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Svetličić E, Dončević L, Ozdanovac L, Janeš A, Tustonić T, Štajduhar A, Brkić AL, Čeprnja M, Cindrić M. Direct Identification of Urinary Tract Pathogens by MALDI-TOF/TOF Analysis and De Novo Peptide Sequencing. Molecules 2022; 27:molecules27175461. [PMID: 36080229 PMCID: PMC9457756 DOI: 10.3390/molecules27175461] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Revised: 08/19/2022] [Accepted: 08/19/2022] [Indexed: 11/16/2022] Open
Abstract
For mass spectrometry-based diagnostics of microorganisms, matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) is currently routinely used to identify urinary tract pathogens. However, it requires a lengthy culture step for accurate pathogen identification, and is limited by a relatively small number of available species in peptide spectral libraries (≤3329). Here, we propose a method for pathogen identification that overcomes the above limitations, and utilizes the MALDI-TOF/TOF MS instrument. Tandem mass spectra of the analyzed peptides were obtained by chemically activated fragmentation, which allowed mass spectrometry analysis in negative and positive ion modes. Peptide sequences were elucidated de novo, and aligned with the non-redundant National Center for Biotechnology Information Reference Sequence Database (NCBInr). For data analysis, we developed a custom program package that predicted peptide sequences from the negative and positive MS/MS spectra. The main advantage of this method over a conventional MALDI-TOF MS peptide analysis is identification in less than 24 h without a cultivation step. Compared to the limited identification with peptide spectra libraries, the NCBI database derived from genome sequencing currently contains 20,917 bacterial species, and is constantly expanding. This paper presents an accurate method that is used to identify pathogens grown on agar plates, and those isolated directly from urine samples, with high accuracy.
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Affiliation(s)
- Ema Svetličić
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Lyngby, Denmark
| | - Lucija Dončević
- Division of Molecular Medicine, Ruđer Bošković Institute, Bijenička 54, 10000 Zagreb, Croatia
| | - Luka Ozdanovac
- Division of Molecular Medicine, Ruđer Bošković Institute, Bijenička 54, 10000 Zagreb, Croatia
| | - Andrea Janeš
- Clinical Department of Laboratory Diagnostics, University Hospital Dubrava, Avenija Gojka Šuška 6, 10000 Zagreb, Croatia
| | | | - Andrija Štajduhar
- Division for Medical Statistics, Andrija Štampar Teaching Institute of Public Health, Mirogojska cesta 16, 10000 Zagreb, Croatia
| | | | - Marina Čeprnja
- Special Hospital Agram, Agram EEIG, Trnjanska cesta 108, 10000 Zagreb, Croatia
| | - Mario Cindrić
- Division of Molecular Medicine, Ruđer Bošković Institute, Bijenička 54, 10000 Zagreb, Croatia
- Correspondence: ; Tel.: +385-16384422
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Lai Z, Zhang M, Zhou J, Chen T, Li D, Shen X, Liu J, Zhou J, Li Z. Fe 3O 4@PANI: a magnetic polyaniline nanomaterial for highly efficient and handy enrichment of intact N-glycopeptides. Analyst 2021; 146:4261-4267. [PMID: 34105527 DOI: 10.1039/d1an00580d] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Glycosylation of proteins plays important roles in the occurrence and development of chronic diseases. In this study, we report an enrichment method of intact N-glycopeptides using a magnetic polyaniline nanomaterial (Fe3O4@PANI). Under the synergistic effect of hydrogen bonding and electrostatic adsorption, Fe3O4@PANI can rapidly and easily enrich N-glycopeptides derived from standard protein (bovine fetuin and transferrin) tryptic digests and serum haptoglobin tryptic digests. Finally we have detected 63 glycopeptides in the glycosylation sites of both N204 and N211 from the serum haptoglobin beta chain using MALDI FTICR MS. Compared with non-magnetic materials, Fe3O4@PANI can achieve complete separation from complex biological samples, meeting the requirement of the high purity of samples for mass spectrometric detection. Overall, Fe3O4@PANI exhibits great application potential in the highly efficient enrichment of intact N-glycopeptides due to its stability and convenient preparation.
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Affiliation(s)
- Zhizhen Lai
- Department of Biophysics and Structural Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & School of Basic Medicine, Peking Union Medical College, 5 Dongdan San Tiao, Beijing 100005, China.
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Rapid Differential Detection of Abrin Isoforms by an Acetonitrile- and Ultrasound-Assisted On-Bead Trypsin Digestion Coupled with LC-MS/MS Analysis. Toxins (Basel) 2021; 13:toxins13050358. [PMID: 34069935 PMCID: PMC8157574 DOI: 10.3390/toxins13050358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 05/11/2021] [Accepted: 05/13/2021] [Indexed: 11/17/2022] Open
Abstract
The high toxic abrin from the plant Abrus precatorius is a type II ribosome-inactivating protein toxin with a human lethal dose of 0.1-1.0 µg/kg body weight. Due to its high toxicity and the potential misuse as a biothreat agent, it is of great importance to developing fast and reliable methods for the identification and quantification of abrin in complex matrices. Here, we report rapid and efficient acetonitrile (ACN)- and ultrasound-assisted on-bead trypsin digestion method combined with HPLC-MS/MS for the quantification of abrin isoforms in complex matrices. Specific peptides of abrin isoforms were generated by direct ACN-assisted trypsin digestion and analyzed by HPLC-HRMS. Combined with in silico digestion and BLASTp database search, fifteen marker peptides were selected for differential detection of abrin isoforms. The abrin in milk and plasma was enriched by immunomagnetic beads prepared by biotinylated anti-abrin polyclonal antibodies conjugated to streptavidin magnetic beads. The ultrasound-assisted on-bead trypsin digestion method was carried out under the condition of 10% ACN as denaturant solvent, the entire digestion time was further shortened from 90 min to 30 min. The four peptides of T3Aa,b,c,d, T12Aa, T15Ab, and T9Ac,d were chosen as quantification for total abrin, abrin-a, abrin-b, and abrin-c/d, respectively. The absolute quantification of abrin and its isoforms was accomplished by isotope dilution with labeled AQUA peptides and analyzed by HPLC-MS/MS (MRM). The developed method was fully validated in milk and plasma matrices with quantification limits in the range of 1.0-9.4 ng/mL for the isoforms of abrin. Furthermore, the developed approach was applied for the characterization of abrin isoforms from various fractions from gel filtration separation of the seeds, and measurement of abrin in the samples of biotoxin exercises organized by the Organization for the Prohibition of Chemical Weapons (OPCW). This study provided a recommended method for the differential identification of abrin isoforms, which are easily applied in international laboratories to improve the capabilities for the analysis of biotoxin samples.
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Liu C, Si X, Yan S, Zhao X, Qian X, Ying W, Zhao L. Development of the C12Im-Cl-assisted method for rapid sample preparation in proteomic application. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2021; 13:776-781. [PMID: 33492312 DOI: 10.1039/d0ay02079f] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Chromatography and mass spectrometry (MS) techniques have greatly improved the power of proteomic analyses. However, sample processing methods used prior to MS, including protein extraction and digestion, remain bottlenecks in the large-scale clinical application of proteomics. Ionic liquids, composed entirely of ions, have high solubility in various solvents. In this study, the effects of the cationic surfactant 1-dodecyl-3-methylimidazolium chloride (C12Im-Cl) on protein digestion were evaluated for clinical proteomic applications. C12Im-Cl was compatible with trypsin and reduced the protein digestion time from 16 h to 1 h. Residual C12Im-Cl was easily removed with a strong anion exchange membrane before MS. We evaluated the performance of C12Im-Cl extraction and rapid protein digestion using formalin-fixed paraffin-embedded liver cancer tissues. The number of proteins and peptides identified was nearly equal to that identified by the traditional filter-aided sample preparation method (2705 vs. 2739 and 16 682 vs. 17 214). In general, the C12Im-Cl-aided rapid sample preparation method is promising for proteomic applications.
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Affiliation(s)
- Chang Liu
- Beijing Key Laboratory of Environmental and Viral Oncology, Faculty of Environment and Life, Beijing University of Technology, Beijing 100124, China.
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Bottom-up sample preparation for the LC-MS/MS quantification of anti-cancer monoclonal antibodies in bio matrices. Bioanalysis 2020; 12:1405-1425. [PMID: 32975434 DOI: 10.4155/bio-2020-0204] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Therapeutic monoclonal antibodies (mAbs) are rapidly taking over the treatment of many malignancies, and an astonishing number of mAbs is in development. This causes a high demand for quantification of mAbs in biomatrices both for measuring therapeutic mAb concentrations and to support pharmacokinetics and pharmacodynamics studies. Conventionally, ligand-binding assays are used for these purposes, but LC-MS is gaining popularity. Although intact (top-down) and subunit (middle-down) mAb quantification is reported, signature peptide (bottom-up) quantification is currently most advantageous. This review provides an overview of the reported bottom-up mAb quantification methods in biomatrices as well as general recommendations regarding signature peptide and internal standard selection, reagent use and optimization of digestion in bottom-up quantification methods.
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Sun Y, Zhang Y, Wu X, Chi P. A Four Gene-Based Risk Score System Associated with Chemoradiotherapy Response and Tumor Recurrence in Rectal Cancer by Co-Expression Network Analysis. Onco Targets Ther 2020; 13:6721-6733. [PMID: 32753901 PMCID: PMC7354918 DOI: 10.2147/ott.s256696] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 05/26/2020] [Indexed: 12/14/2022] Open
Abstract
Aim Resistance to neoadjuvant chemoradiotherapy (NCRT) and tumor recurrence presents a major clinical problem in locally advanced rectal cancer (LARC) patients. This study aimed to explore a genetic risk score related to NCRT response and tumor recurrence in rectal cancer after NCRT. Materials and Methods Weighted gene co-expression network analysis was employed to identify hub genes associated with NCRT response from the GSE93375 dataset. Prognostic hub genes were determined using Cox regression analysis and associated with disease-free survival (DFS). A risk score system was constructed and the prognostic significance of the risk score was validated in our patient cohort. A predictive nomogram for DFS was developed and validated internally. Results The Tan module had the highest correlations with NCRT response. Ten hub genes (COL15A1, THBS2, ITGB1, MMP2, CD34, SPARC, NOTCH3, PDGFRB, DCN, and SERPINH1) were associated with NCRT response. Immunostaining expression of four genes (NOTCH3, SPARC, DCN, and ITGB1) was found to be significantly associated with both NCRT response and DFS in our patient cohort and was selected to build a prognostic risk score for DFS as follows: risk score= (0.6188×Exp NOTCH3 ) + (0.6511×Exp SPARC ) + (-0.2976×Exp DCN ) + (1.0035×Exp ITGB1 ). Using this risk score, patients could be separated into high- and low-risk groups for tumor recurrence. A nomogram that incorporated the risk score, ypTNM stage, and tumor regression grade (TRG) was constructed and utilized to predict DFS in LARC patients. Conclusion The four-gene expression-based risk score system presented here could be potentially used for predicting tumor recurrence in LARC patients after NCRT.
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Affiliation(s)
- Yanwu Sun
- Department of Colorectal Surgery, Fujian Medical University Union Hospital, Fuzhou, Fujian Province, People's Republic of China
| | - Yiyi Zhang
- Fujian Medical University, Fuzhou, Fujian Province, People's Republic of China
| | - Xuejing Wu
- Department of Pathology, Fujian Medical University Union Hospital, Fuzhou, Fujian Province, People's Republic of China
| | - Pan Chi
- Department of Colorectal Surgery, Fujian Medical University Union Hospital, Fuzhou, Fujian Province, People's Republic of China
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Robinson MR, Vasicek LA, Hoppmann C, Li M, Jokhadze G, Spellman DS. Improving the throughput of immunoaffinity purification and enzymatic digestion of therapeutic proteins using membrane-immobilized reagent technology. Analyst 2020; 145:3148-3156. [PMID: 32191233 DOI: 10.1039/d0an00190b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Continued interest in protein therapeutics has motivated the development of improved bioanalytical tools to support development programs. LC-MS offers specificity, sensitivity, and multiplexing capabilities without the need for target-specific reagents, making it a valuable alternative to ligand binding assays. Immunoaffinity purification (IP) and enzymatic digestion are critical, yet extensive and time-consuming components of the "gold standard" bottom-up approach to LC-MS-based protein quantitation. In the present work, commercially available technology, based on membrane-immobilized reagents in spin column and plate format, is applied to reduce IP and digestion times from hours to minutes. For a standard monoclonal antibody, the lower limit of quantitation was 0.1 ng μL-1 compared to 0.05 ng μL-1 for the standard method. A pharmacokinetics (PK) study dosing Herceptin in rat was analyzed by both the membrane and the standard method with a total sample processing time of 4 h and 20 h, respectively. The calculated concentrations at each time point agreed within 8% between both methods, and PK values including area under the curve (AUC), half-life (T1/2), mean residence time (MRT), clearance (CL), and volume of distribution (Vdss) agreed within 6% underscoring the utility of the membrane methodology for quantitative bioanalysis workflows.
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Affiliation(s)
- Michelle R Robinson
- Department of Pharmacokinetics Pharmacodynamics and Drug Metabolism, Merck & Co., Inc., West Point, PA, USA.
| | - Lisa A Vasicek
- Department of Pharmacokinetics Pharmacodynamics and Drug Metabolism, Merck & Co., Inc., West Point, PA, USA.
| | | | - Mandy Li
- Takara Bio USA, Inc., Mountain View, CA, USA
| | | | - Daniel S Spellman
- Department of Pharmacokinetics Pharmacodynamics and Drug Metabolism, Merck & Co., Inc., West Point, PA, USA.
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Feldberg L, Schuster O, Elhanany E, Laskar O, Yitzhaki S, Gura S. Rapid and sensitive identification of ricin in environmental samples based on lactamyl agarose beads using LC-MS/MS (MRM). JOURNAL OF MASS SPECTROMETRY : JMS 2020; 55:e4482. [PMID: 31782217 DOI: 10.1002/jms.4482] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2019] [Revised: 11/16/2019] [Accepted: 11/22/2019] [Indexed: 06/10/2023]
Abstract
Ricin, a plant-derived toxin extracted from the seeds of Ricinus communis (castor bean plant), is one of the most toxic proteins known. Ricin's high toxicity, widespread availability, and ease of its extraction make it a potential agent for bioterrorist attacks. Most ricin detection methods are based on immunoassays. These methods may suffer from low efficiency in matrices containing interfering substances, or from false positive results due to antibody cross reactivity, with highly homologous proteins. In this study, we have developed a simple, rapid, sensitive, and selective mass spectrometry assay, for the identification of ricin in complex environmental samples. This assay involves three main stages: (a) Ricin affinity capture by commercial lactamyl-agarose (LA) beads. (b) Tryptic digestion. (c) LC-MS/MS (MRM) analysis of tryptic fragments. The assay was validated using 60 diverse environmental samples such as soil, asphalt, and vegetation, taken from various geographic regions. The assay's selectivity was established in the presence of high concentrations of competing lectin interferences. Based on our findings, we have defined strict criteria for unambiguous identification of ricin. Our novel method, which combines affinity capture beads followed by MRM-based analysis, enabled the identification of 1 ppb ricin spiked into complex environmental matrices. This methodology has the potential to be extended for the identification of ricin in body fluids from individuals exposed (deliberately or accidentally) to the toxin, contaminated food or for the detection of the entire family of RIP-II toxins, by applying multiplex format.
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Affiliation(s)
- Liron Feldberg
- Department of Analytical Chemistry, Israel Institute for Biological Research, Ness Ziona, Israel
| | - Ofir Schuster
- Department of Infectious Diseases, Israel Institute for Biological Research, Ness Ziona, Israel
| | - Eytan Elhanany
- Department of Biochemistry, Israel Institute for Biological Research, Ness Ziona, Israel
| | - Orly Laskar
- Department of Infectious Diseases, Israel Institute for Biological Research, Ness Ziona, Israel
| | - Shmuel Yitzhaki
- Department of Infectious Diseases, Israel Institute for Biological Research, Ness Ziona, Israel
| | - Sigalit Gura
- Department of Analytical Chemistry, Israel Institute for Biological Research, Ness Ziona, Israel
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9
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Acetonitrile-assisted enzymatic digestion can facilitate the bottom-up identification of proteins of cancer origin. Anal Biochem 2019; 570:1-4. [DOI: 10.1016/j.ab.2019.01.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Revised: 01/09/2019] [Accepted: 01/14/2019] [Indexed: 02/07/2023]
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10
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Ladner Y, Mas S, Coussot G, Montels J, Perrin C. In-line tryptic digestion of therapeutic molecules by capillary electrophoresis with temperature control. Talanta 2019; 193:146-151. [DOI: 10.1016/j.talanta.2018.09.090] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Revised: 09/20/2018] [Accepted: 09/24/2018] [Indexed: 12/26/2022]
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Perspectives on potentiating immunocapture-LC-MS for the bioanalysis of biotherapeutics and biomarkers. Bioanalysis 2018; 10:1679-1690. [PMID: 30371100 DOI: 10.4155/bio-2018-0205] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The integration of ligand-binding assay and LC-MS/MS (immunocapture-LC-MS) has unleashed the combined advantages of both powerful techniques for addressing the ever increasing bioanalytical challenges for biotherapeutics and biomarker assays. The highly specific, selective and sensitive characteristics of the immunocapture-LC-MS-based assays have enabled the determination of biotherapeutics and biomarkers in biomatrices with ease of method development, less requirements on key reagents as well as structural specificity for endogenous and engineered biomolecules. In addition, the versatile immunocapture-LC-MS technology has expanded into many challenging areas to enhance mechanistic studies of drug interactions with their targets. This paper intends to summarize our perspectives on enhancing the use of immunocapture-LC-MS in drug discovery and development for emerging new modalities.
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Hansbauer EM, Worbs S, Volland H, Simon S, Junot C, Fenaille F, Dorner BG, Becher F. Rapid Detection of Abrin Toxin and Its Isoforms in Complex Matrices by Immuno-Extraction and Quantitative High Resolution Targeted Mass Spectrometry. Anal Chem 2017; 89:11719-11727. [PMID: 28984440 DOI: 10.1021/acs.analchem.7b03189] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Abrin expressed by the tropical plant Abrus precatorius is highly dangerous with an estimated human lethal dose of 0.1-1 μg/kg body weight. Due to the potential misuse as a biothreat agent, abrin is in the focus of surveillance. Fast and reliable methods are therefore of great importance for early identification. Here, we have developed an innovative and rapid multiepitope immuno-mass spectrometry workflow which is capable of unambiguously differentiating abrin and its isoforms in complex matrices. Toxin-containing samples were incubated with magnetic beads coated with multiple abrin-specific antibodies, thereby concentrating and extracting all the isoforms. Using an ultrasonic bath for digestion enhancement, on-bead trypsin digestion was optimized to obtain efficient and reproducible peptide recovery in only 30 min. Improvements made to the workflow reduced total analysis time to less than 3 h. A large panel of common and isoform-specific peptides was monitored by multiplex LC-MS/MS through the parallel reaction monitoring mode on a quadrupole-Orbitrap high resolution mass spectrometer. Additionally, absolute quantification was accomplished by isotope dilution with labeled AQUA peptides. The newly established method was demonstrated as being sensitive and reproducible with quantification limits in the low ng/mL range in various food and clinical matrices for the isoforms of abrin and also the closely related, less toxic Abrus precatorius agglutinin. This method allows for the first time the rapid detection, differentiation, and simultaneous quantification of abrin and its isoforms by mass spectrometry.
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Affiliation(s)
- Eva-Maria Hansbauer
- Service de Pharmacologie et Immunoanalyse (SPI), Laboratoire d'Etude du Métabolisme des Médicaments, CEA, INRA, Université Paris Saclay , F-91191 Gif-sur-Yvette cedex, France
| | - Sylvia Worbs
- Biological Toxins, Centre for Biological Threats and Special Pathogens, Robert Koch Institute , Berlin, Germany
| | - Hervé Volland
- Service de Pharmacologie et Immunoanalyse (SPI), Laboratoire d'Etudes et de Recherches en Immunoanalyse, CEA, INRA, Université Paris Saclay , F-91191 Gif-sur-Yvette cedex, France
| | - Stéphanie Simon
- Service de Pharmacologie et Immunoanalyse (SPI), Laboratoire d'Etudes et de Recherches en Immunoanalyse, CEA, INRA, Université Paris Saclay , F-91191 Gif-sur-Yvette cedex, France
| | - Christophe Junot
- Service de Pharmacologie et Immunoanalyse (SPI), CEA, INRA, Université Paris Saclay , F-91191 Gif-sur-Yvette cedex, France
| | - François Fenaille
- Service de Pharmacologie et Immunoanalyse (SPI), Laboratoire d'Etude du Métabolisme des Médicaments, CEA, INRA, Université Paris Saclay , F-91191 Gif-sur-Yvette cedex, France
| | - Brigitte G Dorner
- Biological Toxins, Centre for Biological Threats and Special Pathogens, Robert Koch Institute , Berlin, Germany
| | - François Becher
- Service de Pharmacologie et Immunoanalyse (SPI), Laboratoire d'Etude du Métabolisme des Médicaments, CEA, INRA, Université Paris Saclay , F-91191 Gif-sur-Yvette cedex, France
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Chen WQ, Obermayr P, Černigoj U, Vidič J, Panić-Janković T, Mitulović G. Immobilized monolithic enzymatic reactor and its application for analysis of in-vitro fertilization media samples. Electrophoresis 2017; 38:2957-2964. [DOI: 10.1002/elps.201700197] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Revised: 05/29/2017] [Accepted: 06/04/2017] [Indexed: 12/12/2022]
Affiliation(s)
- Wei-Qiang Chen
- Clinical Institute of Laboratory Medicine; Medical University of Vienna; Vienna Austria
| | | | | | - Jana Vidič
- BIA Separations d.o.o; Ajdovščina Slovenia
| | - Tanta Panić-Janković
- Clinical Institute of Laboratory Medicine; Medical University of Vienna; Vienna Austria
| | - Goran Mitulović
- Clinical Institute of Laboratory Medicine; Medical University of Vienna; Vienna Austria
- Proteomics Core Facility; Medical University of Vienna; Vienna Austria
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Fakhry SS, Jessim AI, Azeez AZ, Alwash SJ, Abdulbaqi AA. Protein binding pigment by Bacillus pumilus SF214. KARBALA INTERNATIONAL JOURNAL OF MODERN SCIENCE 2017. [DOI: 10.1016/j.kijoms.2017.04.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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15
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Cheng S, Wang J, Cai Y, Loo JA, Chen H. Enhancing Performance of Liquid Sample Desorption Electrospray Ionization Mass Spectrometry Using Trap and Capillary Columns. INTERNATIONAL JOURNAL OF MASS SPECTROMETRY 2015; 392:73-79. [PMID: 27239159 PMCID: PMC4878830 DOI: 10.1016/j.ijms.2015.09.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Desorption electrospray ionization mass spectrometry (DESI-MS) is a recent and important advance in the field that has extensive applications in surface analysis of solid samples but has also been extended to analysis of liquid samples. The liquid sample DESI typically employs a piece of fused silica capillary to transfer liquid sample for ionization. In this study, we present the improvement of liquid sample DESI-MS by replacing the sample transfer silica capillary with a trap column filled with chromatographic stationary phase materials (e.g., C4, C18). This type of trap column/liquid sample DESI can be used for trace analysis of organics and biomolecules such as proteins/peptides (in nM concentration) in high salt content matrices. Furthermore, when the sample transfer capillary is modified with enzyme covalently bound on its inside capillary wall, fast digestion (< 6 min) of proteins such as phosphoproteins can be achieved and the online digested proteins can be directly ionized using DESI with high sensitivity. The latter is ascribed to the freedom to select favorable spray solvent for the DESI analysis. Our data shows that liquid sample DESI-MS with a modified sample transfer capillary has significantly expanded its utility in bioanalysis.
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Affiliation(s)
- Si Cheng
- Center for Intelligent Chemical Instrumentation, Department of Chemistry and Biochemistry, Edison Biotechnology Institute, Ohio University, Athens, OH, 45701, USA
| | - Jun Wang
- Center for Intelligent Chemical Instrumentation, Department of Chemistry and Biochemistry, Edison Biotechnology Institute, Ohio University, Athens, OH, 45701, USA ; Department of forensic science, Jiangsu Police Institute, Nanjing, Jiang Su, 210031, China
| | - Yi Cai
- Center for Intelligent Chemical Instrumentation, Department of Chemistry and Biochemistry, Edison Biotechnology Institute, Ohio University, Athens, OH, 45701, USA
| | - Joseph A Loo
- Department of Chemistry and Biochemistry, Department of Biological Chemistry, David Geffen School of Medicine at UCLA, and UCLA/DOE Institute for Genomics and Proteomics, University of California-Los Angeles, Los Angeles, California 90095, USA
| | - Hao Chen
- Center for Intelligent Chemical Instrumentation, Department of Chemistry and Biochemistry, Edison Biotechnology Institute, Ohio University, Athens, OH, 45701, USA
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LIU FJ, YE ML, PAN YB, ZOU HF. High Concentration Trypsin Assisted Fast In-Gel Digestion for Phosphoproteome Analysis. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2015. [DOI: 10.1016/s1872-2040(15)60864-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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17
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Dittrich J, Becker S, Hecht M, Ceglarek U. Sample preparation strategies for targeted proteomics via proteotypic peptides in human blood using liquid chromatography tandem mass spectrometry. Proteomics Clin Appl 2014; 9:5-16. [PMID: 25418444 DOI: 10.1002/prca.201400121] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2014] [Revised: 10/29/2014] [Accepted: 11/18/2014] [Indexed: 11/07/2022]
Abstract
The simultaneous quantification of protein concentrations via proteotypic peptides in human blood by liquid chromatography coupled to quadrupole MS/MS is an important field of bioanalytical research with a high potential for routine diagnostic applications. This review summarizes currently available sample preparation procedures and trends for absolute protein quantification in blood using LC-MS/MS. It discusses approaches of transferring established qualitative protocols to a quantitative analysis regarding their reliability and reproducibility. Techniques used to enhance method sensitivity such as the depletion of high-abundant proteins or the immunoaffinity enrichment of proteins and peptides are described. Furthermore, workflows for (i) protein denaturation, (ii) disulfide bridge reduction and (iii) thiol alkylation as well as (iv) enzymatic digestion for absolute protein quantification are presented. The main focus is on the tryptic digestion as a bottleneck of protein quantification via proteotypic peptides. Conclusively, requirements for a high-throughput application are discussed.
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Affiliation(s)
- Julia Dittrich
- Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, University Hospital Leipzig, Leipzig, Germany; LIFE - Leipzig Research Center for Civilization Diseases, University Leipzig, Leipzig, Germany
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Liu F, Ye M, Pan Y, Zhang Y, Bian Y, Sun Z, Zhu J, Cheng K, Zou H. Integration of cell lysis, protein extraction, and digestion into one step for ultrafast sample preparation for phosphoproteome analysis. Anal Chem 2014; 86:6786-91. [PMID: 24958348 DOI: 10.1021/ac5002146] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Conventional sample preparation protocols for phosphoproteome analysis require multiple time-consuming and labor-intensive steps, including cell lysis, protein extraction, protein digestion, and phosphopeptide enrichment. In this study, we found that the presence of a large amount of trypsin in the sample did not interfere with phosphopeptide enrichment and subsequent LC-MS/MS analysis. Taking advantage of fast digestion achieved with high trypsin-to-protein ratio, we developed a novel concurrent lysis-digestion method for phosphoproteome analysis. In this method, the harvested cells were first placed in a lysis buffer containing a huge amount of trypsin. After ultrasonication, the cells were lysed and the proteins were efficiently digested into peptides within one step. Thereafter, tryptic digest was subjected to phosphopeptide enrichment, in which unphosphorylated peptides, trypsin, and other components incompatible with LC-MS/MS analysis were removed. Compared with conventional methods, better phosphoproteome coverage was achieved in this new one-step method. Because protein solubilization and cell lysis were facilitated by fast protein digestion, the complete transformation of cell pellets into the peptide mixture could be finished within 25 min, while it would take at least 16 h for conventional methods. Hence, our method, which integrated cell lysis, protein extraction, and protein digestion into one step, is rapid and convenient. It is expected to have broad applications in phosphoproteomics analysis.
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Affiliation(s)
- Fangjie Liu
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences , Dalian, Liaoning 116023, China
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Araújo J, Oliveira E, Kouvonen P, Corthals G, Lodeiro C, Santos H, Capelo J. A journey through PROTEOSONICS. Talanta 2014; 121:71-80. [DOI: 10.1016/j.talanta.2013.12.054] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2013] [Revised: 12/16/2013] [Accepted: 12/24/2013] [Indexed: 10/25/2022]
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Zheng Q, Zhang H, Chen H. Integration of online digestion and electrolytic reduction with mass spectrometry for rapid disulfide-containing protein structural analysis. INTERNATIONAL JOURNAL OF MASS SPECTROMETRY 2013; 353:84-92. [PMID: 25419170 PMCID: PMC4240030 DOI: 10.1016/j.ijms.2013.04.009] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Bottom-up structural analysis of disulfide-bond containing proteins usually involves time-consuming offline enzymatic digestion, chemical reduction and thiol protection prior to mass spectrometric detection, which takes many hours. This paper presents an expedited bottom-up approach, employing desorption electrospray ionization-mass spectrometry (DESI-MS) coupled with online pepsin digestion and online electrochemical reduction of disulfide bonds. Peptides are generated in high digestion yield as its precursor protein in acidic aqueous solution flows through a pepsin column, which can undergo direct electrolysis. The electrolytic behaviors of peptides, as online monitored by DESI-MS, suggest the presence or absence of disulfide bonds in the peptides, and also provide information to relate disulfide bond-containing peptide precursors to their corresponding reduced products. Furthermore, selective electrolysis simply using different reduction potentials can be adopted to generate either partially or fully reduced peptides to assist disulfide bond mapping. In addition, it turns out that DESI is suitable for ionizing peptides in water without organic solvent additives (organic solvent additives would not be compatible with the use of pepsin column). The feasibility of this method was demonstrated using insulin, a protein carrying three pairs of disulfide-bonds as an example, in which all disulfide bond linkages and most of the protein sequence were successfully determined. Strikingly, this method shortens the sample digestion, reduction and MS detection from hours to less than 7 min, which could be of high value in high-throughput proteomics research.
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Affiliation(s)
- Qiuling Zheng
- Center for Intelligent Chemical Instrumentation, Department of Chemistry and Biochemistry, Ohio University, Athens, OH 45701, USA
| | - Hao Zhang
- Department of Chemistry, Washington University, St. Louis, MO 63130, USA
- Corresponding author. Tel.: +1 314 935 7486
| | - Hao Chen
- Center for Intelligent Chemical Instrumentation, Department of Chemistry and Biochemistry, Ohio University, Athens, OH 45701, USA
- Corresponding author. Tel.: +1 740 593 0719; fax: +1 740 597 3157
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21
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Kalli A, Smith GT, Sweredoski MJ, Hess S. Evaluation and optimization of mass spectrometric settings during data-dependent acquisition mode: focus on LTQ-Orbitrap mass analyzers. J Proteome Res 2013; 12:3071-86. [PMID: 23642296 DOI: 10.1021/pr3011588] [Citation(s) in RCA: 114] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Mass-spectrometry-based proteomics has evolved as the preferred method for the analysis of complex proteomes. Undoubtedly, recent advances in mass spectrometry instrumentation have greatly enhanced proteomic analysis. A popular instrument platform in proteomics research is the LTQ-Orbitrap mass analyzer. In this tutorial, we discuss the significance of evaluating and optimizing mass spectrometric settings on the LTQ-Orbitrap during CID data-dependent acquisition (DDA) mode to improve protein and peptide identification rates. We focus on those MS and MS/MS parameters that have been systematically examined and evaluated by several researchers and are commonly used during DDA. More specifically, we discuss the effect of mass resolving power, preview mode for FTMS scan, monoisotopic precursor selection, signal threshold for triggering MS/MS events, number of microscans per MS/MS scan, number of MS/MS events, automatic gain control target value (ion population) for MS and MS/MS, maximum ion injection time for MS/MS, rapid and normal scan rate, and prediction of ion injection time. We furthermore present data from the latest generation LTQ-Orbitrap system, the Orbitrap Elite, along with recommended MS and MS/MS parameters. The Orbitrap Elite outperforms the Orbitrap Classic in terms of scan speed, sensitivity, dynamic range, and resolving power and results in higher identification rates. Several of the optimized MS parameters determined on the LTQ-Orbitrap Classic and XL were easily transferable to the Orbitrap Elite, whereas others needed to be reevaluated. Finally, the Q Exactive and HCD are briefly discussed, as well as sample preparation, LC-optimization, and bioinformatics analysis. We hope this tutorial will serve as guidance for researchers new to the field of proteomics and assist in achieving optimal results.
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Affiliation(s)
- Anastasia Kalli
- Proteome Exploration Laboratory, Division of Biology, Beckman Institute, California Institute of Technology, Pasadena, California 91125, USA
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22
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Kim JS, Lee Y, Lee MY, Shin J, Han JM, Yang EG, Yu MH, Kim S, Hwang D, Lee C. Multiple reaction monitoring of multiple low-abundance transcription factors in whole lung cancer cell lysates. J Proteome Res 2013; 12:2582-96. [PMID: 23586733 DOI: 10.1021/pr3011414] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Lung cancer-related transcription factors (TFs) were identified by integrating previously reported genomic, transcriptomic, and proteomic data and were quantified by multiple reaction monitoring (MRM) in various cell lines. All experiments were performed without affinity depletion or subfractionation of cell lysates. Since the target proteins were expected to be present in low abundance, we experimentally optimized MRM transition parameters with chemically synthesized peptides. Quantitation was based on stable isotope-labeled standard peptides (SIS peptides). Out of 288 MRM measurements (36 peptides representing 28 TFs × 8 cell lines), 241 were successfully obtained within a quantitation limit of 15 amol, 221 measurements (91.7%) showed coefficients of variation (CVs) of ≤ 20%, and 149 (61.8%) showed CVs of ≤ 10%, quantifying as low as 19.4 amol/μg protein for STAT2 with a CV of 6.3% in an A549 cell. Comparisons between MRM measurements and levels of the corresponding mRNAs revealed linear, nonlinear, or no relationship between protein and mRNA levels, indicating the need for an MRM assay. An integrative analysis of MRM and gene expression profiles from doxorubicin-resistant H69AR and sensitive H69 cells further showed that 14 differentially expressed TFs, such as STAT1 and SMAD4, regulated genes associated with drug resistance and cell differentiation-related processes. Thus, the analytical performance of MRM for the quantitation of low abundance TFs suggests its usefulness for biological application.
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Affiliation(s)
- Jun Seok Kim
- Theragnosis Research Center, Korea Institute of Science and Technology, Seoul, Korea
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Switzar L, Giera M, Niessen WMA. Protein Digestion: An Overview of the Available Techniques and Recent Developments. J Proteome Res 2013; 12:1067-77. [DOI: 10.1021/pr301201x] [Citation(s) in RCA: 164] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Linda Switzar
- AIMMS Division of BioMolecular
Analysis, Faculty of Sciences, VU University Amsterdam, De Boelelaan 1083, 1081 HV, Amsterdam, The Netherlands
| | - Martin Giera
- Division of Molecular Cell Physiology,
Faculty of Earth and Life Sciences, VU University Amsterdam, De Boelelaan 1085, 1081 HV, Amsterdam, The Netherlands
- Biomolecular Mass Spectrometry
Unit, Department of Parasitology, Leiden University Medical Center, P.O. Box 9600, 2300 RC Leiden, The Netherlands
| | - Wilfried M. A. Niessen
- AIMMS Division of BioMolecular
Analysis, Faculty of Sciences, VU University Amsterdam, De Boelelaan 1083, 1081 HV, Amsterdam, The Netherlands
- hyphen MassSpec, de Wetstraat 8, 2332 XT Leiden, The Netherlands
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Drabik A, Bodzon-Kulakowska A, Suder P. Application of the ETD/PTR reactions in top-down proteomics as a faster alternative to bottom-up nanoLC-MS/MS protein identification. JOURNAL OF MASS SPECTROMETRY : JMS 2012; 47:1347-1352. [PMID: 23019167 DOI: 10.1002/jms.3086] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Our goal was to compare two popular analytical techniques used nowadays in proteomic investigations for proteins/peptides sequencing and identification, a widely used nanoLC-MS/MS approach applied in the bottom-up proteomics and electron transfer dissociation/proton transfer reaction fragmentation preferably used when top-down strategy is applied. Comparison was carried out with the aid of the ESI-quadrupole ion-trap instrument using the following criteria: total time of analysis including sample preparation, sequence coverage, Mascot scoring, capability to detect modifications, quality of the results as a function of protein molecular weight and sample consumption.
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