabricated heating-instrument with a fast thermal response. Our results will significantly simplify micromixing and a subsequent biochemical reaction that involves reagent heating in microfluidic networks.
Collapse
Affiliation(s)
- Sung-Jin Kim
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, Michigan 48109, USA
| | | | | | | |
Collapse
|