1
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Beltekin B, Alharthi S, Aydoğan C. Novel open‐tubular columns with highly hydrophobic stationary phase for peptide and protein separation by nano‐liquid chromatography. SEPARATION SCIENCE PLUS 2023. [DOI: 10.1002/sscp.202200111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- Büşra Beltekin
- Food Analysis and Research Laboratory Bingöl University Bingöl Türkiye
| | - Sarah Alharthi
- Department of Chemistry, College of Science Taif University Taif Saudi Arabia
| | - Cemil Aydoğan
- Food Analysis and Research Laboratory Bingöl University Bingöl Türkiye
- Department of Chemistry Bingöl University Bingöl Türkiye
- Department of Food Engineering Bingöl University Bingöl Türkiye
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2
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Kano K, Noda S, Sato S, Kuwata K, Mishiro‐Sato E. An efficient in‐gel digestion method on small amounts of protein sample from large intact gel pieces. SEPARATION SCIENCE PLUS 2023. [DOI: 10.1002/sscp.202200121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- Keiko Kano
- Molecular Structure Center, Institute of Transformative Bio‐Molecules (WPI‐ITbM) Nagoya University Nagoya Japan
| | - Saki Noda
- Molecular Structure Center, Institute of Transformative Bio‐Molecules (WPI‐ITbM) Nagoya University Nagoya Japan
| | - Shinya Sato
- Molecular Structure Center, Institute of Transformative Bio‐Molecules (WPI‐ITbM) Nagoya University Nagoya Japan
| | - Keiko Kuwata
- Molecular Structure Center, Institute of Transformative Bio‐Molecules (WPI‐ITbM) Nagoya University Nagoya Japan
| | - Emi Mishiro‐Sato
- Molecular Structure Center, Institute of Transformative Bio‐Molecules (WPI‐ITbM) Nagoya University Nagoya Japan
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3
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Synovec RE, Mikaliunaite L. Application of Porous Layer Open Tubular Columns: Beyond Permanent Gases. LCGC NORTH AMERICA 2022. [DOI: 10.56530/lcgc.na.ew7472z7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
Porous layer open tubular (PLOT) columns are traditionally built with particles that are adhered to the tubing walls. These columns have unique selectivity and provide a great alternative when gaseous samples need to be separated, but these columns also have been used to separate higher boiling point analytes. There are many different commercially available stationary phases of PLOT columns, including alumina-based columns, molecular sieves, and porous polymers. Alumina-based columns have an aluminum oxide stationary phase that is then deactivated with different salts. These columns have high capacity, superior loading ability, and produce symmetrical peaks. Molecular sieve columns are designed specifically for permanent gas separations because the columns have high retention. Porous polymer columns are highly hydrophobic, making them more applicable to analyzing a wider range of samples.
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4
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Liang Y, Wang C, Liang Z, Zhang L, Zhang Y. C18-Functionalized Amine-Bridged Hybrid Monoliths for Mass Spectrometry-Friendly Peptide Separation and Highly Sensitive Proteomic Analysis. Anal Chem 2022; 94:6084-6088. [PMID: 35404572 DOI: 10.1021/acs.analchem.1c04405] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
For proteomic analysis based on mass spectrometry (MS), high-performance peptide separation under MS-friendly conditions is of importance. To this end, a novel kind of amine-bridged hybrid monolith was developed by the sol-gel reaction of bis[3-(trimethoxysilyl)propyl]amine and allyltrimethoxysilane, followed by "thiol-ene" click functionalization of C18 groups. With the secondary amino groups bridged in the framework, the nonspecific adsorption from silanol groups could be decreased, so that peptide peak tailing under MS-friendly conditions was reduced, and half peak width was narrowed. Furthermore, such materials were facilely in situ prepared in the very narrow bore capillary with low backpressure for proteomic analysis of limited amounts of samples. Finally, 16,692 unique peptides corresponding to 3698 protein groups could be averagely identified from 10 ng Hela cell digests in a single 65 min run, and 5257 peptides corresponding to 1062 protein groups could be averagely identified from 200 pg digests in a single 60 min run. Such high sensitivity could be attributed to the decreased nonspecific adsorption, the narrowed peak width, and the miniaturization of the column. It is shown that such monoliths are promising for highly sensitive proteomic analysis, including single-cell proteomics.
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Affiliation(s)
- Yu Liang
- CAS Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Chao Wang
- CAS Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhen Liang
- CAS Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Lihua Zhang
- CAS Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Yukui Zhang
- CAS Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
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5
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Alexovič M, Sabo J, Longuespée R. Microproteomic sample preparation. Proteomics 2021; 21:e2000318. [PMID: 33547857 DOI: 10.1002/pmic.202000318] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 01/23/2021] [Accepted: 01/27/2021] [Indexed: 12/11/2022]
Abstract
Multiple applications of proteomics in life and health science, pathology and pharmacology, require handling size-limited cell and tissue samples. During proteomic sample preparation, analyte loss in these samples arises when standard procedures are used. Thus, specific considerations have to be taken into account for processing, that are summarised under the term microproteomics (μPs). Microproteomic workflows include: sampling (e.g., flow cytometry, laser capture microdissection), sample preparation (possible disruption of cells or tissue pieces via lysis, protein extraction, digestion in bottom-up approaches, and sample clean-up) and analysis (chromatographic or electrophoretic separation, mass spectrometric measurements and statistical/bioinformatic evaluation). All these steps must be optimised to reach wide protein dynamic ranges and high numbers of identifications. Under optimal conditions, sampling is adapted to the studied sample types and nature, sample preparation isolates and enriches the whole protein content, clean-up removes salts and other interferences such as detergents or chaotropes, and analysis identifies as many analytes as the instrumental throughput and sensitivity allow. In the suggested review, we present and discuss the current state in μP applications for processing of small number of cells (cell μPs) and microscopic tissue regions (tissue μPs).
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Affiliation(s)
- Michal Alexovič
- Department of Medical and Clinical Biophysics, Faculty of Medicine, University of P.J. Šafárik in Košice, Košice, Slovakia
| | - Ján Sabo
- Department of Medical and Clinical Biophysics, Faculty of Medicine, University of P.J. Šafárik in Košice, Košice, Slovakia
| | - Rémi Longuespée
- Department of Clinical Pharmacology and Pharmacoepidemiology, Heidelberg University Hospital, Heidelberg, Germany
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6
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Alyethodi RR, Karthik S, Muniswamy K, Ravi SK, Perumal P, Bhattacharya D, Bala PA, De AK, Sujatha T, Sunder J, Kundu A. Assessment of Protein Profiles of RNAlater Stored and Fresh PBMC Cells Using Different Protein Extraction Buffers. Protein J 2020; 39:291-300. [DOI: 10.1007/s10930-020-09888-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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7
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Channaveerappa D, Ngounou Wetie AG, Darie CC. Bottlenecks in Proteomics: An Update. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1140:753-769. [PMID: 31347083 DOI: 10.1007/978-3-030-15950-4_45] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
Abstract
Mass spectrometry (MS) is the core for advanced methods in proteomic experiments. When effectively used, proteomics may provide extensive information about proteins and their post-translational modifications, as well as their interaction partners. However, there are also many problems that one can encounter during a proteomic experiment, including, but not limited to sample preparation, sample fractionation, sample analysis, data analysis & interpretation and biological significance. Here we discuss some of the problems that researchers should be aware of when performing a proteomic experiment.
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Affiliation(s)
- Devika Channaveerappa
- Biochemistry and Proteomics Group, Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, NY, USA
| | - Armand G Ngounou Wetie
- Biochemistry and Proteomics Group, Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, NY, USA
| | - Costel C Darie
- Biochemistry and Proteomics Group, Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, NY, USA.
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8
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Almeida JMFD, Silva EMF, Veríssimo LM, Fernandes NS. Salting-out assisted liquid-liquid extraction method combined with GC-MS for the determination of topiramate in aqueous solutions: development and application of the methodology. SEP SCI TECHNOL 2019. [DOI: 10.1080/01496395.2019.1624570] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
| | | | - Lourena Mafra Veríssimo
- Departamento de Ciências Farmacêuticas, Universidade Federal do Rio Grande do Norte, Natal, RN, Brazil
| | - Nedja Suely Fernandes
- Instituto de Química, Universidade Federal do Rio Grande do Norte, Campus Central, Natal, RN, Brazil
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9
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Davis S, Scott C, Ansorge O, Fischer R. Development of a Sensitive, Scalable Method for Spatial, Cell-Type-Resolved Proteomics of the Human Brain. J Proteome Res 2019; 18:1787-1795. [PMID: 30768908 PMCID: PMC6456870 DOI: 10.1021/acs.jproteome.8b00981] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
![]()
While nearly comprehensive proteome
coverage can be achieved from
bulk tissue or cultured cells, the data usually lacks spatial resolution.
As a result, tissue based proteomics averages protein abundance across
multiple cell types and/or localizations. With proteomics platforms
lacking sensitivity and throughput to undertake deep single-cell proteome
studies in order to resolve spatial or cell type dependent protein
expression gradients within tissue, proteome analysis has been combined
with sorting techniques to enrich for certain cell populations. However,
the spatial resolution and context is lost after cell sorting. Here,
we report an optimized method for the proteomic analysis of neurons
isolated from post-mortem human brain by laser capture microdissection
(LCM). We tested combinations of sample collection methods, lysis
buffers and digestion methods to maximize the number of identifications
and quantitative performance, identifying 1500 proteins from 60 000
μm2 of 10 μm thick cerebellar molecular layer
with excellent reproducibility. To demonstrate the ability of our
workflow to resolve cell type specific proteomes within human brain
tissue, we isolated sets of individual Betz and Purkinje cells. Both
neuronal cell types are involved in motor coordination and were found
to express highly specific proteomes to a depth of 2800 to 3600 proteins.
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Affiliation(s)
- Simon Davis
- Target Discovery Institute, Nuffield Department of Medicine , University of Oxford , Roosevelt Drive , Oxford , OX3 7FZ , U.K
| | - Connor Scott
- Academic Unit of Neuropathology, Nuffield Department of Clinical Neurosciences , University of Oxford, John Radcliffe Hospital , Oxford , OX3 9DU , U.K
| | - Olaf Ansorge
- Academic Unit of Neuropathology, Nuffield Department of Clinical Neurosciences , University of Oxford, John Radcliffe Hospital , Oxford , OX3 9DU , U.K
| | - Roman Fischer
- Target Discovery Institute, Nuffield Department of Medicine , University of Oxford , Roosevelt Drive , Oxford , OX3 7FZ , U.K
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10
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Lam SC, Sanz Rodriguez E, Haddad PR, Paull B. Recent advances in open tubular capillary liquid chromatography. Analyst 2019; 144:3464-3482. [DOI: 10.1039/c9an00329k] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
This review covers advances and applications of open tubular capillary liquid chromatography (OT-LC) over the period 2007–2018.
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Affiliation(s)
- Shing Chung Lam
- ASTech
- ARC Training Centre for Portable Analytical Separation Technologies (ASTech)
- and Australian Centre for Research on Separation Science (ACROSS)
- School of Natural Sciences
- University of Tasmania
| | - Estrella Sanz Rodriguez
- ASTech
- ARC Training Centre for Portable Analytical Separation Technologies (ASTech)
- and Australian Centre for Research on Separation Science (ACROSS)
- School of Natural Sciences
- University of Tasmania
| | - Paul R. Haddad
- ASTech
- ARC Training Centre for Portable Analytical Separation Technologies (ASTech)
- and Australian Centre for Research on Separation Science (ACROSS)
- School of Natural Sciences
- University of Tasmania
| | - Brett Paull
- ASTech
- ARC Training Centre for Portable Analytical Separation Technologies (ASTech)
- and Australian Centre for Research on Separation Science (ACROSS)
- School of Natural Sciences
- University of Tasmania
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11
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Rodriguez ES, Lam SC, Haddad PR, Paull B. Reversed-Phase Functionalised Multi-lumen Capillary as Combined Concentrator, Separation Column, and ESI Emitter in Capillary-LC–MS. Chromatographia 2018. [DOI: 10.1007/s10337-018-3629-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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12
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Feist PE, Loughran EA, Stack MS, Hummon AB. Quantitative proteomic analysis of murine white adipose tissue for peritoneal cancer metastasis. Anal Bioanal Chem 2017; 410:1583-1594. [PMID: 29282499 DOI: 10.1007/s00216-017-0813-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 11/30/2017] [Accepted: 12/06/2017] [Indexed: 12/15/2022]
Abstract
Cancer metastasis risk increases in older individuals, but the mechanisms for this risk increase are unclear. Many peritoneal cancers, including ovarian cancer, preferentially metastasize to peritoneal fat depots. However, there is a dearth of studies exploring aged peritoneal adipose tissue in the context of cancer. Because adipose tissue produces signals which influence several diseases including cancer, proteomics of adipose tissue in aged and young mice may provide insight into metastatic mechanisms. We analyzed mesenteric, omental, and uterine adipose tissue groups from the peritoneal cavities of young and aged C57BL/6J mouse cohorts with a low-fraction SDS-PAGE gelLC-MS/MS method. We identified 2308 protein groups and quantified 2167 groups, among which several protein groups showed twofold or greater abundance differences between the aged and young cohorts. Cancer-related gene products previously identified as significant in another age-related study were found altered in this study. Several gene products known to suppress proliferation and cellular invasion were found downregulated in the aged cohort, including R-Ras, Arid1a, and heat shock protein β1. In addition, multiple protein groups were identified within single cohorts, including the proteins Cd11a, Stat3, and Ptk2b. These data suggest that adipose tissue is a strong candidate for analysis to identify possible contributors to cancer metastasis in older subjects. The results of this study, the first of its kind using uterine adipose tissue, contribute to the understanding of the role of adipose tissue in age-related alteration of oncogenic pathways, which may help elucidate the mechanisms of increased metastatic tumor burden in the aged. Graphical abstract We analyzed mesenteric, omental, and uterine adipose tissue groups from the peritoneal cavities of young and aged C57BL/6J mouse cohorts with a low-fraction SDS-PAGE gelLC-MS/MS method. These fat depots are preferential sites for many peritoneal cancers. The results of this study, the first of its kind using uterine adipose tissue, contribute to the understanding of the role of adipose tissue in age-related alteration of oncogenic pathways, which may help elucidate the mechanisms of increased metastatic tumor burden in the aged.
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Affiliation(s)
- Peter E Feist
- Integrated Biomedical Sciences Program, University of Notre Dame, Notre Dame, IN, 46556, USA
- Department of Chemistry and Biochemistry, Harper Cancer Research Institute, University of Notre Dame, 251 140B McCourtney Hall, Notre Dame, IN, 46556, USA
| | - Elizabeth A Loughran
- Integrated Biomedical Sciences Program, University of Notre Dame, Notre Dame, IN, 46556, USA
- Department of Chemistry and Biochemistry, Harper Cancer Research Institute, University of Notre Dame, 251 140B McCourtney Hall, Notre Dame, IN, 46556, USA
| | - M Sharon Stack
- Department of Chemistry and Biochemistry, Harper Cancer Research Institute, University of Notre Dame, 251 140B McCourtney Hall, Notre Dame, IN, 46556, USA
| | - Amanda B Hummon
- Department of Chemistry and Biochemistry, Harper Cancer Research Institute, University of Notre Dame, 251 140B McCourtney Hall, Notre Dame, IN, 46556, USA.
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13
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LI RN, WANG YN, PENG MH, WANG XY, GUO GS. Preparation and Application of Porous Layer Open Tubular Capillary Columns with Narrow Bore in Liquid Chromatography. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2017. [DOI: 10.1016/s1872-2040(17)61057-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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14
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Su Y, Shi Q, Wei W. Single cell proteomics in biomedicine: High-dimensional data acquisition, visualization, and analysis. Proteomics 2017; 17. [PMID: 28128880 DOI: 10.1002/pmic.201600267] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Revised: 01/20/2017] [Accepted: 01/23/2017] [Indexed: 11/11/2022]
Abstract
New insights on cellular heterogeneity in the last decade provoke the development of a variety of single cell omics tools at a lightning pace. The resultant high-dimensional single cell data generated by these tools require new theoretical approaches and analytical algorithms for effective visualization and interpretation. In this review, we briefly survey the state-of-the-art single cell proteomic tools with a particular focus on data acquisition and quantification, followed by an elaboration of a number of statistical and computational approaches developed to date for dissecting the high-dimensional single cell data. The underlying assumptions, unique features, and limitations of the analytical methods with the designated biological questions they seek to answer will be discussed. Particular attention will be given to those information theoretical approaches that are anchored in a set of first principles of physics and can yield detailed (and often surprising) predictions.
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Affiliation(s)
- Yapeng Su
- NanoSystems Biology Cancer Center, Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Qihui Shi
- Key Laboratory of Systems Biomedicine (Ministry of Education), School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Wei Wei
- NanoSystems Biology Cancer Center, Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA.,Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California - Los Angeles, Los Angeles, CA, USA
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15
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An automated and self-cleaning nano liquid chromatography mass spectrometry platform featuring an open tubular multi-hole crystal fiber solid phase extraction column and an open tubular separation column. J Chromatogr A 2017; 1518:104-110. [DOI: 10.1016/j.chroma.2017.08.071] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Revised: 08/21/2017] [Accepted: 08/24/2017] [Indexed: 11/24/2022]
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16
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Lynch KB, Chen A, Liu S. Miniaturized high-performance liquid chromatography instrumentation. Talanta 2017; 177:94-103. [PMID: 29108588 DOI: 10.1016/j.talanta.2017.09.016] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Revised: 09/04/2017] [Accepted: 09/06/2017] [Indexed: 12/26/2022]
Abstract
Miniaturized high performance liquid chromatography (HPLC) has attracted increasing attention for its potential in high-throughput analyses and point-of-care applications. In this review we highlight the recent advancements in HPLC system miniaturization. We focus on the major components that constitute these instruments along with their respective advantages and drawbacks as well as present a few representative miniaturized HPLC systems. We discuss briefly some of the applications and also anticipate the future development trends of these instrumental platforms.
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Affiliation(s)
- Kyle B Lynch
- Department of Chemistry and Biochemistry, University of Oklahoma, USA.
| | - Apeng Chen
- Department of Chemistry and Biochemistry, University of Oklahoma, USA
| | - Shaorong Liu
- Department of Chemistry and Biochemistry, University of Oklahoma, USA
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17
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Preparation of open tubular capillary columns by in situ ring-opening polymerization and their applications in cLC-MS/MS analysis of tryptic digest. Anal Chim Acta 2017; 979:58-65. [DOI: 10.1016/j.aca.2017.05.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Revised: 04/30/2017] [Accepted: 05/06/2017] [Indexed: 11/23/2022]
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18
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Ceciliani F, Roccabianca P, Giudice C, Lecchi C. Application of post-genomic techniques in dog cancer research. MOLECULAR BIOSYSTEMS 2017; 12:2665-79. [PMID: 27345606 DOI: 10.1039/c6mb00227g] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Omics techniques have been widely applied to veterinary science, although mostly on farm animal productions and infectious diseases. In canine oncology, on the contrary, the use of omics methodologies is still far behind. This review presents the most recent achievement in the application of postgenomic techniques, such as transcriptomics, proteomics, and metabolomics, to canine cancer research. The protocols to recover material suitable for omics analyses from formalin-fixed, paraffin-embedded tissues are presented, and omics applications for biomarker discovery and their potential for cancer diagnostics in veterinary medicine are highlighted.
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Affiliation(s)
- F Ceciliani
- Department of Veterinary Medicine, Università di Milano, Via Celoria 02, 20133 Milano, Italy.
| | - P Roccabianca
- Department of Veterinary Medicine, Università di Milano, Via Celoria 02, 20133 Milano, Italy.
| | - C Giudice
- Department of Veterinary Medicine, Università di Milano, Via Celoria 02, 20133 Milano, Italy.
| | - C Lecchi
- Department of Veterinary Medicine, Università di Milano, Via Celoria 02, 20133 Milano, Italy.
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19
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Li R, Shao Y, Yu Y, Wang X, Guo G. Pico-HPLC system integrating an equal inner diameter femtopipette into a 900 nm I.D. porous layer open tubular column. Chem Commun (Camb) 2017; 53:4104-4107. [DOI: 10.1039/c7cc00799j] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A pico-HPLC method was developed using a bifunctional chromatographic column enabling femtoliter volume sampling and separation.
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Affiliation(s)
- Ruonan Li
- Beijing Key Laboratory for Green Catalysis and Separation
- Department of Chemistry and Chemistry Engineering
- Beijing University of Technology
- Beijing 100124
- China
| | - Yunlong Shao
- Beijing Key Laboratory for Green Catalysis and Separation
- Department of Chemistry and Chemistry Engineering
- Beijing University of Technology
- Beijing 100124
- China
| | - Yanmin Yu
- Beijing Key Laboratory for Green Catalysis and Separation
- Department of Chemistry and Chemistry Engineering
- Beijing University of Technology
- Beijing 100124
- China
| | - Xiayan Wang
- Beijing Key Laboratory for Green Catalysis and Separation
- Department of Chemistry and Chemistry Engineering
- Beijing University of Technology
- Beijing 100124
- China
| | - Guangsheng Guo
- Beijing Key Laboratory for Green Catalysis and Separation
- Department of Chemistry and Chemistry Engineering
- Beijing University of Technology
- Beijing 100124
- China
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20
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Quanico J, Franck J, Wisztorski M, Salzet M, Fournier I. Progress and Potential of Imaging Mass Spectrometry Applied to Biomarker Discovery. Methods Mol Biol 2017; 1598:21-43. [PMID: 28508356 DOI: 10.1007/978-1-4939-6952-4_2] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Mapping provides a direct means to assess the impact of protein biomarkers and puts into context their relevance in the type of cancer being examined. To this end, mass spectrometry imaging (MSI) was developed to provide the needed spatial information which is missing in traditional liquid-based mass spectrometric proteomics approaches. Aptly described as a "molecular histology" technique, MSI gives an additional dimension in characterizing tumor biopsies, allowing for mapping of hundreds of molecules in a single analysis. A decade of developments focused on improving and standardizing MSI so that the technique can be translated into the clinical setting. This review describes the progress made in addressing the technological development that allows to bridge local protein detection by MSI to its identification and to illustrate its potential in studying various aspects of cancer biomarker discovery.
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Affiliation(s)
- Jusal Quanico
- Université de Lille 1, INSERM, U1192-Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), 59000, Lille, France
| | - Julien Franck
- Université de Lille 1, INSERM, U1192-Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), 59000, Lille, France
| | - Maxence Wisztorski
- Université de Lille 1, INSERM, U1192-Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), 59000, Lille, France
| | - Michel Salzet
- Université de Lille 1, INSERM, U1192-Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), 59000, Lille, France
| | - Isabelle Fournier
- Université de Lille 1, INSERM, U1192-Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), 59000, Lille, France.
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21
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Peng L, Zhu M, Zhang L, Liu H, Zhang W. Preparation and evaluation of 3 m open tubular capillary columns with a zwitterionic polymeric porous layer for liquid chromatography. J Sep Sci 2016; 39:3736-3744. [DOI: 10.1002/jssc.201600535] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Revised: 07/29/2016] [Accepted: 08/01/2016] [Indexed: 12/30/2022]
Affiliation(s)
- Li Peng
- Shanghai Key Laboratory of Functional Materials Chemistry, School of Chemistry and Molecular Engineering; East China University of Science and Technology; Shanghai P. R. China
| | - Manman Zhu
- Shanghai Key Laboratory of Functional Materials Chemistry, School of Chemistry and Molecular Engineering; East China University of Science and Technology; Shanghai P. R. China
| | - Lingyi Zhang
- Shanghai Key Laboratory of Functional Materials Chemistry, School of Chemistry and Molecular Engineering; East China University of Science and Technology; Shanghai P. R. China
| | - Haiyan Liu
- Shanghai Key Laboratory of Functional Materials Chemistry, School of Chemistry and Molecular Engineering; East China University of Science and Technology; Shanghai P. R. China
| | - Weibing Zhang
- Shanghai Key Laboratory of Functional Materials Chemistry, School of Chemistry and Molecular Engineering; East China University of Science and Technology; Shanghai P. R. China
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22
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Wall modified photonic crystal fibre capillaries as porous layer open tubular columns for in-capillary micro-extraction and capillary chromatography. Anal Chim Acta 2016; 905:1-7. [DOI: 10.1016/j.aca.2015.10.005] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Revised: 10/01/2015] [Accepted: 10/07/2015] [Indexed: 12/15/2022]
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23
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Staunton L, Tonry C, Lis R, Finn S, O Leary J, Loda M, Bowden M, Pennington SR. Profiling the tumor microenvironment proteome in prostate cancer using laser capture microdissection coupled to LCMSA technical report. EUPA OPEN PROTEOMICS 2015; 10:19-23. [PMID: 29900095 PMCID: PMC5988569 DOI: 10.1016/j.euprot.2015.11.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Revised: 11/03/2015] [Accepted: 11/09/2015] [Indexed: 10/27/2022]
Abstract
Laser capture microdissection (LCM) allows microscopic procurement of specific cell types from tissue sections. Here, we present an optimized workflow for coupling LCM to LCMS/MS including: sectioning of tissue, a standard LCM workflow, protein digestion and advanced LCMS/MS. Soluble proteins extracted from benign epithelial cells, their associated stroma, tumor epithelial cells and their associated stromal cells from a single patient tissue sample were digested and profiled using advanced LCMS/MS. The correlation between technical replicates was R2 = 0.99 with a mean % CV of 9.55% ± 8.73. The correlation between sample replicates was R2 = 0.97 with a mean % CV of 13.83% ± 10.17. This represents a robust, systematic approach for profiling of the tumor microenvironment using LCM coupled to label-free LCMS/MS.
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Affiliation(s)
- L Staunton
- Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - C Tonry
- Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - R Lis
- Center for Molecular Oncologic Pathology, Dana-Farber Cancer Institute, 450 Brookline Ave., Boston, MA, USA
| | - S Finn
- St Jamess Hospital, Jamess St., Dublin 8, Ireland
| | - J O Leary
- St Jamess Hospital, Jamess St., Dublin 8, Ireland
| | - M Loda
- Center for Molecular Oncologic Pathology, Dana-Farber Cancer Institute, 450 Brookline Ave., Boston, MA, USA
| | - M Bowden
- Center for Molecular Oncologic Pathology, Dana-Farber Cancer Institute, 450 Brookline Ave., Boston, MA, USA
| | - S R Pennington
- Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland
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24
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Nazario CED, Silva MR, Franco MS, Lanças FM. Evolution in miniaturized column liquid chromatography instrumentation and applications: An overview. J Chromatogr A 2015; 1421:18-37. [PMID: 26381569 DOI: 10.1016/j.chroma.2015.08.051] [Citation(s) in RCA: 77] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Revised: 08/24/2015] [Accepted: 08/25/2015] [Indexed: 02/01/2023]
Abstract
The purpose of this article is to underline the miniaturized LC instrumental system and describe the evolution of commercially available systems by discussing their advantages and drawbacks. Nowadays, there are already many miniaturized LC systems available with a great variety of pump design, interface and detectors as well as efficient columns technologies and reduced connections devices. The solvent delivery systems are able to drive the mobile phase without flow splitters and promote gradient elution using either dual piston reciprocating or syringe-type pumps. The mass spectrometry as detection system is the most widely used detection system; among many alternative ionization sources direct-EI LC-MS is a promising alternative to APCI. In addition, capillary columns are now available showing many possibilities of stationary phases, inner diameters and hardware materials. This review provides a discussion about miniaturized LC demonstrating fundamentals and instrumentals' aspects of the commercially available miniaturized LC instrumental system mainly nano and micro LC formats. This review also covers the recent developments and trends in instrumentation, capillary and nano columns, and several applications of this very important and promising field.
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Affiliation(s)
| | - Meire R Silva
- Institute of Chemistry of Sao Carlos, University of Sao Paulo, Sao Carlos, SP, Brazil
| | - Maraíssa S Franco
- Institute of Chemistry of Sao Carlos, University of Sao Paulo, Sao Carlos, SP, Brazil
| | - Fernando M Lanças
- Institute of Chemistry of Sao Carlos, University of Sao Paulo, Sao Carlos, SP, Brazil.
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25
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Abstract
In proteomics, nano-LC is arguably the most common tool for separating peptides/proteins prior to MS. The main advantage of nano-LC is enhanced sensitivity, as compounds enter the MS in more concentrated bands. This is particularly relevant for determining low abundant compounds in limited samples. Nano-LC columns can produce peak capacities of 1000 or more, and very narrow columns can be used to perform proteomics of 1000 cells or less. Also, nano-LC can be coupled with online add-ons such as selective trap columns or enzymatic reactors, for faster and more automated analysis. Nano-LC is today an established tool for research laboratories; but can nano-LC-based systems soon be ready for more routine settings, such as in clinics?
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26
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Feist P, Hummon AB. Proteomic challenges: sample preparation techniques for microgram-quantity protein analysis from biological samples. Int J Mol Sci 2015; 16:3537-63. [PMID: 25664860 PMCID: PMC4346912 DOI: 10.3390/ijms16023537] [Citation(s) in RCA: 180] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Accepted: 01/29/2015] [Indexed: 12/22/2022] Open
Abstract
Proteins regulate many cellular functions and analyzing the presence and abundance of proteins in biological samples are central focuses in proteomics. The discovery and validation of biomarkers, pathways, and drug targets for various diseases can be accomplished using mass spectrometry-based proteomics. However, with mass-limited samples like tumor biopsies, it can be challenging to obtain sufficient amounts of proteins to generate high-quality mass spectrometric data. Techniques developed for macroscale quantities recover sufficient amounts of protein from milligram quantities of starting material, but sample losses become crippling with these techniques when only microgram amounts of material are available. To combat this challenge, proteomicists have developed micro-scale techniques that are compatible with decreased sample size (100 μg or lower) and still enable excellent proteome coverage. Extraction, contaminant removal, protein quantitation, and sample handling techniques for the microgram protein range are reviewed here, with an emphasis on liquid chromatography and bottom-up mass spectrometry-compatible techniques. Also, a range of biological specimens, including mammalian tissues and model cell culture systems, are discussed.
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Affiliation(s)
- Peter Feist
- Department of Chemistry and Biochemistry, Integrated Biomedical Sciences Program, and the Harper Cancer Research Institute, 251 Nieuwland Science Hall, University of Notre Dame, Notre Dame, IN 46556, USA.
| | - Amanda B Hummon
- Department of Chemistry and Biochemistry, Integrated Biomedical Sciences Program, and the Harper Cancer Research Institute, 251 Nieuwland Science Hall, University of Notre Dame, Notre Dame, IN 46556, USA.
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27
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Sun J, Zhang GL, Li S, Ivanov AR, Fenyo D, Lisacek F, Murthy SK, Karger BL, Brusic V. Pathway analysis and transcriptomics improve protein identification by shotgun proteomics from samples comprising small number of cells--a benchmarking study. BMC Genomics 2014; 15 Suppl 9:S1. [PMID: 25521637 PMCID: PMC4290587 DOI: 10.1186/1471-2164-15-s9-s1] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Proteomics research is enabled with the high-throughput technologies, but our ability to identify expressed proteome is limited in small samples. The coverage and consistency of proteome expression are critical problems in proteomics. Here, we propose pathway analysis and combination of microproteomics and transcriptomics analyses to improve mass-spectrometry protein identification from small size samples. RESULTS Multiple proteomics runs using MCF-7 cell line detected 4,957 expressed proteins. About 80% of expressed proteins were present in MCF-7 transcripts data; highly expressed transcripts are more likely to have expressed proteins. Approximately 1,000 proteins were detected in each run of the small sample proteomics. These proteins were mapped to gene symbols and compared with gene sets representing canonical pathways, more than 4,000 genes were extracted from the enriched gene sets. The identified canonical pathways were largely overlapping between individual runs. Of identified pathways 182 were shared between three individual small sample runs. CONCLUSIONS Current technologies enable us to directly detect 10% of expressed proteomes from small sample comprising as few as 50 cells. We used knowledge-based approaches to elucidate the missing proteome that can be verified by targeted proteomics. This knowledge-based approach includes pathway analysis and combination of gene expression and protein expression data for target prioritization. Genes present in both the enriched gene sets (canonical pathways collection) and in small sample proteomics data correspond to approximately 50% of expressed proteomes in larger sample proteomics data. In addition, 90% of targets from canonical pathways were estimated to be expressed. The comparison of proteomics and transcriptomics data, suggests that highly expressed transcripts have high probability of protein expression. However, approximately 10% of expressed proteins could not be matched with the expressed transcripts.
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28
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Cheong WJ, Zaidi SA, Kim YS. An Open Tubular CEC Column of Excellent Separation Efficiency for Proteomic Analysis. B KOREAN CHEM SOC 2014. [DOI: 10.5012/bkcs.2014.35.10.3115] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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29
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Hustoft HK, Vehus T, Brandtzaeg OK, Krauss S, Greibrokk T, Wilson SR, Lundanes E. Open tubular lab-on-column/mass spectrometry for targeted proteomics of nanogram sample amounts. PLoS One 2014; 9:e106881. [PMID: 25222838 PMCID: PMC4164520 DOI: 10.1371/journal.pone.0106881] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2014] [Accepted: 08/09/2014] [Indexed: 12/28/2022] Open
Abstract
A novel open tubular nanoproteomic platform featuring accelerated on-line protein digestion and high-resolution nano liquid chromatography mass spectrometry (LC-MS) has been developed. The platform features very narrow open tubular columns, and is hence particularly suited for limited sample amounts. For enzymatic digestion of proteins, samples are passed through a 20 µm inner diameter (ID) trypsin + endoproteinase Lys-C immobilized open tubular enzyme reactor (OTER). Resulting peptides are subsequently trapped on a monolithic pre-column and transferred on-line to a 10 µm ID porous layer open tubular (PLOT) liquid chromatography LC separation column. Wnt/ß-catenein signaling pathway (Wnt-pathway) proteins of potentially diagnostic value were digested+detected in targeted-MS/MS mode in small cell samples and tumor tissues within 120 minutes. For example, a potential biomarker Axin1 was identifiable in just 10 ng of sample (protein extract of ∼1,000 HCT15 colon cancer cells). In comprehensive mode, the current OTER-PLOT set-up could be used to identify approximately 1500 proteins in HCT15 cells using a relatively short digestion+detection cycle (240 minutes), outperforming previously reported on-line digestion/separation systems. The platform is fully automated utilizing common commercial instrumentation and parts, while the reactor and columns are simple to produce and have low carry-over. These initial results point to automated solutions for fast and very sensitive MS based proteomics, especially for samples of limited size.
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Affiliation(s)
| | - Tore Vehus
- Department of Chemistry, University of Oslo, Oslo, Norway
| | | | - Stefan Krauss
- Unit for Cell Signaling, Cancer Stem Cell Innovation Center, Oslo University Hospital, Oslo, Norway
| | - Tyge Greibrokk
- Department of Chemistry, University of Oslo, Oslo, Norway
| | | | - Elsa Lundanes
- Department of Chemistry, University of Oslo, Oslo, Norway
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30
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Longuespée R, Fléron M, Pottier C, Quesada-Calvo F, Meuwis MA, Baiwir D, Smargiasso N, Mazzucchelli G, De Pauw-Gillet MC, Delvenne P, De Pauw E. Tissue Proteomics for the Next Decade? Towards a Molecular Dimension in Histology. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2014; 18:539-52. [DOI: 10.1089/omi.2014.0033] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Rémi Longuespée
- Mass Spectrometry Laboratory, GIGA-Research, Department of Chemistry, University of Liège, Liège, Belgium
| | - Maximilien Fléron
- Mammalian Cell Culture Laboratory, GIGA-Research, Department of Biomedical and Preclinical Sciences, University of Liège, Liège, Belgium
| | - Charles Pottier
- Laboratory of Experimental Pathology, GIGA-Cancer, Department of Pathology, University of Liège, Liège, Belgium
| | - Florence Quesada-Calvo
- Hepato-Gastroenterology and Digestive Oncology Department, Liège University Hospital, University of Liège, Liège, Belgium
| | - Marie-Alice Meuwis
- Hepato-Gastroenterology and Digestive Oncology Department, Liège University Hospital, University of Liège, Liège, Belgium
| | - Dominique Baiwir
- GIGA-R, GIGA Proteomic Facilities, University of Liège, Liège, Belgium
| | - Nicolas Smargiasso
- Mass Spectrometry Laboratory, GIGA-Research, Department of Chemistry, University of Liège, Liège, Belgium
| | - Gabriel Mazzucchelli
- Mass Spectrometry Laboratory, GIGA-Research, Department of Chemistry, University of Liège, Liège, Belgium
| | - Marie-Claire De Pauw-Gillet
- Mammalian Cell Culture Laboratory, GIGA-Research, Department of Biomedical and Preclinical Sciences, University of Liège, Liège, Belgium
| | - Philippe Delvenne
- Laboratory of Experimental Pathology, GIGA-Cancer, Department of Pathology, University of Liège, Liège, Belgium
| | - Edwin De Pauw
- Mass Spectrometry Laboratory, GIGA-Research, Department of Chemistry, University of Liège, Liège, Belgium
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31
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Magdeldin S, Moresco JJ, Yamamoto T, Yates JR. Off-Line Multidimensional Liquid Chromatography and Auto Sampling Result in Sample Loss in LC/LC-MS/MS. J Proteome Res 2014; 13:3826-36. [PMID: 25040086 PMCID: PMC4123945 DOI: 10.1021/pr500530e] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2014] [Indexed: 01/09/2023]
Abstract
Large-scale proteomics often employs two orthogonal separation methods to fractionate complex peptide mixtures. Fractionation can involve ion exchange separation coupled to reversed-phase separation or, more recently, two reversed-phase separations performed at different pH values. When multidimensional separations are combined with tandem mass spectrometry for protein identification, the strategy is often referred to as multidimensional protein identification technology (MudPIT). MudPIT has been used in either an automated (online) or manual (offline) format. In this study, we evaluated the performance of different MudPIT strategies by both label-free and tandem mass tag (TMT) isobaric tagging. Our findings revealed that online MudPIT provided more peptide/protein identifications and higher sequence coverage than offline platforms. When employing an off-line fractionation method with direct loading of samples onto the column from an eppendorf tube via a high-pressure device, a 5.3% loss in protein identifications is observed. When off-line fractionated samples are loaded via an autosampler, a 44.5% loss in protein identifications is observed compared with direct loading of samples onto a triphasic capillary column. Moreover, peptide recovery was significantly lower after offline fractionation than in online fractionation. Signal-to-noise (S/N) ratio, however, was not significantly altered between experimental groups. It is likely that offline sample collection results in stochastic peptide loss due to noncovalent adsorption to solid surfaces. Therefore, the use of the offline approaches should be considered carefully when processing minute quantities of valuable samples.
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Affiliation(s)
- Sameh Magdeldin
- Department
of Chemical Physiology, The Scripps Research
Institute, 10550 North
Torrey Pines Road, SR11, La Jolla, California 92037, United States
- Department
of Structural Pathology, Institute of Nephrology, Graduate School
of Medical and Dental Sciences, Niigata
University, 1-757 Asahimachi-dori, Niigata 951-8510, Japan
- Department
of Physiology, Faculty of Veterinary Medicine, Suez Canal University, Ismailia 41522, Egypt
| | - James J. Moresco
- Department
of Chemical Physiology, The Scripps Research
Institute, 10550 North
Torrey Pines Road, SR11, La Jolla, California 92037, United States
| | - Tadashi Yamamoto
- Department
of Structural Pathology, Institute of Nephrology, Graduate School
of Medical and Dental Sciences, Niigata
University, 1-757 Asahimachi-dori, Niigata 951-8510, Japan
| | - John R. Yates
- Department
of Chemical Physiology, The Scripps Research
Institute, 10550 North
Torrey Pines Road, SR11, La Jolla, California 92037, United States
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32
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Wang N, Tang Y, Chen L, Li L. Microbore liquid chromatography ultraviolet detection for quantification of total peptide amount and its application for assessing sample quality in shotgun proteome analysis of hundreds of cells. J Chromatogr A 2014; 1338:51-7. [PMID: 24630977 DOI: 10.1016/j.chroma.2014.02.050] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2013] [Revised: 02/15/2014] [Accepted: 02/17/2014] [Indexed: 11/30/2022]
Abstract
Mass spectrometric profiling of the proteome of a small number of cells requires not only a sensitive instrument for protein/peptide separation and detection, but also a robust sample preparation protocol to process a very small amount of proteins (<1μg) present in few cells. We have developed and evaluated the performance of a microbore liquid chromatography (LC) UV detection system for quantifying the total amount of peptides in a shotgun proteome analysis workflow that is tailored for the analysis of hundreds of cancer cells. Upon the sample injection into a 1-mm-diameter reversed phase column, a step-gradient was used to first remove salts and other impurities and then elute the peptides quickly without much separation. The UV absorbance of eluted peptides at 214nm was used for peptide quantification with the aid of a calibration curve of a tryptic digest of a mixture of four standard proteins. Two linear calibration regions could be obtained in the peptide amount ranging from 0.03μg to 0.3μg and from 0.6μg to 5μg. The limit of quantification (LOQ) was determined to be 30ng (or 39ng in the linear calibration range). However, the presence of background proteins, mainly keratins, introduced during the sample preparation process was found to be the limiting factor in quantifying a lower amount of peptides from a cell lysate digest. With background absorbance from the digest of contaminant proteins in a solution, the LOQ was found to be 200ng. This nondestructive microbore LC-UV method should be useful in assessing sample quality during the development and applications of an efficient sample preparation method for proteome analysis of a small number of cells. As an example, this method was used for quantifying the peptides generated from breast cancer MCF-7 cell extracts with a limited number of cells: 250, 500 and 1000 cells. Using capillary LC quadrupole time-of-flight mass spectrometry, 81-126, 122-154 and 256-282 proteins could be identified from 250, 500, and 1000 cells, respectively, in duplicate experiments. This method was also applied for the analysis of biological triplicate samples of MCF-7 cells. The average numbers of peptides and proteins detected from the experimental triplicate analyses of biological triplicate samples were 400±71 (9 datasets) and 124±14, respectively, from 250 cells, and 531±44 and 162±16, respectively, from 500 cells.
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Affiliation(s)
- Nan Wang
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada
| | - Yanan Tang
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada
| | - Lu Chen
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada
| | - Liang Li
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada.
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33
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Pham TV, Piersma SR, Oudgenoeg G, Jimenez CR. Label-free mass spectrometry-based proteomics for biomarker discovery and validation. Expert Rev Mol Diagn 2014; 12:343-59. [DOI: 10.1586/erm.12.31] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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34
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Collins DA, Nesterenko EP, Paull B. Infrared photo-initiated fabrication of monolithic porous layer open tubular (monoPLOT) capillary columns for chromatographic applications. RSC Adv 2014. [DOI: 10.1039/c4ra03792h] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Investigation into the development of a fabrication approach for capillary porous layer open tubular (PLOT) chromatographic columns via infrared (IR) photo-initiated polymerisation and the optimisation of the technique is presented in this work.
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Affiliation(s)
- David A. Collins
- Irish Separation Science Cluster
- Dublin City University
- Dublin 9, Ireland
| | | | - Brett Paull
- Australian Centre for Research on Separation Science
- School of Physical Sciences
- University of Tasmania
- Hobart, Australia
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35
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Collins DA, Nesterenko EP, Paull B. Porous layer open tubular columns in capillary liquid chromatography. Analyst 2014; 139:1292-302. [DOI: 10.1039/c3an01869e] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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36
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On-line solid phase extraction–liquid chromatography, with emphasis on modern bioanalysis and miniaturized systems. J Pharm Biomed Anal 2014; 87:120-9. [DOI: 10.1016/j.jpba.2013.05.006] [Citation(s) in RCA: 101] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2013] [Revised: 05/06/2013] [Accepted: 05/07/2013] [Indexed: 11/24/2022]
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37
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Hustoft HK, Brandtzaeg OK, Rogeberg M, Misaghian D, Torsetnes SB, Greibrokk T, Reubsaet L, Wilson SR, Lundanes E. Integrated enzyme reactor and high resolving chromatography in "sub-chip" dimensions for sensitive protein mass spectrometry. Sci Rep 2013; 3:3511. [PMID: 24336509 PMCID: PMC3863811 DOI: 10.1038/srep03511] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2013] [Accepted: 11/28/2013] [Indexed: 12/29/2022] Open
Abstract
Reliable, sensitive and automatable analytical methodology is of great value in e.g. cancer diagnostics. In this context, an on-line system for enzymatic cleavage of proteins, subsequent peptide separation by liquid chromatography (LC) with mass spectrometric detection has been developed using "sub-chip" columns (10-20 μm inner diameter, ID). The system could detect attomole amounts of isolated cancer biomarker progastrin-releasing peptide (ProGRP), in a more automatable fashion compared to previous methods. The workflow combines protein digestion using an 20 μm ID immobilized trypsin reactor with a polymeric layer of 2-hydroxyethyl methacrylate-vinyl azlactone (HEMA-VDM), desalting on a polystyrene-divinylbenzene (PS-DVB) monolithic trap column, and subsequent separation of resulting peptides on a 10 μm ID (PS-DVB) porous layer open tubular (PLOT) column. The high resolution of the PLOT columns was maintained in the on-line system, resulting in narrow chromatographic peaks of 3-5 seconds. The trypsin reactors provided repeatable performance and were compatible with long-term storage.
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Affiliation(s)
- Hanne Kolsrud Hustoft
- Department of Chemistry, University of Oslo, Post Box 1033 Blindern, NO-0315 Oslo, Norway
| | | | - Magnus Rogeberg
- Department of Chemistry, University of Oslo, Post Box 1033 Blindern, NO-0315 Oslo, Norway
- Department of Neurology, Akershus University Hospital, 1478 Lørenskog, Norway
| | - Dorna Misaghian
- Department of Chemistry, University of Oslo, Post Box 1033 Blindern, NO-0315 Oslo, Norway
| | - Silje Bøen Torsetnes
- School of Pharmacy, University of Oslo, Post Box 1068 Blindern, NO-0316 Oslo, Norway
| | - Tyge Greibrokk
- Department of Chemistry, University of Oslo, Post Box 1033 Blindern, NO-0315 Oslo, Norway
| | - Léon Reubsaet
- School of Pharmacy, University of Oslo, Post Box 1068 Blindern, NO-0316 Oslo, Norway
| | - Steven Ray Wilson
- Department of Chemistry, University of Oslo, Post Box 1033 Blindern, NO-0315 Oslo, Norway
| | - Elsa Lundanes
- Department of Chemistry, University of Oslo, Post Box 1033 Blindern, NO-0315 Oslo, Norway
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38
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Rogeberg M, Vehus T, Grutle L, Greibrokk T, Wilson SR, Lundanes E. Separation optimization of long porous-layer open-tubular columns for nano-LC-MS of limited proteomic samples. J Sep Sci 2013; 36:2838-47. [DOI: 10.1002/jssc.201300499] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2013] [Revised: 05/31/2013] [Accepted: 05/31/2013] [Indexed: 11/09/2022]
Affiliation(s)
- Magnus Rogeberg
- Department of Chemistry; University of Oslo; Blindern Oslo Norway
| | - Tore Vehus
- Department of Chemistry; University of Oslo; Blindern Oslo Norway
| | - Lene Grutle
- Department of Chemistry; University of Oslo; Blindern Oslo Norway
| | - Tyge Greibrokk
- Department of Chemistry; University of Oslo; Blindern Oslo Norway
| | | | - Elsa Lundanes
- Department of Chemistry; University of Oslo; Blindern Oslo Norway
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39
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Cheong WJ, Ali F, Kim YS, Lee JW. Comprehensive overview of recent preparation and application trends of various open tubular capillary columns in separation science. J Chromatogr A 2013; 1308:1-24. [DOI: 10.1016/j.chroma.2013.07.107] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2013] [Revised: 07/26/2013] [Accepted: 07/31/2013] [Indexed: 12/15/2022]
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40
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Wei W, Shin YS, Ma C, Wang J, Elitas M, Fan R, Heath JR. Microchip platforms for multiplex single-cell functional proteomics with applications to immunology and cancer research. Genome Med 2013; 5:75. [PMID: 23998271 PMCID: PMC3978720 DOI: 10.1186/gm479] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Single-cell functional proteomics assays can connect genomic information to biological function through quantitative and multiplex protein measurements. Tools for single-cell proteomics have developed rapidly over the past 5 years and are providing approaches for directly elucidating phosphoprotein signaling networks in cancer cells or for capturing high-resolution snapshots of immune system function in patients with various disease conditions. We discuss advances in single-cell proteomics platforms, with an emphasis on microchip methods. These methods can provide a direct correlation of morphological, functional and molecular signatures at the single-cell level. We also provide examples of how those platforms are being applied to both fundamental biology and clinical studies, focusing on immune-system monitoring and phosphoprotein signaling networks in cancer.
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Affiliation(s)
- Wei Wei
- NanoSystems Biology Cancer Center, Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA ; Department of Applied Physics and Materials Science, California Institute of Technology, Pasadena, CA 91125, USA
| | - Young Shik Shin
- NanoSystems Biology Cancer Center, Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Chao Ma
- NanoSystems Biology Cancer Center, Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Jun Wang
- NanoSystems Biology Cancer Center, Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Meltem Elitas
- Department of Biomedical Engineering, Yale University, New Haven, CT 06520, USA
| | - Rong Fan
- Department of Biomedical Engineering, Yale University, New Haven, CT 06520, USA
| | - James R Heath
- NanoSystems Biology Cancer Center, Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
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Kojima K, Bowersock GJ, Kojima C, Klug CA, Grizzle WE, Mobley JA. Validation of a robust proteomic analysis carried out on formalin-fixed paraffin-embedded tissues of the pancreas obtained from mouse and human. Proteomics 2013; 12:3393-402. [PMID: 22997103 DOI: 10.1002/pmic.201100663] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2011] [Revised: 08/17/2012] [Accepted: 09/05/2012] [Indexed: 01/02/2023]
Abstract
A number of reports have recently emerged with focus on extraction of proteins from formalin-fixed paraffin-embedded (FFPE) tissues for MS analysis; however, reproducibility and robustness as compared to flash frozen controls is generally overlooked. The goal of this study was to identify and validate a practical and highly robust approach for the proteomics analysis of FFPE tissues. FFPE and matched frozen pancreatic tissues obtained from mice (n = 8) were analyzed using 1D-nanoLC-MS(MS)(2) following work up with commercially available kits. The chosen approach for FFPE tissues was found to be highly comparable to that of frozen. In addition, the total number of unique peptides identified between the two groups was highly similar, with 958 identified for FFPE and 1070 identified for frozen, with protein identifications that corresponded by approximately 80%. This approach was then applied to archived human FFPE pancreatic cancer specimens (n = 11) as compared to uninvolved tissues (n = 8), where 47 potential pancreatic ductal adenocarcinoma markers were identified as significantly increased, of which 28 were previously reported. Further, these proteins share strongly overlapping pathway associations to pancreatic cancer that include estrogen receptor α. Together, these data support the validation of an approach for the proteomic analysis of FFPE tissues that is straightforward and highly robust, which can also be effectively applied toward translational studies of disease.
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Affiliation(s)
- Kyoko Kojima
- Department of Surgery, University of Alabama at Birmingham, Birmingham, AL 35294, USA
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Wiśniewski JR, Duś K, Mann M. Proteomic workflow for analysis of archival formalin-fixed and paraffin-embedded clinical samples to a depth of 10 000 proteins. Proteomics Clin Appl 2013; 7:225-33. [PMID: 23090905 DOI: 10.1002/prca.201200046] [Citation(s) in RCA: 113] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2012] [Revised: 08/03/2012] [Accepted: 09/28/2012] [Indexed: 02/06/2023]
Abstract
PURPOSE Archival formalin-fixed and paraffin-embedded clinical samples represent a very diverse source of material for proteomic investigation of diseases, often with follow-up patient information. Here, we describe an analytical workflow for analysis of laser-capture microdissected formalin-fixed and paraffin-embedded samples that allows studying proteomes to a depth of 10 000 proteins per sample. EXPERIMENTAL DESIGN The workflow involves lysis of tissue in SDS-containing buffer, detergent removal, and consecutive digestion of the proteins with two enzymes by the multienzyme digestion filter-aided sample preparation method. Resulting peptides are fractionated by pipette-tip based strong anion exchange into six fractions and analyzed by LC-MS/MS on a bench top quadrupole Orbitrap mass spectrometer. RESULTS Analysis of the data using the MaxQuant software resulted in the identification of 9502 ± 28 protein groups per a 110 nL sample of microdissected cells from human colonic adenoma. This depth of proteome analysis enables systemic insights into the organization of the adenoma cells and an estimation of the abundances of known biomarkers. It also allows the identification of proteins expressed from tumor suppressors, oncogenes, and other key players in the development and progression of the colorectal cancer. CONCLUSION AND CLINICAL RELEVANCE Our proteomic platform can be used for quantitative comparisons between samples representing different stages of diseases and thus can be applied to the discovery of biomarkers or drug targets.
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Affiliation(s)
- Jacek R Wiśniewski
- Department of Proteomics and Signal Transduction, Max-Planck-Institute of Biochemistry, Martinsried, Germany.
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43
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Performance evaluation of thick film open tubular silica capillary by reversed phase liquid chromatography. J Chromatogr A 2013; 1283:110-5. [DOI: 10.1016/j.chroma.2013.01.107] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2012] [Revised: 01/25/2013] [Accepted: 01/28/2013] [Indexed: 11/23/2022]
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Jahn M, Seifert J, von Bergen M, Schmid A, Bühler B, Müller S. Subpopulation-proteomics in prokaryotic populations. Curr Opin Biotechnol 2013; 24:79-87. [DOI: 10.1016/j.copbio.2012.10.017] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2012] [Revised: 10/15/2012] [Accepted: 10/24/2012] [Indexed: 10/27/2022]
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45
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Quanico J, Franck J, Dauly C, Strupat K, Dupuy J, Day R, Salzet M, Fournier I, Wisztorski M. Development of liquid microjunction extraction strategy for improving protein identification from tissue sections. J Proteomics 2013; 79:200-18. [DOI: 10.1016/j.jprot.2012.11.025] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2012] [Revised: 11/20/2012] [Accepted: 11/30/2012] [Indexed: 12/22/2022]
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46
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Mukherjee S, Rodriguez-Canales J, Hanson J, Emmert-Buck MR, Tangrea MA, Prieto DA, Blonder J, Johann DJ. Proteomic analysis of frozen tissue samples using laser capture microdissection. Methods Mol Biol 2013; 1002:71-83. [PMID: 23625395 DOI: 10.1007/978-1-62703-360-2_6] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
The discovery of effective cancer biomarkers is essential for the development of both advanced molecular diagnostics and new therapies/medications. Finding and exploiting useful clinical biomarkers for cancer patients is fundamentally linked to improving outcomes. Towards these aims, the heterogeneous nature of tumors represents a significant problem. Thus, methods establishing an effective functional linkage between laser capture microdissection (LCM) and mass spectrometry (MS) provides for an enhanced molecular profiling of homogenous, specifically targeted cell populations from solid tumors. Utilizing frozen tissue avoids molecular degradation and bias that can be induced by other preservation techniques. Since clinical samples are often of a small quantity, tissue losses must be minimized. Therefore, all steps are carried out in the same single tube. Proteins are identified through peptide sequencing and subsequent matching against a specific proteomic database. Using such an approach enhances clinical biomarker discovery in the following ways. First, LCM allows for the complexity of a solid tumor to be reduced. Second, MS provides for the profiling of proteins, which are the ultimate bio-effectors. Third, by selecting for tumor proper or microenvironment-specific cells from clinical samples, the heterogeneity of individual solid tumors is directly addressed. Finally, since proteins are the targets of most pharmaceuticals, the enriched protein data streams can then be further analyzed for potential biomarkers, drug targets, pathway elucidation, as well as an enhanced understanding of the various pathologic processes under study. Within this context, the following method illustrates in detail a synergy between LCM and MS for an enhanced molecular profiling of solid tumors and clinical biomarker discovery.
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47
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Affiliation(s)
- Gert Desmet
- Department of Chemical Engineering, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels,
Belgium
| | - Sebastiaan Eeltink
- Department of Chemical Engineering, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels,
Belgium
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48
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Abstract
Multidimensional liquid chromatography (LC) combined with mass spectrometry (MS) has become a standard technique in proteomics to reduce sample complexity and to tackle the dynamic range in protein abundance. Fractionation is necessary to obtain a comprehensive analysis of complex biological samples such as tissue and mammalian cell lines. However, extensive fractionation comes at the expense of sample loss, presenting a bottleneck in the analysis of limited amounts of material. In this protocol, we describe a two-dimensional chromatographic strategy based on a combination of hydrophilic interaction liquid chromatography (HILIC; with a zwitterionic packing material, ZIC-cHILIC) and reversed-phase chromatography, which allows proteomic analyses with minimal sample loss. Experimental aspects related to obtaining maximum recovery are discussed, including how to optimally prepare samples for this system. Examples involving protein lysates originating from cultured cell lines and cells sorted by flow cytometry are used to show the power, sensitivity and versatility of the technique. Once the ZIC-cHILIC fractionation system has been optimized and standardized, this protocol requires ∼5-6 d, including sample preparation and fraction analysis.
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49
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Forster S, Kolmar H, Altmaier S. Synthesis and characterization of new generation open tubular silica capillaries for liquid chromatography. J Chromatogr A 2012; 1265:88-94. [PMID: 23084484 DOI: 10.1016/j.chroma.2012.09.054] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2012] [Revised: 09/14/2012] [Accepted: 09/18/2012] [Indexed: 10/27/2022]
Abstract
The chromatographic performance gain of open tubular (OT) silica capillaries over packed beds has been demonstrated theoretically. However, experimental progress in the preparative realization of these columns is still lacking behind as thick films are required for a sufficient mass loadability. Here, silica sol-gel chemistry in confined spaces was applied to the preparation of thick-film OT capillaries comprising a mesoporous layer with a thickness of approximately 500 nm covalently attached to the capillary wall. Samples were synthesized varying both in length and inner diameter (ID) and the resulting layer morphology was investigated using scanning electron microscopy. The chromatographic performance of these first generation columns was evaluated by normal phase chromatography utilizing standard capillary-LC equipment. Separations of small molecules in a 15 μm ID column provided high theoretical plate numbers (up to 170,000) and a good retention capacity within reasonable retention times (<1 h), bearing the unavoidable trade-off between column efficiency and analysis time.
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Affiliation(s)
- Simon Forster
- Technische Universität Darmstadt, Petersenstraße 22, 64287 Darmstadt, Germany
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50
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Jafari M, Primo V, Smejkal GB, Moskovets EV, Kuo WP, Ivanov AR. Comparison of in-gel protein separation techniques commonly used for fractionation in mass spectrometry-based proteomic profiling. Electrophoresis 2012; 33:2516-26. [PMID: 22899259 PMCID: PMC4234072 DOI: 10.1002/elps.201200031] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Fractionation of complex samples at the cellular, subcellular, protein, or peptide level is an indispensable strategy to improve the sensitivity in mass spectrometry-based proteomic profiling. This study revisits, evaluates, and compares the most common gel-based protein separation techniques i.e. 1D SDS-PAGE, 1D preparative SDS-PAGE, IEF-IPG, and 2D-PAGE in their performance as fractionation approaches in nano LC-ESI-MS/MS analysis of a mixture of protein standards and mitochondrial extracts isolated from rat liver. This work demonstrates that all the above techniques provide complementary protein identification results, but 1D SDS-PAGE and IEF-IPG had the highest number of identifications. The IEF-IPG technique resulted in the highest average number of detected peptides per protein. The 2D-PAGE was evaluated as a protein fractionation approach. This work shows that the recovery of proteins and resulting proteolytic digests is highly dependent on the total volume of the gel matrix. The performed comparison of the fractionation techniques demonstrates the potential of a combination of orthogonal 1D SDS-PAGE and IEF-IPG for the improved sensitivity of profiling without significant decrease in throughput.
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Affiliation(s)
- Mohieddin Jafari
- HSPH Proteomics Resource, Department of Genetics and Complex Diseases, Harvard School of Public Health, Boston, MA, USA
- School of Paramedical Science, Shahid Beheshti University of Medical Science, Tehran, Iran
- School of Computer Science, Institute for Research in Fundamental Sciences (IPM), Tehran, Iran
| | - Vincent Primo
- Harvard Catalyst, The Harvard Clinical and Translational Science Center, Laboratory for Innovative Translational Technologies, Boston, MA, USA
| | - Gary B. Smejkal
- Harvard Catalyst, The Harvard Clinical and Translational Science Center, Laboratory for Innovative Translational Technologies, Boston, MA, USA
| | | | - Winston P. Kuo
- Harvard Catalyst, The Harvard Clinical and Translational Science Center, Laboratory for Innovative Translational Technologies, Boston, MA, USA
- Harvard School of Dental Medicine, Department of Developmental Biology, Boston, MA, USA
| | - Alexander R. Ivanov
- HSPH Proteomics Resource, Department of Genetics and Complex Diseases, Harvard School of Public Health, Boston, MA, USA
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