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Chen L, Zhang Z, Matsumoto C, Gao Y. High-Throughput Proteomics Enabled by a Fully Automated Dual-Trap and Dual-Column LC-MS. Anal Chem 2024; 96:9761-9766. [PMID: 38887087 DOI: 10.1021/acs.analchem.3c03182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/20/2024]
Abstract
This Technical Note describes a dual-column liquid chromatography system coupled to mass spectrometry (LC-MS) for high-throughput bottom-up proteomic analysis. This system made full use of two 2-position 10-port valves and a binary pump with an integrated loading pump of a commercial LC instrument to provide successive operation of two parallel subsystems. Each subsystem consisted of a set of trap columns and an analytical column. A T-junction union was used to split the mobile phase from the loading pump into two parts. This allowed one set of columns to be washed and equilibrated, followed by the injection of the next sample, while the previous sample was eluting and being analyzed on the other set of columns, thereby greatly increasing the analysis throughput. This approach showed high reproducibility for the analysis of HeLa tryptic digests with average relative standard deviation (RSD) values of 1.75%, 6.90%, and 5.19% for the identification number of proteins, peptides, and peptide-spectrum matches (PSMs), respectively, across 10 consecutive runs. The capacity for peptide and protein identification, as well as proteome depth, of the dual-column LC system was comparable to a conventional single-column system. Due to its simple equipment requirements and set up process, this method should be highly accessible for other laboratories.
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Affiliation(s)
- Liang Chen
- College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois 60612, United States
| | - Ziwei Zhang
- College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois 60612, United States
| | - Cory Matsumoto
- College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois 60612, United States
| | - Yu Gao
- College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois 60612, United States
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Staes A, Boucher K, Dufour S, Maia TM, Timmerman E, Haver DV, Pauwels J, Demol H, Vandenbussche J, Gevaert K, Impens F, Devos S. High-Throughput Nanoflow Proteomics Using a Dual-Column Electrospray Source. Anal Chem 2024; 96:6534-6539. [PMID: 38647218 DOI: 10.1021/acs.analchem.4c00845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2024]
Abstract
With current trends in proteomics, especially regarding clinical and low input (to single cell) samples, it is increasingly important to both maximize the throughput of the analysis and maintain as much sensitivity as possible. The new generation of mass spectrometers (MS) are taking a huge leap in sensitivity, allowing analysis of samples with shorter liquid chromatography (LC) methods while digging as deep in the proteome. However, the throughput can be doubled by implementing a dual column nano-LC-MS configuration. For this purpose, we used a dual-column setup with a two-outlet electrospray source and compared it to a classic dual-column setup with a single-outlet source.
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Affiliation(s)
- An Staes
- VIB Center for Medical Biotechnology, Technologiepark-Zwijnaarde 75, B9052 Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Technologiepark-Zwijnaarde 75, B9052 Ghent, Belgium
- VIB Proteomics Core, Technologiepark-Zwijnaarde 75, B9052 Ghent, Belgium
| | - Katie Boucher
- VIB Center for Medical Biotechnology, Technologiepark-Zwijnaarde 75, B9052 Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Technologiepark-Zwijnaarde 75, B9052 Ghent, Belgium
- VIB Proteomics Core, Technologiepark-Zwijnaarde 75, B9052 Ghent, Belgium
| | - Sara Dufour
- VIB Center for Medical Biotechnology, Technologiepark-Zwijnaarde 75, B9052 Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Technologiepark-Zwijnaarde 75, B9052 Ghent, Belgium
- VIB Proteomics Core, Technologiepark-Zwijnaarde 75, B9052 Ghent, Belgium
| | - Teresa Mendes Maia
- VIB Center for Medical Biotechnology, Technologiepark-Zwijnaarde 75, B9052 Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Technologiepark-Zwijnaarde 75, B9052 Ghent, Belgium
- VIB Proteomics Core, Technologiepark-Zwijnaarde 75, B9052 Ghent, Belgium
| | - Evy Timmerman
- VIB Center for Medical Biotechnology, Technologiepark-Zwijnaarde 75, B9052 Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Technologiepark-Zwijnaarde 75, B9052 Ghent, Belgium
- VIB Proteomics Core, Technologiepark-Zwijnaarde 75, B9052 Ghent, Belgium
| | - Delphi Van Haver
- VIB Center for Medical Biotechnology, Technologiepark-Zwijnaarde 75, B9052 Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Technologiepark-Zwijnaarde 75, B9052 Ghent, Belgium
- VIB Proteomics Core, Technologiepark-Zwijnaarde 75, B9052 Ghent, Belgium
| | - Jarne Pauwels
- VIB Center for Medical Biotechnology, Technologiepark-Zwijnaarde 75, B9052 Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Technologiepark-Zwijnaarde 75, B9052 Ghent, Belgium
| | - Hans Demol
- VIB Center for Medical Biotechnology, Technologiepark-Zwijnaarde 75, B9052 Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Technologiepark-Zwijnaarde 75, B9052 Ghent, Belgium
- VIB Proteomics Core, Technologiepark-Zwijnaarde 75, B9052 Ghent, Belgium
| | | | - Kris Gevaert
- VIB Center for Medical Biotechnology, Technologiepark-Zwijnaarde 75, B9052 Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Technologiepark-Zwijnaarde 75, B9052 Ghent, Belgium
| | - Francis Impens
- VIB Center for Medical Biotechnology, Technologiepark-Zwijnaarde 75, B9052 Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Technologiepark-Zwijnaarde 75, B9052 Ghent, Belgium
- VIB Proteomics Core, Technologiepark-Zwijnaarde 75, B9052 Ghent, Belgium
| | - Simon Devos
- VIB Center for Medical Biotechnology, Technologiepark-Zwijnaarde 75, B9052 Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Technologiepark-Zwijnaarde 75, B9052 Ghent, Belgium
- VIB Proteomics Core, Technologiepark-Zwijnaarde 75, B9052 Ghent, Belgium
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3
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Hosp F, Scheltema RA, Eberl HC, Kulak NA, Keilhauer EC, Mayr K, Mann M. A Double-Barrel Liquid Chromatography-Tandem Mass Spectrometry (LC-MS/MS) System to Quantify 96 Interactomes per Day. Mol Cell Proteomics 2015; 14:2030-41. [PMID: 25887394 PMCID: PMC4587330 DOI: 10.1074/mcp.o115.049460] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Indexed: 12/12/2022] Open
Abstract
The field of proteomics has evolved hand-in-hand with technological advances in LC-MS/MS systems, now enabling the analysis of very deep proteomes in a reasonable time. However, most applications do not deal with full cell or tissue proteomes but rather with restricted subproteomes relevant for the research context at hand or resulting from extensive fractionation. At the same time, investigation of many conditions or perturbations puts a strain on measurement capacity. Here, we develop a high-throughput workflow capable of dealing with large numbers of low or medium complexity samples and specifically aim at the analysis of 96-well plates in a single day (15 min per sample). We combine parallel sample processing with a modified liquid chromatography platform driving two analytical columns in tandem, which are coupled to a quadrupole Orbitrap mass spectrometer (Q Exactive HF). The modified LC platform eliminates idle time between measurements, and the high sequencing speed of the Q Exactive HF reduces required measurement time. We apply the pipeline to the yeast chromatin remodeling landscape and demonstrate quantification of 96 pull-downs of chromatin complexes in about 1 day. This is achieved with only 500 μg input material, enabling yeast cultivation in a 96-well format. Our system retrieved known complex-members and the high throughput allowed probing with many bait proteins. Even alternative complex compositions were detectable in these very short gradients. Thus, sample throughput, sensitivity and LC/MS-MS duty cycle are improved severalfold compared with established workflows. The pipeline can be extended to different types of interaction studies and to other medium complexity proteomes.
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Affiliation(s)
- Fabian Hosp
- From the ‡Department of Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Am Klopferspitz 18, D-82152 Martinsried, Germany
| | - Richard A Scheltema
- From the ‡Department of Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Am Klopferspitz 18, D-82152 Martinsried, Germany
| | - H Christian Eberl
- From the ‡Department of Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Am Klopferspitz 18, D-82152 Martinsried, Germany
| | - Nils A Kulak
- From the ‡Department of Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Am Klopferspitz 18, D-82152 Martinsried, Germany
| | - Eva C Keilhauer
- From the ‡Department of Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Am Klopferspitz 18, D-82152 Martinsried, Germany
| | - Korbinian Mayr
- From the ‡Department of Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Am Klopferspitz 18, D-82152 Martinsried, Germany
| | - Matthias Mann
- From the ‡Department of Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Am Klopferspitz 18, D-82152 Martinsried, Germany
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4
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Lee H, Lee JH, Kim H, Kim SJ, Bae J, Kim HK, Lee SW. A fully automated dual-online multifunctional ultrahigh pressure liquid chromatography system for high-throughput proteomics analysis. J Chromatogr A 2014; 1329:83-9. [PMID: 24412000 DOI: 10.1016/j.chroma.2013.12.084] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2013] [Revised: 12/25/2013] [Accepted: 12/28/2013] [Indexed: 11/19/2022]
Abstract
A fully automated dual-online multifunctional ultrahigh pressure liquid chromatography (DO-MULTI-UPLC) system has been developed for high throughput proteome analyses of complex peptide mixtures. The system employs two online solid phase extraction (SPE) columns (150μm inner diameter×3cm), two capillary reverse phase (RP) columns (75μm×100cm) and a strong cation exchange (SCX) column (150μm×15cm) on a single system utilizing one binary pump and one isocratic pump. With the automated operation of six switching valves, the selection of LC experiments between single-dimensional RPLC and online two-dimensional SCX/RPLC were achieved automatically, without manual intervention, while two RPLC columns were used independently and alternatively. By essentially removing the dead time for column equilibration between experiments, in either 1D mode or 2D experimental mode, the current system was demonstrated to increase the experimental throughput by about two folds, while keeping the inter-column reproducibility of peptide elution time in less than 1% of gradient time. The advantageous features of the proposed system were demonstrated by its application to proteome samples of varying complexities.
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Affiliation(s)
- Hangyeore Lee
- Department of Chemistry, Research Institute for Natural Sciences, Korea University, Seoul 136-701, South Korea.
| | - Jung Hwa Lee
- Department of Chemistry, Research Institute for Natural Sciences, Korea University, Seoul 136-701, South Korea.
| | - Hokeun Kim
- Department of Chemistry, Research Institute for Natural Sciences, Korea University, Seoul 136-701, South Korea.
| | - Su-Jin Kim
- Department of Chemistry, Research Institute for Natural Sciences, Korea University, Seoul 136-701, South Korea.
| | - Jingi Bae
- Department of Chemistry, Research Institute for Natural Sciences, Korea University, Seoul 136-701, South Korea.
| | - Hark Kyun Kim
- National Cancer Center, Goyang 410-769, South Korea.
| | - Sang-Won Lee
- Department of Chemistry, Research Institute for Natural Sciences, Korea University, Seoul 136-701, South Korea.
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5
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Orton DJ, Wall MJ, Doucette AA. Dual LC-MS platform for high-throughput proteome analysis. J Proteome Res 2013; 12:5963-70. [PMID: 24090060 DOI: 10.1021/pr400738a] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We describe a dual-column interface for parallel chromatography to improve throughput during LC-MS experimentation. The system employs a high-voltage switch to operate two capillary column/nanospray emitters fixed at the MS orifice. Sequentially loading one column while operating the second nearly doubles the LC-MS duty cycle. Given the innate run-to-run variation of a nanospray LC-MS (12% RSD peak area; 2% retention time), the intercolumn variability of the platform showed no meaningful difference for proteome analysis, with equal numbers of proteins and peptides identified per column. Applied to GeLC analysis of an E. coli extract, throughput was increased using one of three methods: doubling the number of replicates, increasing the LC gradient length, or sectioning the gel into twice as many fractions. Each method increased the total number of identifications as well as detection throughput (number of peptides/proteins identified per hour). The greatest improvement was achieved by doubling the number of gel slices (10 vs 5). Analysis on the dual column platform provided a 26% increase in peptides identified per hour (24% proteins). This translates into ~50% more total proteins and peptides identified in the experiment using the dual LC-MS platform.
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Affiliation(s)
- Dennis J Orton
- Department of Pathology, Dalhousie University , 11th Floor Tupper Medical Building, Room 11B, Halifax, NS B3H 4R2, Canada
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6
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Wang J, Bourne PE, Bandeira N. Peptide identification by database search of mixture tandem mass spectra. Mol Cell Proteomics 2011; 10:M111.010017. [PMID: 21862760 DOI: 10.1074/mcp.m111.010017] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
In high-throughput proteomics the development of computational methods and novel experimental strategies often rely on each other. In certain areas, mass spectrometry methods for data acquisition are ahead of computational methods to interpret the resulting tandem mass spectra. Particularly, although there are numerous situations in which a mixture tandem mass spectrum can contain fragment ions from two or more peptides, nearly all database search tools still make the assumption that each tandem mass spectrum comes from one peptide. Common examples include mixture spectra from co-eluting peptides in complex samples, spectra generated from data-independent acquisition methods, and spectra from peptides with complex post-translational modifications. We propose a new database search tool (MixDB) that is able to identify mixture tandem mass spectra from more than one peptide. We show that peptides can be reliably identified with up to 95% accuracy from mixture spectra while considering only a 0.01% of all possible peptide pairs (four orders of magnitude speedup). Comparison with current database search methods indicates that our approach has better or comparable sensitivity and precision at identifying single-peptide spectra while simultaneously being able to identify 38% more peptides from mixture spectra at significantly higher precision.
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Affiliation(s)
- Jian Wang
- Bioinformatics Program, University of California, San Diego, La Jolla, CA 92093, USA
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7
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Kim K, Jung HS, Song JY, Lee MR, Kim KS, Suh KY. Rapid detection ofMycoplasma pneumoniain a microfluidic device using immunoagglutination assay and static light scattering. Electrophoresis 2009; 30:3206-11. [DOI: 10.1002/elps.200900136] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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8
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Zhou Y, Shen H, Yi T, Wen D, Pang N, Liao J, Liu H. Synergistic design of electric field and membrane in facilitating continuous adsorption for cleanup and enrichment of proteins in direct ESI-MS analysis. Anal Chem 2009; 80:8920-9. [PMID: 18954078 DOI: 10.1021/ac800816k] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We designed and fabricated a novel microdevice to facilitate continuous adsorption phenomena for biological sample preparation. Using the device, we also developed an online, highly integrated, multifunctional strategy, with a promise of accepting a large volume of crude tissue extracts with the end point generation of a reliable MS identification within 20 min. Under an external electric field, charged membranes can adsorb multiple layers of proteins, which exceed the capacity limit of common resins or membranes. It enlarges sample loading and trapping efficiency, thus bypasses the tradeoff between sample capacity and downstream detection sensitivity. This integrated approach, formed by synergistic utilization among electric field, membrane, and fluidic handling at the microscale, reduces the overall complexity of crude samples in one step for direct MS analysis. The sample preparation goals, including enrichment, desalting, removal of noncharged contaminants, and initial fractionation, can be rapidly performed in a single device. The strategy facilitates reproducible MS quantification by circumventing traditional laborious and time-consuming sample preparation steps. In addition, MEPD extended the ion trap linear dynamic range from 2 to at least 4 orders of magnitude by eliminating ion suppression effect, enriching target analyte(s), and decreasing sample loss during integrated sample preparation.
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Affiliation(s)
- Yu Zhou
- Beijing National Laboratory for Molecular Sciences, Key Lab of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Inst. of Analytical Chemistry, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
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9
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Hammerling U, Tallsjö A, Grafström R, Ilbäck NG. Comparative Hazard Characterization in Food Toxicology. Crit Rev Food Sci Nutr 2009; 49:626-69. [DOI: 10.1080/10408390802145617] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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10
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Chambery A, Vissers JPC, Langridge JI, Lonardo E, Minchiotti G, Ruvo M, Parente A. Qualitative and Quantitative Proteomic Profiling of Cripto−/− Embryonic Stem Cells by Means of Accurate Mass LC−MS Analysis. J Proteome Res 2009; 8:1047-58. [DOI: 10.1021/pr800485c] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Angela Chambery
- Dipartimento di Scienze della Vita, Seconda Università di Napoli, I-81100 Caserta, Italy, Waters Corporation, MS Technologies Center, M22 5PP Manchester, United Kingdom, Istituto di Genetica e Biofisica “A Buzzati-Traverso”, CNR, I-80131 Napoli, Italy, and Istituto di Biostrutture e Bioimmagini, CNR, I-80134, Napoli, Italy
| | - Johannes P. C. Vissers
- Dipartimento di Scienze della Vita, Seconda Università di Napoli, I-81100 Caserta, Italy, Waters Corporation, MS Technologies Center, M22 5PP Manchester, United Kingdom, Istituto di Genetica e Biofisica “A Buzzati-Traverso”, CNR, I-80131 Napoli, Italy, and Istituto di Biostrutture e Bioimmagini, CNR, I-80134, Napoli, Italy
| | - James I. Langridge
- Dipartimento di Scienze della Vita, Seconda Università di Napoli, I-81100 Caserta, Italy, Waters Corporation, MS Technologies Center, M22 5PP Manchester, United Kingdom, Istituto di Genetica e Biofisica “A Buzzati-Traverso”, CNR, I-80131 Napoli, Italy, and Istituto di Biostrutture e Bioimmagini, CNR, I-80134, Napoli, Italy
| | - Enza Lonardo
- Dipartimento di Scienze della Vita, Seconda Università di Napoli, I-81100 Caserta, Italy, Waters Corporation, MS Technologies Center, M22 5PP Manchester, United Kingdom, Istituto di Genetica e Biofisica “A Buzzati-Traverso”, CNR, I-80131 Napoli, Italy, and Istituto di Biostrutture e Bioimmagini, CNR, I-80134, Napoli, Italy
| | - Gabriella Minchiotti
- Dipartimento di Scienze della Vita, Seconda Università di Napoli, I-81100 Caserta, Italy, Waters Corporation, MS Technologies Center, M22 5PP Manchester, United Kingdom, Istituto di Genetica e Biofisica “A Buzzati-Traverso”, CNR, I-80131 Napoli, Italy, and Istituto di Biostrutture e Bioimmagini, CNR, I-80134, Napoli, Italy
| | - Menotti Ruvo
- Dipartimento di Scienze della Vita, Seconda Università di Napoli, I-81100 Caserta, Italy, Waters Corporation, MS Technologies Center, M22 5PP Manchester, United Kingdom, Istituto di Genetica e Biofisica “A Buzzati-Traverso”, CNR, I-80131 Napoli, Italy, and Istituto di Biostrutture e Bioimmagini, CNR, I-80134, Napoli, Italy
| | - Augusto Parente
- Dipartimento di Scienze della Vita, Seconda Università di Napoli, I-81100 Caserta, Italy, Waters Corporation, MS Technologies Center, M22 5PP Manchester, United Kingdom, Istituto di Genetica e Biofisica “A Buzzati-Traverso”, CNR, I-80131 Napoli, Italy, and Istituto di Biostrutture e Bioimmagini, CNR, I-80134, Napoli, Italy
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11
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Alves G, Ogurtsov AY, Kwok S, Wu WW, Wang G, Shen RF, Yu YK. Detection of co-eluted peptides using database search methods. Biol Direct 2008; 3:27. [PMID: 18597684 PMCID: PMC2483259 DOI: 10.1186/1745-6150-3-27] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2008] [Accepted: 07/02/2008] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Current experimental techniques, especially those applying liquid chromatography mass spectrometry, have made high-throughput proteomic studies possible. The increase in throughput however also raises concerns on the accuracy of identification or quantification. Most experimental procedures select in a given MS scan only a few relatively most intense parent ions, each to be fragmented (MS2) separately, and most other minor co-eluted peptides that have similar chromatographic retention times are ignored and their information lost. RESULTS We have computationally investigated the possibility of enhancing the information retrieval during a given LC/MS experiment by selecting the two or three most intense parent ions for simultaneous fragmentation. A set of spectra is created via superimposing a number of MS2 spectra, each can be identified by all search methods tested with high confidence, to mimick the spectra of co-eluted peptides. The generated convoluted spectra were used to evaluate the capability of several database search methods - SEQUEST, Mascot, X!Tandem, OMSSA, and RAId_DbS - in identifying true peptides from superimposed spectra of co-eluted peptides. We show that using these simulated spectra, all the database search methods will gain eventually in the number of true peptides identified by using the compound spectra of co-eluted peptides. OPEN PEER REVIEW Reviewed by Vlad Petyuk (nominated by Arcady Mushegian), King Jordan and Shamil Sunyaev. For the full reviews, please go to the Reviewers' comments section.
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Affiliation(s)
- Gelio Alves
- National Center for Biotechnology Information, National Library of Medicine, NIH, Bethesda, MD, 20894, USA
| | - Aleksey Y Ogurtsov
- National Center for Biotechnology Information, National Library of Medicine, NIH, Bethesda, MD, 20894, USA
| | - Siwei Kwok
- Department of Mathematics, University of Maryland, College Park, MD, 20742, USA
| | - Wells W Wu
- Proteomics Core Facility, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD, 20892, USA
| | - Guanghui Wang
- Proteomics Core Facility, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD, 20892, USA
| | - Rong-Fong Shen
- Proteomics Core Facility, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD, 20892, USA
| | - Yi-Kuo Yu
- National Center for Biotechnology Information, National Library of Medicine, NIH, Bethesda, MD, 20894, USA
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12
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Wang H, Hanash SM. Increased throughput and reduced carryover of mass spectrometry-based proteomics using a high-efficiency nonsplit nanoflow parallel dual-column capillary HPLC system. J Proteome Res 2008; 7:2743-55. [PMID: 18512973 DOI: 10.1021/pr700876g] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We report a new design of a fully automated, high-efficiency parallel nonsplit nanoflow capillary HPLC system, coupled on-line with linear ion trap (LTQ) and high performance nanoelectrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (nanoESI LTQ-FTICR MS). The system, intended for high-throughput proteome analysis of complex protein mixtures, notably serum and plasma, consists of two reversed-phase trap columns for large volume sample injection with high speed sample loading and desalting and two reversed-phase analytical capillary columns. Through a nanoscale two-position, 10-port switching valve, the whole system is terminated by a 10 microm i.d. of nanoemitter mounted on the nanoelectrospray source in front of the sampling cone of the LTQ-FTICR MS. Gradient elution to both nanoflow-rate capillary columns is simultaneously delivered by a single HPLC system via two independent binary gradient pump systems. The parallel capillary column approach eliminates the time delays for column regeneration/equilibration since one capillary column is used for separating the sample mixtures and delivering the separated fractions to the MS, while the other capillary column is being regenerated and equilibrated. The reproducibility of retention time and peak intensity of the present automated parallel nanoflow-rate capillary HPLC system is comparable to that obtained using a single column configuration. Replicate injections of tryptic digests indicated that this system provided good reproducibility of retention time and peak area on both columns with average CV values of less than 1.08% and 7.04%, respectively. Throughput was increased to 100% for 2-h LC-MS analysis compared to the single capillary column LC-MS pipeline. Application of this system is demonstrated in a plasma proteomic study. A total of 312 868 MSMS events were acquired and 1564 proteins identified with high confidence (Protein Prophet > or = 0.9, and peptides matched > or = 2). Comparison of a series of plasma fractions run using the single-column LC-MS versus the parallel-column LC-MS demonstrated that parallel-column LC-MS system significantly reduced the sample carryover, improved MS data quality and increased the number of MS/MS sequence scan events.
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Affiliation(s)
- Hong Wang
- Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA.
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13
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Lucas LJ, Chesler JN, Yoon JY. Lab-on-a-chip immunoassay for multiple antibodies using microsphere light scattering and quantum dot emission. Biosens Bioelectron 2007; 23:675-81. [PMID: 17869502 DOI: 10.1016/j.bios.2007.08.004] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2007] [Revised: 08/01/2007] [Accepted: 08/03/2007] [Indexed: 11/21/2022]
Abstract
Double detection of microsphere light scattering and quantum dot emission was demonstrated for lab-on-a-chip immunoassay without using stationary support. We conjugated quantum dots (QDs) onto microspheres to enable multiplex assays as well as to enhance the limit of detection (LOD). We named this configuration "nano-on-micro" or "NOM". Upon radiation with UV light (380nm), a stronger light scattering signal is observed with NOMs than QDs or microspheres alone. Additionally, NOMs are easier to handle than QDs. Since QDs also provide fluorescent emission, we are able to utilize an increase in light scattering for detecting antigen-antibody reaction and a decrease in QD emission to identify which antibody (or antigen) is present. Two types of NOM combinations were used. One batch of microspheres was coated with QDs emitting at 655 nm and mouse IgG (mIgG); the other with QDs emitting at 605 nm and bovine serum albumin (BSA). A mixture of these two NOMs was used to identify either anti-mIgG or anti-BSA. NOM particles and target solutions were mixed in a microfluidic device (using highly carboxylated microspheres as previously demonstrated by our group) and on-chip detection was performed using proximity optical fibers. Forward light scattering at 380 nm was collected. With the positive target, the scattering signal was increased. The LOD was as low as 50 ng ml(-1) (330 pM) with p<0.05. Fluorescent emission (655 or 605 nm) was simultaneously collected. With the positive target, the emission signal was attenuated. Therefore, we were able to detect two different antibodies simultaneously with two different detection protocols. We believe this NOM bioassay has the ability to screen for and detect multiple antibodies with minimal sample processing and handling (one-step lab-on-a-chip immunoassay).
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Affiliation(s)
- Lonnie J Lucas
- Department of Agricultural and Biosystems Engineering, The University of Arizona, Tucson, AZ 85721-0038, USA
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14
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Yuan H, Zhang L, Liang Z, Zhang Y. Novel chromatography techniques for high-throughput analysis of proteomes. Anal Bioanal Chem 2007; 390:273-6. [PMID: 17901948 DOI: 10.1007/s00216-007-1597-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2007] [Accepted: 09/03/2007] [Indexed: 11/27/2022]
Affiliation(s)
- Huiming Yuan
- National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, The Chinese Academy of Sciences, Dalian, 116023, People's Republic of China
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15
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Jiang X, Feng S, Tian R, Han G, Jiang X, Ye M, Zou H. Automation of nanoflow liquid chromatography-tandem mass spectrometry for proteome analysis by using a strong cation exchange trap column. Proteomics 2007; 7:528-539. [PMID: 17309098 DOI: 10.1002/pmic.200600661] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
An approach was developed to automate sample introduction for nanoflow LC-MS/MS (microLC-MS/MS) analysis using a strong cation exchange (SCX) trap column. The system consisted of a 100 microm id x 2 cm SCX trap column and a 75 microm id x 12 cm C18 RP analytical column. During the sample loading step, the flow passing through the SCX trap column was directed to waste for loading a large volume of sample at high flow rate. Then the peptides bound on the SCX trap column were eluted onto the RP analytical column by a high salt buffer followed by RP chromatographic separation of the peptides at nanoliter flow rate. It was observed that higher performance of separation could be achieved with the system using SCX trap column than with the system using C18 trap column. The high proteomic coverage using this approach was demonstrated in the analysis of tryptic digest of BSA and yeast cell lysate. In addition, this system was also applied to two-dimensional separation of tryptic digest of human hepatocellular carcinoma cell line SMMC-7721 for large scale proteome analysis. This system was fully automated and required minimum changes on current microLC-MS/MS system. This system represented a promising platform for routine proteome analysis.
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Affiliation(s)
- Xiaogang Jiang
- National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
- School of Medicine, Suzhou University, Suzhou, Jiangsu, China
| | - Shun Feng
- National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - Ruijun Tian
- National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - Guanghui Han
- National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - Xinning Jiang
- National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - Mingliang Ye
- National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - Hanfa Zou
- National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
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16
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Ahn NG, Shabb JB, Old WM, Resing KA. Achieving in-depth proteomics profiling by mass spectrometry. ACS Chem Biol 2007; 2:39-52. [PMID: 17243782 DOI: 10.1021/cb600357d] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Proteomics addresses the important goal of determining the chemistry and composition of proteins in biological samples. Mass-spectrometry-based strategies have been highly successful in identifying and profiling proteins in complex mixtures; however, although depth of sampling continues to improve, a general recognition exists that no study has yet achieved complete protein coverage in any tissue, cell type, subcellular component, or fluid. The development of new approaches for comprehensively surveying highly complex protein mixtures, distinguishing protein isoforms, quantifying changes in protein abundance between different samples, and mapping post-translational modifications are areas of active research. These will be needed to achieve the "systems-wide" protein profiling goals of defining molecular responses to cell perturbations and obtaining biomarker information for disease detection, prognosis, and responses to therapy. We review recent progress in approaching these problems and present examples of successful applications and the outlook for the future.
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Affiliation(s)
- Natalie G Ahn
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309, USA.
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17
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Dayon L, Abonnenc M, Prudent M, Lion N, Girault HH. Multitrack electrospray chips. JOURNAL OF MASS SPECTROMETRY : JMS 2006; 41:1484-90. [PMID: 17083086 DOI: 10.1002/jms.1119] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Multitrack electrospray chips (MTEC) were fabricated by UV-photoablation of polyethylene terephthalate (PET) substrates. They are composed of an array of up to six microchannels that are successively used as electrospray ionization (ESI) emitters for mass spectrometry (MS). There is no requirement for alignment of the different spraying microchannels with the mass spectrometer orifice. The MTEC is thus fixed in front of the mass spectrometer and the successive MS analyses are performed without moving the chip. The sequential electrospraying by successive application of an identical high voltage in each off-axis microchannel was evaluated for the fast screening of peptides and proteins. The counting of cysteines in peptides through chemical modification and the relative quantification of a peptide in two samples are presented herein as two original strategies based on this new analytical tool.
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Affiliation(s)
- Loïc Dayon
- Laboratoire d'Electrochimie Physique et Analytique, Ecole Polytechnique Fédérale de Lausanne (EPFL), Station 6, CH-1015 Lausanne, Switzerland
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