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Truong CM, Jair YC, Chen HP, Chen WC, Liu YH, Chen PC, Chen PS. Streamlining regular liquid chromatography with MALDI-TOF MS and NMR spectroscopy using automatic full-contact splitless spotting interface and flash-tap fractioning collection. Anal Chim Acta 2024; 1298:342401. [PMID: 38462340 DOI: 10.1016/j.aca.2024.342401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 02/18/2024] [Accepted: 02/20/2024] [Indexed: 03/12/2024]
Abstract
BACKGROUND High-resolution matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS) and nuclear magnetic resonance (NMR) spectroscopy are powerful tools to identify unknown psychoactive substances. However, in complex matrices, trace levels of unknown substances usually require additional fractionation and concentration. Specialized liquid chromatography systems are necessary for both techniques. The small flow rate of nano LC, typically paired with MALDI-TOF MS, often results in prolonged fractionation times. Conversely, the larger flow rate of semi-preparative LC, used for NMR analysis, can be time-consuming and labor-intensive when concentrating samples. To address these issues, we developed an integrated automatic system that integrated to regular LC. RESULT Automatic spot collector (ASC) and automatic fraction collector (AFC) were present in this study. The ASC utilized in-line matrix mixing, full-contact spotting and real time heating (50 °C), achieving great capacity of 5 μL droplet on MALDI plate, high recovery (76-116%) and rapid evaporation in 2 min. The analytes were concentrated 4-8 times, forming even crystallization, reaching the detection limit at the concentration of 50 μg L-1 for 12 psychoactive substances in urine. The AFC utilizes flexible tubing which flash-tapped the microtube's upper rim (3 mm depth) instead of reaching the bottom. This method prevents sample loss and minimizes the robotic arm's movement, providing a high fractionating speed at 6 s 12 psychoactive compounds were fractionated in a single round analysis (recovery: 81%-114%). Methamphetamine and nitrazepam obtained from drug-laced coffee samples were successful analyzed with photodiode array (PDA) after one AFC round and NMR after five rounds. SIGNIFICANCE The ASC device employed real-time heating, in-line matrix mixing, and full-contact spotting to facilitate the samples spotting onto the MALDI target plate, thereby enhancing detection sensitivity in low-concentration and complex samples. The AFC device utilized the novel flash-tapping method to achieve rapid fractionation and high recovery rate. These devices were assembled using commercially available components, making them affordable (400 USD) for most laboratories while still meeting the required performance for advanced commercialized systems.
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Affiliation(s)
- Chi-Minh Truong
- Department of Mechanical Engineering, National Taiwan University of Science and Technology, Taipei, Taiwan
| | - Yung-Cheng Jair
- Institute of Toxicology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Hong-Po Chen
- Department of Chemistry, National Taiwan Normal University, Taipei, Taiwan
| | - Wei-Chih Chen
- Department of Mechanical Engineering, National Taiwan University of Science and Technology, Taipei, Taiwan
| | - Yi-Hsin Liu
- Department of Chemistry, National Taiwan Normal University, Taipei, Taiwan
| | - Pin-Chuan Chen
- Department of Mechanical Engineering, National Taiwan University of Science and Technology, Taipei, Taiwan.
| | - Pai-Shan Chen
- Institute of Toxicology, College of Medicine, National Taiwan University, Taipei, Taiwan.
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Ferrick L, Lee YSL, Gardner DK. Reducing time to pregnancy and facilitating the birth of healthy children through functional analysis of embryo physiology†. Biol Reprod 2020; 101:1124-1139. [PMID: 30649216 DOI: 10.1093/biolre/ioz005] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Revised: 12/21/2018] [Accepted: 01/09/2019] [Indexed: 12/12/2022] Open
Abstract
An ever-increasing number of couples rely on assisted reproductive technologies (ART) in order to conceive a child. Although advances in embryo culture have led to increases in the success rates of clinical ART, it often takes more than one treatment cycle to conceive a child. Ensuring patients conceive as soon as possible with a healthy embryo is a priority for reproductive medicine. Currently, selection of embryos for transfer relies predominantly on the morphological assessment of the preimplantation embryo; however, morphology is not an absolute link to embryo physiology, nor the health of the resulting child. Non-invasive quantitation of individual embryo physiology, a key regulator of both embryo viability and health, could provide valuable information to assist in the selection of the most viable embryo for transfer, hence reducing the time to pregnancy. Further, according to the Barker Hypothesis, the environment to which a fetus is exposed to during gestation affects subsequent offspring health. If the environment of the preimplantation period is capable of affecting metabolism, which in turn will affect gene expression through the metaboloepigenetic link, then assessment of embryo metabolism should represent an indirect measure of future offspring health. Previously, the term viable embryo has been used in association with the potential of an embryo to establish a pregnancy. Here, we propose the term healthy embryo to reflect the capacity of that embryo to lead to a healthy child and adult.
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Affiliation(s)
- Laura Ferrick
- School of BioSciences, University of Melbourne, VIC, Australia
| | | | - David K Gardner
- School of BioSciences, University of Melbourne, VIC, Australia.,Melbourne IVF, East Melbourne, VIC, Australia
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3
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Zietek BM, Still KBM, Jaschusch K, Bruyneel B, Ariese F, Brouwer TJF, Luger M, Limburg RJ, Rosier JC, V Iperen DJ, Casewell NR, Somsen GW, Kool J. Bioactivity Profiling of Small-Volume Samples by Nano Liquid Chromatography Coupled to Microarray Bioassaying Using High-Resolution Fractionation. Anal Chem 2019; 91:10458-10466. [PMID: 31373797 PMCID: PMC6706796 DOI: 10.1021/acs.analchem.9b01261] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
![]()
High-throughput
screening platforms for the identification of bioactive
compounds in mixtures have become important tools in the drug discovery
process. Miniaturization of such screening systems may overcome problems
associated with small sample volumes and enhance throughput and sensitivity.
Here we present a new screening platform, coined picofractionation
analytics, which encompasses microarray bioassays and mass spectrometry
(MS) of components from minute amounts of samples after their nano
liquid chromatographic (nanoLC) separation. Herein, nanoLC was coupled
to a low-volume liquid dispenser equipped with pressure-fed solenoid
valves, enabling 50-nL volumes of column effluent (300 nL/min) to
be discretely deposited on a glass slide. The resulting fractions
were dried and subsequently bioassayed by sequential printing of nL-volumes
of reagents on top of the spots. Unwanted evaporation of bioassay
liquids was circumvented by employing mineral oil droplets. A fluorescence
microscope was used for assay readout in kinetic mode. Bioassay data
were correlated to MS data obtained using the same nanoLC conditions
in order to assign bioactives. The platform provides the possibility
of freely choosing a wide diversity of bioassay formats, including
those requiring long incubation times. The new method was compared
to a standard bioassay approach, and its applicability was demonstrated
by screening plasmin inhibitors and fibrinolytic bioactives from mixtures
of standards and snake venoms, revealing active peptides and coagulopathic
proteases.
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Affiliation(s)
- Barbara M Zietek
- Division of BioAnalytical Chemistry, Amsterdam Institute of Molecules, Medicines and Systems , Vrije Universiteit Amsterdam , Amsterdam 1081 HZ , The Netherlands
| | - Kristina B M Still
- Division of BioAnalytical Chemistry, Amsterdam Institute of Molecules, Medicines and Systems , Vrije Universiteit Amsterdam , Amsterdam 1081 HZ , The Netherlands
| | - Kevin Jaschusch
- Division of BioAnalytical Chemistry, Amsterdam Institute of Molecules, Medicines and Systems , Vrije Universiteit Amsterdam , Amsterdam 1081 HZ , The Netherlands
| | - Ben Bruyneel
- Division of BioAnalytical Chemistry, Amsterdam Institute of Molecules, Medicines and Systems , Vrije Universiteit Amsterdam , Amsterdam 1081 HZ , The Netherlands
| | - Freek Ariese
- LaserLaB , Vrije Universiteit Amsterdam , Amsterdam 1081 HZ , The Netherlands
| | - Tinco J F Brouwer
- Electronic Engineering , Vrije Universiteit Amsterdam , Amsterdam 1081 HZ , The Netherlands
| | - Matthijs Luger
- Electronic Engineering , Vrije Universiteit Amsterdam , Amsterdam 1081 HZ , The Netherlands
| | - Rob J Limburg
- Electronic Engineering , Vrije Universiteit Amsterdam , Amsterdam 1081 HZ , The Netherlands
| | - Joost C Rosier
- Fine Mechanics and Engineering Beta-VU , Vrije Universiteit Amsterdam , Amsterdam 1081 HZ , The Netherlands
| | - Dick J V Iperen
- Fine Mechanics and Engineering Beta-VU , Vrije Universiteit Amsterdam , Amsterdam 1081 HZ , The Netherlands
| | - Nicholas R Casewell
- Centre for Snakebite Research & Interventions , Liverpool School of Tropical Medicine , Pembroke Place , Liverpool L3 5QA , U.K.,Centre for Drugs and Diagnostics , Liverpool School of Tropical Medicine , Pembroke Place , Liverpool L3 5QA , U.K
| | - Govert W Somsen
- Division of BioAnalytical Chemistry, Amsterdam Institute of Molecules, Medicines and Systems , Vrije Universiteit Amsterdam , Amsterdam 1081 HZ , The Netherlands
| | - Jeroen Kool
- Division of BioAnalytical Chemistry, Amsterdam Institute of Molecules, Medicines and Systems , Vrije Universiteit Amsterdam , Amsterdam 1081 HZ , The Netherlands
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Zhu J, Warner E, Parikh ND, Lubman DM. Glycoproteomic markers of hepatocellular carcinoma-mass spectrometry based approaches. MASS SPECTROMETRY REVIEWS 2019; 38:265-290. [PMID: 30472795 PMCID: PMC6535140 DOI: 10.1002/mas.21583] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Accepted: 10/19/2018] [Indexed: 05/03/2023]
Abstract
Hepatocellular carcinoma (HCC) is the third most-common cause of cancer-related death worldwide. Most cases of HCC develop in patients that already have liver cirrhosis and have been recommended for surveillance for an early onset of HCC. Cirrhosis is the final common pathway for several etiologies of liver disease, including hepatitis B and C, alcohol, and increasingly non-alcoholic fatty liver disease. Only 20-30% of patients with HCC are eligible for curative therapy due primarily to inadequate early-detection strategies. Reliable, accurate biomarkers for HCC early detection provide the highest likelihood of curative therapy and survival; however, current early-detection methods that use abdominal ultrasound and serum alpha fetoprotein are inadequate due to poor adherence and limited sensitivity and specificity. There is an urgent need for convenient and highly accurate validated biomarkers for HCC early detection. The theme of this review is the development of new methods to discover glycoprotein-based markers for detection of HCC with mass spectrometry approaches. We outline the non-mass spectrometry based methods that have been used to discover HCC markers including immunoassays, capillary electrophoresis, 2-D gel electrophoresis, and lectin-FLISA assays. We describe the development and results of mass spectrometry-based assays for glycan screening based on either MALDI-MS or ESI analysis. These analyses might be based on the glycan content of serum or on glycan screening for target molecules from serum. We describe some of the specific markers that have been developed as a result, including for proteins such as Haptoglobin, Hemopexin, Kininogen, and others. We discuss the potential role for other technologies, including PGC chromatography and ion mobility, to separate isoforms of glycan markers. Analyses of glycopeptides based on new technologies and innovative softwares are described and also their potential role in discovery of markers of HCC. These technologies include new fragmentation methods such as EThcD and stepped HCD, which can identify large numbers of glycopeptide structures from serum. The key role of lectin extraction in various assays for intact glycopeptides or their truncated versions is also described, where various core-fucosylated and hyperfucosylated glycopeptides have been identified as potential markers of HCC. Finally, we describe the role of LC-MRMs or lectin-FLISA MRMs as a means to validate these glycoprotein markers from patient samples. These technological advancements in mass spectrometry have the potential to lead to novel biomarkers to improve the early detection of HCC.
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Affiliation(s)
- Jianhui Zhu
- Department of Surgery, The University of Michigan, Ann Arbor 48109, Michigan
| | - Elisa Warner
- Department of Surgery, The University of Michigan, Ann Arbor 48109, Michigan
| | - Neehar D. Parikh
- Department of Internal Medicine, The University of Michigan, Ann Arbor 48109, Michigan
| | - David M. Lubman
- Department of Surgery, The University of Michigan, Ann Arbor 48109, Michigan
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5
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Küster SK, Pabst M, Jefimovs K, Zenobi R, Dittrich PS. High-resolution droplet-based fractionation of nano-LC separations onto microarrays for MALDI-MS analysis. Anal Chem 2014; 86:4848-55. [PMID: 24725135 DOI: 10.1021/ac4041982] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
We present a robust droplet-based device, which enables the fractionation of ultralow flow rate nanoflow liquid chromatography (nano-LC) eluate streams at high frequencies and high peak resolution. This is achieved by directly interfacing the separation column to a micro T-junction, where the eluate stream is compartmentalized into picoliter droplets. This immediate compartmentalization prevents peak dispersion during eluate transport and conserves the chromatographic performance. Subsequently, nanoliter eluate fractions are collected at a rate of one fraction per second on a high-density microarray to retain the separation with high temporal resolution. Chromatographic separations of up to 45 min runtime can thus be archived on a single microarray possessing 2700 sample spots. The performance of this device is demonstrated by fractionating the separation of a tryptic digest of a known protein mixture onto the microarray chip and subsequently analyzing the sample archive using matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS). Resulting peak widths are found to be significantly reduced compared to standard continuous flow spotting technologies as well as in comparison to a conventional nano-LC-electrospray ionization-mass spectrometry interface. Moreover, we demonstrate the advantage of our high-definition nanofractionation device by applying two different MALDI matrices to all collected fractions in an alternating fashion. Since the information that is obtained from a MALDI-MS measurement depends on the choice of MALDI matrix, we can extract complementary information from neighboring spots containing almost identical composition but different matrices.
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Affiliation(s)
- Simon K Küster
- Department of Chemistry and Applied Biosciences, ETH Zürich , Vladimir-Prelog-Weg 3, 8093 Zürich, Switzerland
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6
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Hioki Y, Tanimura R, Iwamoto S, Tanaka K. Nano-LC/MALDI-MS Using a Column-Integrated Spotting Probe for Analysis of Complex Biomolecule Samples. Anal Chem 2014; 86:2549-58. [DOI: 10.1021/ac4037069] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Yusaku Hioki
- Koichi Tanaka Laboratory
of Advanced Science and Technology, Shimadzu Corporation, 1, Nishinokyo-Kuwabara-cho,
Nakagyo-ku, Kyoto 604-8511, Japan
| | - Ritsuko Tanimura
- Koichi Tanaka Laboratory
of Advanced Science and Technology, Shimadzu Corporation, 1, Nishinokyo-Kuwabara-cho,
Nakagyo-ku, Kyoto 604-8511, Japan
| | - Shinichi Iwamoto
- Koichi Tanaka Laboratory
of Advanced Science and Technology, Shimadzu Corporation, 1, Nishinokyo-Kuwabara-cho,
Nakagyo-ku, Kyoto 604-8511, Japan
| | - Koichi Tanaka
- Koichi Tanaka Laboratory
of Advanced Science and Technology, Shimadzu Corporation, 1, Nishinokyo-Kuwabara-cho,
Nakagyo-ku, Kyoto 604-8511, Japan
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7
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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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8
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Condina MR, Gustafsson JOR, Klingler-Hoffmann M, Bagley CJ, McColl SR, Hoffmann P. EZYprep LC-coupled MALDI-TOF/TOF MS: an improved matrix spray application for phosphopeptide characterisation. Proteomics 2010; 10:2516-30. [PMID: 20432483 DOI: 10.1002/pmic.200900800] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
The quality of MALDI-TOF mass spectrometric analysis is highly dependent on the matrix and its deposition strategy. Although different matrix-deposition methods have specific advantages, one major problem in the field of proteomics, particularly with respect to quantitation, is reproducibility between users or laboratories. Compounding this is the varying crystal homogeneity of matrices depending on the deposition strategy used. Here, we describe a novel optimised matrix-deposition strategy for LC-MALDI-TOF/TOF MS using an automated instrument that produces a nebulised matrix "mist" under controlled atmospheric conditions. Comparisons of this with previously reported strategies showed the method to be advantageous for the atypical matrix, 2,5-DHB, and improved phosphopeptide ionisation when compared with deposition strategies for CHCA. This optimised DHB matrix-deposition strategy with LC-MALDI-TOF/TOF MS, termed EZYprep LC, was subsequently optimised for phosphoproteome analysis and compared to LC-ESI-IT-MS and a previously reported approach for phosphotyrosine identification and characterisation. These methods were used to map phosphorylation on epidermal growth factor-stimulated epidermal growth factor receptor to gauge the sensitivity of the proposed method. EZYprep DHB LC-MALDI-TOF/TOF MS was able to identify more phosphopeptides and characterise more phosphorylation sites than the other two proteomic strategies, thus proving to be a sensitive approach for phosphoproteome analysis.
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Affiliation(s)
- Mark R Condina
- School of Molecular and Biomedical Science, The University of Adelaide, Adelaide, SA, Australia
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9
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Peš O, Preisler J. Off-line coupling of microcolumn separations to desorption mass spectrometry. J Chromatogr A 2010; 1217:3966-77. [DOI: 10.1016/j.chroma.2010.02.058] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2009] [Revised: 02/22/2010] [Accepted: 02/24/2010] [Indexed: 01/13/2023]
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10
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Wang P, Lo A, Young JB, Song JH, Lai R, Kneteman NM, Hao C, Li L. Targeted Quantitative Mass Spectrometric Identification of Differentially Expressed Proteins between Bax-Expressing and Deficient Colorectal Carcinoma Cells. J Proteome Res 2009; 8:3403-14. [DOI: 10.1021/pr9000477] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Peng Wang
- Departments of Chemistry, Laboratory Medicine & Pathology and Surgery, University of Alberta, Edmonton, Alberta T6G 2G2, Canada, and Department of Pathology & Laboratory Medicine, Winship Cancer Institute, Emory University, Atlanta, Georgia 30322
| | - Andy Lo
- Departments of Chemistry, Laboratory Medicine & Pathology and Surgery, University of Alberta, Edmonton, Alberta T6G 2G2, Canada, and Department of Pathology & Laboratory Medicine, Winship Cancer Institute, Emory University, Atlanta, Georgia 30322
| | - J. Bryce Young
- Departments of Chemistry, Laboratory Medicine & Pathology and Surgery, University of Alberta, Edmonton, Alberta T6G 2G2, Canada, and Department of Pathology & Laboratory Medicine, Winship Cancer Institute, Emory University, Atlanta, Georgia 30322
| | - Jin H. Song
- Departments of Chemistry, Laboratory Medicine & Pathology and Surgery, University of Alberta, Edmonton, Alberta T6G 2G2, Canada, and Department of Pathology & Laboratory Medicine, Winship Cancer Institute, Emory University, Atlanta, Georgia 30322
| | - Raymond Lai
- Departments of Chemistry, Laboratory Medicine & Pathology and Surgery, University of Alberta, Edmonton, Alberta T6G 2G2, Canada, and Department of Pathology & Laboratory Medicine, Winship Cancer Institute, Emory University, Atlanta, Georgia 30322
| | - Norman M. Kneteman
- Departments of Chemistry, Laboratory Medicine & Pathology and Surgery, University of Alberta, Edmonton, Alberta T6G 2G2, Canada, and Department of Pathology & Laboratory Medicine, Winship Cancer Institute, Emory University, Atlanta, Georgia 30322
| | - Chunhai Hao
- Departments of Chemistry, Laboratory Medicine & Pathology and Surgery, University of Alberta, Edmonton, Alberta T6G 2G2, Canada, and Department of Pathology & Laboratory Medicine, Winship Cancer Institute, Emory University, Atlanta, Georgia 30322
| | - Liang Li
- Departments of Chemistry, Laboratory Medicine & Pathology and Surgery, University of Alberta, Edmonton, Alberta T6G 2G2, Canada, and Department of Pathology & Laboratory Medicine, Winship Cancer Institute, Emory University, Atlanta, Georgia 30322
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Abstract
Liquid chromatography (LC) can be combined with matrix-assisted laser-desorption ionization (MALDI) mass-spectrometry (MS) by using automated off-line fraction collection of eluates onto a MALDI plate. Commercial tandem MS systems are available for generating product ion spectra of MALDI-produced peptide ions. The MALDI MS/MS spectra can be searched against a proteome database for protein identification. In this chapter, a protocol of sequential solubilization and digestion of membrane proteins involving methanol- and SDS-assisted trypsin digestion and microwave-assisted acid hydrolysis is presented. The process of LC eluate deposition onto a MALDI plate along with practical considerations for achieving optimal performance of eluate deposition is described. Issues related to MALDI MS and MS/MS spectral acquisition are discussed. Database searching and manual inspection of MS/MS spectra of singly charged MALDI-produced peptide ions for positive protein identification are also addressed.
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12
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Recent applications of capillary electrophoresis–mass spectrometry (CE–MS): CE performing functions beyond separation. Anal Chim Acta 2008; 627:3-24. [DOI: 10.1016/j.aca.2008.04.023] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2008] [Revised: 04/02/2008] [Accepted: 04/08/2008] [Indexed: 11/18/2022]
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Schmidt JJ, McIlwain S, Page D, Christie AE, Li L. Combining MALDI-FTMS and bioinformatics for rapid peptidomic comparisons. J Proteome Res 2008; 7:887-96. [PMID: 18205299 DOI: 10.1021/pr070390p] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Increasing research efforts in large-scale mass spectral analyses of peptides and proteins have led to many advances in technology and method development for collecting data and improving the quality of data. However, the resultant large data sets often pose significant challenges in extracting useful information in a high-throughput manner. Here, we describe one such method where we analyzed a large mass spectral data set collected using decapod crustacean nervous tissue extracts separated via high-performance liquid chromatography (HPLC) coupled to high-resolution matrix-assisted laser desorption/ionization Fourier transform mass spectrometry (MALDI-FTMS). Following their acquisition, the data collected from discrete LC fractions was compiled and analyzed using an in-house developed software package that deisotoped, compressed, calibrated, and matched peaks to a list of known crustacean neuropeptides. By processing these data via bioinformatics tools such as hierarchical clustering, more than 110 neuropeptides that belong to 14 peptide families were mapped in five crustacean species. Overall, we demonstrate the utility of MALDI-FTMS in combination with a bioinformatics software package for the elucidation and comparison of peptidomes of varying crustacean species. This study established an effective methodology and will provide the basis for future investigations into more comprehensive comparative peptidomics with larger collection of species and phyla in order to gain a deeper understanding of the evolution and diversification of peptide families.
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Affiliation(s)
- Joshua J Schmidt
- School of Pharmacy, University of Wisconsin, Madison, Wisconsin 53705, USA
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14
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Young JB, Li L. Impulse-Driven Heated-Droplet Deposition Interface for Capillary and Microbore LC−MALDI MS and MS/MS. Anal Chem 2007; 79:5927-34. [PMID: 17605467 DOI: 10.1021/ac070383k] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
An automated off-line liquid chromatography-matrix-assisted laser desorption ionization (LC-MALDI) interface capable of coupling both capillary and microbore LC separations with MALDI mass spectrometry (MS) and tandem mass spectrometry (MS/MS) has been developed. The interface is a combination of two concepts: analyte concentration from heated hanging droplets and impulse-driven droplet deposition of LC fractions onto a MALDI sample plate. At room temperature the interface allows the coupling of capillary LC separations (i.e., flow rate of <5 microL/min) with MALDI MS. With heating, it can be used to combine microbore LC operated at a relatively high flow rate of up to 50 microL/min with MALDI MS. The collected fractions can be analyzed by MALDI MS and MS/MS instruments, such as time-of-flight (TOF) and quadrupole-TOF MS. Performance of the interface was examined using several peptide and protein standards. It was shown that, using MALDI-TOF MS, [GLU1]-fibrinopeptide B could be detected with a total injection amount of 5 fmol to microbore LC. Chromatographic performance was also monitored. A peak width of 12 s at half-height for [GLU1]-fibrinopeptide B showed no evidence of band broadening due to the interface. The ability of the interface to mitigate ion suppression was studied using a mixture of 100 fmol of [GLU1]-fibrinopeptide B and 10 pmol of cytochrome c tryptic digest. Although fully suppressed under direct MALDI conditions, LC-MALDI analysis was able to detect the 100 fmol peptide with 10 s fraction collection. Finally, the ability to inject relatively large sample amounts to improve detectability of low-abundance peptides was illustrated in the analysis of phosphopeptides from alpha-casein tryptic digests. A digest loaded on column to 2.4 microg and analyzed by LC-MALDI MS/MS resulted in 82% sequence coverage and detection of all nine phosphoserine residues. It is concluded that, being able to handle both high- and low-flow LC separations, the impulse-driven heated-droplet interface provides the flexibility to carry out MALDI analysis of peptides and proteins depending on the information sought after, analysis speed, and sample size.
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Affiliation(s)
- J Bryce Young
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
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15
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Hu L, Ye M, Jiang X, Feng S, Zou H. Advances in hyphenated analytical techniques for shotgun proteome and peptidome analysis--a review. Anal Chim Acta 2007; 598:193-204. [PMID: 17719892 DOI: 10.1016/j.aca.2007.07.046] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2007] [Revised: 07/17/2007] [Accepted: 07/18/2007] [Indexed: 01/30/2023]
Abstract
Proteomics is defined as the analysis of part or all of the protein components of a complex biological system (a cell, organ or tissue) at a given moment. Due to the huge number of proteins encoded by the genome, novel analytical techniques must be developed to meet the need of large scale analysis. This has led to the hyphenation of multiple techniques to achieve this object. Here current status of the hyphenated analytical techniques of one-dimensional and multidimensional liquid chromatography-mass spectrometry for shotgun proteomic analysis is reviewed, and on-line techniques for automated sample preparation and injection are also covered. In addition, the hyphenated techniques for peptidome analysis are also covered.
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Affiliation(s)
- Lianghai Hu
- National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Graduate School of the Chinese Academy of Sciences, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China
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Perlman DH, Huang H, Dauly C, Costello CE, McComb ME. Coupling of protein HPLC to MALDI-TOF MS using an on-target device for fraction collection, concentration, digestion, desalting, and matrix/analyte cocrystallization. Anal Chem 2007; 79:2058-66. [PMID: 17256876 DOI: 10.1021/ac061919p] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Multidimensional protein chromatography offers an alternative to gel-based separations for large-scale proteomic analyses of highly complex mixtures. However, these liquid separations divide the original mixtures into multitudes of discrete samples, each of which may require numerous steps of sample manipulation, such as fraction collection, buffer exchange, protease digestion, peptide desalting, and, in the case of MALDI-MS, matrix and analyte cocrystallization on target. When traditional high-flow liquid chromatography is used, large volumes of solvent must also be removed from fractions to maximize MS sensitivity. Although robotic liquid-handling devices can facilitate these steps and reduce analyst/sample contact, they remain prototypic and expensive. Here, we explore the use of a novel, one-piece elastomeric device, the BD MALDI sample concentrator, which affixes to a MALDI target to create a prestructured 96-well sample array on the target surface. We have developed methodologies to process high-flow HPLC fractions by collecting them directly into the elastomeric device and then subjecting them to sequential on-target sample concentration, buffer exchange, digestion, desalting, and matrix/analyte cocrystallization for MALDI-MS analyses. We demonstrate that this methodology enables the rapid digestion and analysis of low amounts of proteins and that it is effective in the characterization of an HPLC-fractionated protein mixture by MALDI-TOF MS followed by peptide mass fingerprinting.
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Affiliation(s)
- David H Perlman
- Cardiovascular Proteomics Center, Mass Spectrometry Resource, Departments of Medicine and Biochemistry, Boston University School of Medicine, Boston, Massachusetts 02118, USA
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Abstract
Liquid chromatography-matrix-assisted laser desorption/ionization mass spectrometry represents a sensitive, hyphenated MS- and MS/MS-technique with a broad range of applications in all areas ofproteome analysis. Whereas a number of interface types have been developed for coupling MALDI MS and liquid chromatography, in this chapter selected on-line and off-line types and techniques will be discussed with respect to their individual properties and performance. The technique is especially attractive in off-line mode where LC-separation and MS analyses are decoupled and each step can be performed at its individual optimum. Different speed of chromatographic separation and achievement of S/N criteria in MS or MS/MS mode can be optimized independently by individual adjustment of specific operating parameters. This flexibility makes LC-MALDI MS attractive for the analysis of peptide mixtures from low to medium complexity. Using sequential MS analysis of parallel LC runs (multiplexing), even highly complex samples can be handled. Quantitation at the MS and MS/MS level can be accomplished by a variety of labeling techniques, where the predominant formation of singly charged ions in MALDI alleviates the assignment of isotopomers. After discussing the level of complementarity between LC-MALDI and LC-ESI MS, selected applications of LC-MALDI MS are presented. Examples of membrane protein analysis applying 1D SDS PAGE are discussed in detail as well as applications in protein interaction analysis. These application examples clearly show that in all respects LC-MALDI MS and MS/MS are flexible and sensitive techniques which can be adapted to a wide range of different workflows.
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Liu C, Zhang X. Multidimensional capillary array liquid chromatography and matrix-assisted laser desorption/ionization tandem mass spectrometry for high-throughput proteomic analysis. J Chromatogr A 2007; 1139:191-8. [PMID: 17126347 DOI: 10.1016/j.chroma.2006.11.019] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2006] [Revised: 11/02/2006] [Accepted: 11/03/2006] [Indexed: 11/23/2022]
Abstract
A two-dimensional capillary array liquid chromatography system coupled with matrix-assisted laser desorption/ionization (MALDI) mass spectrometry (MS) was developed for high-throughput comprehensive proteomic analysis, in which one strong cation-exchange (SCX) capillary chromatographic column was used as the first separation dimension and 10 parallel reversed-phase liquid chromatographic (RPLC) capillary columns were used as the second separation dimension. A novel multi-channel interface was designed and fabricated for on-line coupling of the SCX to RPLC column array system. Besides the high resolution based on the combination of SCX and RPLC separation, the developed new system provided the most rapid two-dimensional liquid chromatography (2D-LC) separation. Ten three-way micro-splitter valves used as stop-and-flow switches in transferring SCX fractions onto RPLC columns. In addition, the three-way valves also acted as mixing chambers of RPLC effluent with matrix. The system enables on-line mixing of the LC array effluents with matrix solution during the elution and directly depositing the analyte/matrix mixtures on MALDI plates from the tenplexed channels in parallel through an array of capillary tips. With the novel system, thousands of peptides were well separated and deposited on MALDI plates only in 150min for a complex proteome sample. Compared with common 2D-LC system, the parallel 2D-LC system showed about 10-times faster analytical procedure. In combination with a high throughput tandem time of flight mass spectrometry, the system was proven to be very effective for proteome analysis by analyzing a complicated sample, soluble proteins extracted from a liver cancer tissue, in which over 1202 proteins were identified.
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Affiliation(s)
- Chunli Liu
- Department of Biochemistry and Molecular Biology, Second Military Medical University, Shanghai 200433, China.
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19
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Current literature in mass spectrometry. JOURNAL OF MASS SPECTROMETRY : JMS 2007; 42:127-38. [PMID: 17199253 PMCID: PMC7166443 DOI: 10.1002/jms.1070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
In order to keep subscribers up‐to‐date with the latest developments in their field, John Wiley & Sons are providing a current awareness service in each issue of the journal. The bibliography contains newly published material in the field of mass spectrometry. Each bibliography is divided into 11 sections: 1 Books, Reviews & Symposia; 2 Instrumental Techniques & Methods; 3 Gas Phase Ion Chemistry; 4 Biology/Biochemistry: Amino Acids, Peptides & Proteins; Carbohydrates; Lipids; Nucleic Acids; 5 Pharmacology/Toxicology; 6 Natural Products; 7 Analysis of Organic Compounds; 8 Analysis of Inorganics/Organometallics; 9 Surface Analysis; 10 Environmental Analysis; 11 Elemental Analysis. Within each section, articles are listed in alphabetical order with respect to author (6 Weeks journals ‐ Search completed at 4th. Oct. 2006)
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McComb ME, Perlman DH, Huang H, Costello CE. Evaluation of an on-target sample preparation system for matrix-assisted laser desorption/ionization time-of-flight mass spectrometry in conjunction with normal-flow peptide high-performance liquid chromatography for peptide mass fingerprint analyses. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2007; 21:44-58. [PMID: 17133622 DOI: 10.1002/rcm.2805] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Large-scale mass spectrometry (MS)-based proteomic analyses require high-throughput sample preparation techniques due to the increasing numbers of samples that make up a typical proteomics experiment. Moreover, extensive sample pre-treatment steps are necessary prior to MS acquisition for even the most rapid and robust MS-based proteomics methodology, matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) MS followed by peptide mass fingerprinting (PMF) analysis. These include sample purification and fractionation, removal of digestion buffers or solvents, and spotting of sample with matrix onto the MALDI target. These multiple steps of time-consuming sample handling can result in high overall analysis costs and the likelihood of sample contamination and loss. In order to overcome some of these limitations in sample processing, we have investigated the use of a novel, simple, inexpensive 96-well elastomeric array that affixes to a MALDI target to create an on-target 96-well plate that accommodates a high solution volume (ca. 200 microL), thereby enabling the on-target processing of samples for MALDI-TOFMS. We explored several factors that influence MALDI sample preparation: type of matrix, solution volume, solution organic composition, solution drying rates and matrix/analyte co-crystallization methods. We also investigated the use of the 96-well elastomeric device for coupling MALDI-TOFMS analysis directly to high flow rate (1 mL/min) reversed-phase (rp)-HPLC. By developing an optimized, robust sample preparation protocol, we were able to obtain mass spectra with a high signal-to-noise ratio from peptide standards present at the 50-fmol level in large starting volumes of solution. PMF analyses were possible from 1-pmol and 500-fmol protein-digest standards. Coupling the device to high-flow HPLC (750 microL/min) yielded a robust and semi-automated means to obtain enhanced MALDI-TOFMS data at 500 ng of protein digest. These methodologies developed for this simple, on-target, elastomeric device show promise for streamlining the sample preparation process from HPLC to MALDI-MS.
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Affiliation(s)
- Mark E McComb
- Cardiovascular Proteomics Center, Boston University School of Medicine, Boston, MA 02118-2646, USA.
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Yoo C, Zhao J, Pal M, Hersberger K, Huber CG, Simeone DM, Beer DG, Lubman DM. Automated integration of monolith-based protein separation with on-plate digestion for mass spectrometric analysis of esophageal adenocarcinoma human epithelial samples. Electrophoresis 2006; 27:3643-51. [PMID: 16927349 DOI: 10.1002/elps.200600117] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
A unique approach of automating the integration of monolithic capillary HPLC-based protein separation and on-plate digestion for subsequent MALDI-MS analysis has been developed. All liquid-handling procedures were performed using a robotic module. This automated high-throughput method minimizes the amount of time and extensive labor required for traditional in-solution digestion followed by exhaustive sample cleanup and analysis. Also, precise positioning of the droplet from the capillary HPLC separation onto the MALDI plate allows for preconcentration effects of analytes for improved sensitivity. Proteins from primary esophageal Barrett's adenocarcinoma tissue were prefractionated by chromatofocusing and analyzed successfully by this automated configuration, obtaining rapid protein identifications through PMF and sequencing analyses with high sequence coverage. Additionally, intact protein molecular weight values were obtained as a means to further confirm protein identification and also to identify potential sequence modifications of proteins. This simple and rapid method is a highly versatile and robust approach for the analysis of complex proteomes.
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Affiliation(s)
- Chul Yoo
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
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