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Vankeerberghen B, Op de Beeck J, Desmet G. Column-Only Band Broadening in a Porous Shell Radially Elongated Pillar Array Column. Anal Chem 2024; 96:3618-3626. [PMID: 38350649 DOI: 10.1021/acs.analchem.3c05756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2024]
Abstract
In the quest for better performing separation media for liquid chromatography, micropillar array columns have received great interest over the past years. While previous research was mainly focused around micropillar array columns (μPACs) filled with cylindrical pillars, this contribution discusses μPACs with rectangular pillars, which, for the first time, have been anodized and hence carry a mesoporous shell. We report on a series of on-chip measurements of the band broadening and flow permeability in a μPAC with very wide radially elongated pillars (3·75 μm) and with an interpillar distance (2 μm) between that of the first (2.5 μm) and second generation (1.25 μm) of cylindrical μPACs. Because of the extreme flow path tortuosity, this type of μPAC can produce very large plate numbers over a short distance. Despite the relatively large interpillar distance, we obtain Hmin = 0.26 μm for a nearly unretained component (phase retention factor, k' ≈ 0.24) and Hmin = 0.79 μm for a retained component with k' ≈ 3. The kinetic performance in terms of separation impedance (Ei = 19) is considerably improved compared to cylindrical pillar μPACs (Ei in range 40-50) and is in excellent agreement with the theoretical value for an open tubular channel with a rectangular cross-section (Ei = 18). This shows that rectangular μPACs can be represented as a parallel bundle of interconnected open-tubular channels.
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Affiliation(s)
- Bert Vankeerberghen
- Department of Chemical Engineering, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
| | - Jeff Op de Beeck
- Thermo Fisher Scientific, Technologiepark-Zwijnaarde 82, 9052 Gent, Belgium
| | - Gert Desmet
- Department of Chemical Engineering, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
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2
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Kømurcu KS, Wilson SR, Røberg-Larsen H. LC-MS Approaches for Oxysterols in Various Biosamples. Adv Exp Med Biol 2024; 1440:57-71. [PMID: 38036875 DOI: 10.1007/978-3-031-43883-7_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/02/2023]
Abstract
Oxysterols are involved in a plethora of biological processes, including a wide variety of diseases. Therefore, monitoring oxysterols is important for obtaining a deeper understanding of their biological roles and utilizing them as, for example, biomarkers. However, oxysterols can be challenging compounds to study, as they can be very similar in chemical structure but still have distinct biological roles. In addition, oxysterols may be difficult to detect, even with advanced analytical instrumentation. We here focus on the use of liquid chromatography-mass spectrometry (LC-MS) for the analysis of oxysterols, with an additional focus on the steps needed to prepare oxysterols for LC-MS. Steps can include chemical modification of the oxysterols for improving LC-MS sensitivity and adding chemicals that can reveal if the oxysterol levels have been perturbed during preparation. We then round off with descriptions and applications of various sample preparations for different biological matrices, from blood to cells, and biosamples with emerging attention, for example, exosomes and organoids. Taken together, oxysterol analysis is highly compatible with a wide variety of biosamples, allowing for a deeper understanding of these challenging analytes.
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3
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Vankeerberghen B, Op de Beeck J, Desmet G. On-Chip Comparison of the Performance of First- and Second-Generation Micropillar Array Columns. Anal Chem 2023; 95:13822-13828. [PMID: 37677150 DOI: 10.1021/acs.analchem.3c01829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/09/2023]
Abstract
Because of its dimensions, the recently introduced micropillar array columns are most suited for high-efficiency liquid chromatography separations in proteomics. Unlike the packed bed columns and capillary-based column formats, the micropillar array concept still has significant room to progress in terms of the reduction of its characteristic size (i.e., pillar diameter and interpillar distance) to open the road to even higher-efficiency separations and their applications. We report here on the on-chip comparison between first-generation (Gen 1) and second-generation (Gen 2) micropillar array columns wherein the pillar and interpillar size have been halved. Because of the on-chip measurements, the observed plate heights H represent the fundamental band broadening, devoid of any extra-column band-broadening effects. The observed reduction of H with a factor of 2 around the uopt-velocity and with a factor of 4 in the C-term dominated regime of the van Deemter-curve is in full agreement with the theoretically expected gain. This shows the pillar and interpillar size reduction could be effectuated without affecting the theoretical separation potential of the micropillar arrays. Compared to Gen 1, Gen 2 offers a 4-fold reduction of the required analysis time around the optimal velocity and about a 16-fold reduction in the C-term-dominated range.
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Affiliation(s)
- Bert Vankeerberghen
- Department of Chemical Engineering, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
| | - Jeff Op de Beeck
- Thermo Fisher Scientific, Technologiepark-Zwijnaarde 82, 9052 Gent, Belgium
| | - Gert Desmet
- Department of Chemical Engineering, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
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4
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Perchepied S, Zhou Z, Mitulović G, Eeltink S. Exploiting ion-mobility mass spectrometry for unraveling proteome complexity. J Sep Sci 2023; 46:e2300512. [PMID: 37746674 DOI: 10.1002/jssc.202300512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 08/17/2023] [Accepted: 08/18/2023] [Indexed: 09/26/2023]
Abstract
Ion mobility spectrometry-mass spectrometry (IMS-MS) is experiencing rapid growth in proteomic studies, driven by its enhancements in dynamic range and throughput, increasing the quantitation precision, and the depth of proteome coverage. The core principle of ion mobility spectrometry is to separate ions in an inert gas under the influence of an electric field based on differences in drift time. This minireview provides an introduction to IMS operation modes and a description of advantages and limitations is presented. Moreover, the principles of trapped IMS-MS (TIMS-MS), including parallel accumulation-serial fragmentation are discussed. Finally, emerging applications linked to TIMS focusing on sample throughput (in clinical proteomics) and sensitivity (single-cell proteomics) are reviewed, and the possibilities of intact protein analysis are discussed.
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Affiliation(s)
- Stan Perchepied
- Department of Chemical Engineering, Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | - Zhuoheng Zhou
- Department of Chemical Engineering, Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | | | - Sebastiaan Eeltink
- Department of Chemical Engineering, Vrije Universiteit Brussel (VUB), Brussels, Belgium
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5
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Greguš M, Ivanov AR, Wilson SR. Ultralow flow liquid chromatography and related approaches: A focus on recent bioanalytical applications. J Sep Sci 2023; 46:e2300440. [PMID: 37528733 PMCID: PMC11087205 DOI: 10.1002/jssc.202300440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 07/25/2023] [Accepted: 07/26/2023] [Indexed: 08/03/2023]
Abstract
Ultralow flow LC employs ultra-narrow bore columns and mid-range pL/min to low nL/min flow rates (i.e., ≤20 nL/min). The separation columns that are used under these conditions are typically 2-30 μm in inner diameter. Ultralow flow LC systems allow for exceptionally high sensitivity and frequently high resolution. There has been an increasing interest in the analysis of scarce biological samples, for example, circulating tumor cells, extracellular vesicles, organelles, and single cells, and ultralow flow LC was efficiently applied to such samples. Hence, advances towards dedicated ultralow flow LC instrumentation, technical approaches, and higher throughput (e.g., tens-to-hundreds of single cells analyzed per day) were recently made. Here, we review the types of ultralow flow LC technology, followed by a discussion of selected representative ultralow flow LC applications, focusing on the progress made in bioanalysis of amount-limited samples during the last 10 years. We also discuss several recently reported high-sensitivity applications utilizing flow rates up to 100 nL/min, which are below commonly used nanoLC flow rates. Finally, we discuss the path forward for future developments of ultralow flow LC.
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Affiliation(s)
- Michal Greguš
- Department of Chemistry and Chemical Biology, Barnett Institute of Chemical and Biological Analysis, Northeastern University, Boston, Massachusetts, USA
| | - Alexander R. Ivanov
- Department of Chemistry and Chemical Biology, Barnett Institute of Chemical and Biological Analysis, Northeastern University, Boston, Massachusetts, USA
| | - Steven Ray Wilson
- Hybrid Technology Hub-Centre of Excellence, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
- Department of Chemistry, University of Oslo, Oslo, Norway
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6
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Aydoğan C, Beltekin B, Alharthi S, Ağca CA, Erdoğan İY. Nano-liquid chromatography with monolithic stationary phase based on naphthyl monomer for proteomics analysis. J Chromatogr A 2023; 1690:463804. [PMID: 36689803 DOI: 10.1016/j.chroma.2023.463804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 01/11/2023] [Accepted: 01/15/2023] [Indexed: 01/18/2023]
Abstract
Monolithic poly(2-vinylnaphthalene-co-divinylbenzene) columns were introduced, for the first time, and were evaluated as the separation media for nano-liquid chromatography (nano-LC). These columns were prepared by in-situ polymerization of 2-vinylnaphthalene (2-VNA) as the functional monomer and divinylbenzene (DVB) as the crosslinker in a fused silica capillary column of 50 µm i.d. Various porogenic solvents, including tetrahydrofuran (THF), dodecanol and toluene were used for morphology optimization. Final monolithic column (referred to as VNA column) was characterized by using scanning electron microscopy (SEM) and chromatographic analyses. Alkylbenzenes (ABs), and polyaromatic hydrocarbons (PAHs) were separated using the VNA column while the column offered excellent hydrophobic and π-π interactions under reversed-phase conditions. Theoretical plates number up to 41,200 plates/m in isocratic mode for ethylbenzene could be achieved. The potential of the final VNA column was demonstrated with a gradient elution in the separation of six intact proteins, including ribonuclease A (RNase A), cytochrome C (Cyt C), lysozyme (Lys), β-lactoglobulin (β-lac), myoglobin (My) and α-chymotrypsinogen (α-chym) in nano LC system. The column was then applied to the peptide analysis of trypsin digested cytochrome C, allowing a high peak capacity up to 1440 and the further proteomics analysis of COS-7 cell line was attempted applying the final monolithic column in nano-LC UV system.
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Affiliation(s)
- Cemil Aydoğan
- Food Analysis and Research Laboratory, Bingöl University, Bingöl, Türkiye; Department of Food Engineering, Bingöl University, Bingöl, Türkiye; Department of Chemistry, Bingöl University, Bingöl, Türkiye.
| | - Büşra Beltekin
- Food Analysis and Research Laboratory, Bingöl University, Bingöl, Türkiye
| | - Sarah Alharthi
- Department of Chemistry, College of Science, Taif University, P.O. Box 11099, Taif, 21944 Saudi Arabia
| | - Can Ali Ağca
- Department of Molecular Biology, Bingöl University, Bingöl, Türkiye
| | - İbrahim Y Erdoğan
- Department of Chemistry, Bingöl University, Bingöl, Türkiye; Faculty of Health Sciences, Bingöl University, Bingöl, Türkiye
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7
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Kogler S, Kømurcu KS, Olsen C, Shoji JY, Skottvoll FS, Krauss S, Wilson SR, Røberg-Larsen H. Organoids, organ-on-a-chip, separation science and mass spectrometry: An update. Trends Analyt Chem 2023. [DOI: 10.1016/j.trac.2023.116996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2023]
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8
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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9
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Liang Y, Zhang L, Zhang Y. Chromatographic separation of peptides and proteins for characterization of proteomes. Chem Commun (Camb) 2023; 59:270-281. [PMID: 36504223 DOI: 10.1039/d2cc05568f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Characterization of proteomes aims to comprehensively characterize proteins in cells or tissues via two main strategies: (1) bottom-up strategy based on the separation and identification of enzymatic peptides; (2) top-down strategy based on the separation and identification of intact proteins. However, it is challenged by the high complexity of proteomes. Consequently, the improvements in peptide and protein separation technologies for simplifying the sample should be critical. In this feature article, separation columns for peptide and protein separation were introduced, and peptide separation technologies for bottom-up proteomic analysis as well as protein separation technologies for top-down proteomic analysis were summarized. The achievement, recent development, limitation and future trends are discussed. Besides, the outlook on challenges and future directions of chromatographic separation in the field of proteomics was also presented.
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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.
| | - 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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10
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Mao S. Recent advances in nanowire sensor assembly using laminar flow in open space. Trends Analyt Chem 2023. [DOI: 10.1016/j.trac.2023.116918] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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11
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Lenčo J, Jadeja S, Naplekov DK, Krokhin OV, Khalikova MA, Chocholouš P, Urban J, Broeckhoven K, Nováková L, Švec F. Reversed-Phase Liquid Chromatography of Peptides for Bottom-Up Proteomics: A Tutorial. J Proteome Res 2022; 21:2846-2892. [PMID: 36355445 DOI: 10.1021/acs.jproteome.2c00407] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The performance of the current bottom-up liquid chromatography hyphenated with mass spectrometry (LC-MS) analyses has undoubtedly been fueled by spectacular progress in mass spectrometry. It is thus not surprising that the MS instrument attracts the most attention during LC-MS method development, whereas optimizing conditions for peptide separation using reversed-phase liquid chromatography (RPLC) remains somewhat in its shadow. Consequently, the wisdom of the fundaments of chromatography is slowly vanishing from some laboratories. However, the full potential of advanced MS instruments cannot be achieved without highly efficient RPLC. This is impossible to attain without understanding fundamental processes in the chromatographic system and the properties of peptides important for their chromatographic behavior. We wrote this tutorial intending to give practitioners an overview of critical aspects of peptide separation using RPLC to facilitate setting the LC parameters so that they can leverage the full capabilities of their MS instruments. After briefly introducing the gradient separation of peptides, we discuss their properties that affect the quality of LC-MS chromatograms the most. Next, we address the in-column and extra-column broadening. The last section is devoted to key parameters of LC-MS methods. We also extracted trends in practice from recent bottom-up proteomics studies and correlated them with the current knowledge on peptide RPLC separation.
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Affiliation(s)
- Juraj Lenčo
- Department of Analytical Chemistry, Faculty of Pharmacy in Hradec Králové, Charles University, Heyrovského 1203/8, 500 05Hradec Králové, Czech Republic
| | - Siddharth Jadeja
- Department of Analytical Chemistry, Faculty of Pharmacy in Hradec Králové, Charles University, Heyrovského 1203/8, 500 05Hradec Králové, Czech Republic
| | - Denis K Naplekov
- Department of Analytical Chemistry, Faculty of Pharmacy in Hradec Králové, Charles University, Heyrovského 1203/8, 500 05Hradec Králové, Czech Republic
| | - Oleg V Krokhin
- Department of Internal Medicine, Manitoba Centre for Proteomics and Systems Biology, University of Manitoba, 799 JBRC, 715 McDermot Avenue, WinnipegR3E 3P4, Manitoba, Canada
| | - Maria A Khalikova
- Department of Analytical Chemistry, Faculty of Pharmacy in Hradec Králové, Charles University, Heyrovského 1203/8, 500 05Hradec Králové, Czech Republic
| | - Petr Chocholouš
- Department of Analytical Chemistry, Faculty of Pharmacy in Hradec Králové, Charles University, Heyrovského 1203/8, 500 05Hradec Králové, Czech Republic
| | - Jiří Urban
- Department of Chemistry, Faculty of Science, Masaryk University, Kamenice 5, 625 00Brno, Czech Republic
| | - Ken Broeckhoven
- Department of Chemical Engineering (CHIS), Faculty of Engineering, Vrije Universiteit Brussel, Pleinlaan 2, 1050Brussel, Belgium
| | - Lucie Nováková
- Department of Analytical Chemistry, Faculty of Pharmacy in Hradec Králové, Charles University, Heyrovského 1203/8, 500 05Hradec Králové, Czech Republic
| | - František Švec
- Department of Analytical Chemistry, Faculty of Pharmacy in Hradec Králové, Charles University, Heyrovského 1203/8, 500 05Hradec Králové, Czech Republic
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Abstract
Cellular heterogeneity is commonly investigated using single-cell genomics and transcriptomics to investigate biological questions such as disease mechanism, therapeutic screening, and genomic and transcriptomic diversity between cellular populations and subpopulations at the cellular level. Single-cell mass spectrometry (MS)-based proteomics enables the high-throughput examination of protein expression at the single-cell level with wide applicability, and with spatial and temporal resolution, applicable to the study of cellular development, disease, effect of treatment, etc. The study of single-cell proteomics has lagged behind genomics and transcriptomics largely because proteins from single-cell samples cannot be amplified as DNA and RNA can using well established techniques such as PCR. Therefore, analytical methods must be robust, reproducible, and sensitive enough to detect the very small amount of protein within a single cell. To this end, nearly every step of the proteomics process has been extensively altered and improved to facilitate the proteomics analysis of single cells including cell counting and sorting, lysis, protein digestion, sample cleanup, separation, MS data acquisition, and data analysis. Here, we have reviewed recent advances in single-cell protein separation using nano reversed phase liquid chromatography (nRPLC) and capillary electrophoresis (CE) to inform application driven selection of separation techniques in the laboratory setting.
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Affiliation(s)
| | - Mulin Fang
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK 73019
| | - Si Wu
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK 73019
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Estrada-Pérez AR, Bakalara N, García-Vázquez JB, Rosales-Hernández MC, Fernández-Pomares C, Correa-Basurto J. LC–MS Based Lipidomics Depict Phosphatidylethanolamine as Biomarkers of TNBC MDA-MB-231 over nTNBC MCF-7 Cells. Int J Mol Sci 2022; 23:ijms232012074. [PMID: 36292927 PMCID: PMC9603493 DOI: 10.3390/ijms232012074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 09/20/2022] [Accepted: 09/22/2022] [Indexed: 11/29/2022] Open
Abstract
Breast cancer (BC) is the first malignant neoplasm in women, with a high death rate despite early diagnoses and treatment advances. Significant differences exist between the most common BC and triple-negative breast cancer (TNBC). TNBC presents molecular differences such as lacking expression of the estrogen receptor (ER), progesterone receptor (PR), and HER2 proteins, making this cancer have a poor clinical prognostic and lack clear strategies for its treatment. However, growing evidence points to metabolic dysregulation as another differential process between stages and types of BC. Therefore, the study of this crucial hallmark could identify new therapeutic targets to treat this aggressive form of BC. These differences induce an in vitro exploration of the metabolic behavior of the MCF7 cells (nTNBC) and MDA-MB-231 (TNBC) cells under lipidomic based LC–MS. The results show more significant differences in lipid regulation (phosphatidylethanolamine) that could be associated with the aggressiveness and difficulties of the treatment of TNBC.
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Affiliation(s)
- Alan Rubén Estrada-Pérez
- Laboratorio de Diseño y Desarrollo de Nuevos Fármacos e Innovación Biotecnológica, Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis y Díaz Mirón, Ciudad de México 11340, Mexico
| | - Norbert Bakalara
- Centre National de la Recherche Scientifique, École Nationale Supérieure de Technologie des Biomolécules de Bordeaux INP, Univeristé de Bordeaux, 146 Rue Léo Saignat, 33000 Bordeaux, France
| | - Juan Benjamín García-Vázquez
- Laboratorio de Diseño y Desarrollo de Nuevos Fármacos e Innovación Biotecnológica, Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis y Díaz Mirón, Ciudad de México 11340, Mexico
| | - Martha Cecilia Rosales-Hernández
- Laboratorio de Biofísica y Biocatálisis, Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional, Ciudad de México 11340, Mexico
| | - Cynthia Fernández-Pomares
- Laboratorio de Diseño y Desarrollo de Nuevos Fármacos e Innovación Biotecnológica, Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis y Díaz Mirón, Ciudad de México 11340, Mexico
| | - José Correa-Basurto
- Laboratorio de Diseño y Desarrollo de Nuevos Fármacos e Innovación Biotecnológica, Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis y Díaz Mirón, Ciudad de México 11340, Mexico
- Correspondence:
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14
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Nix C, Cobraiville G, Gou MJ, Fillet M. Potential of Single Pulse and Multiplexed Drift-Tube Ion Mobility Spectrometry Coupled to Micropillar Array Column for Proteomics Studies. Int J Mol Sci 2022; 23:ijms23147497. [PMID: 35886845 PMCID: PMC9319919 DOI: 10.3390/ijms23147497] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2022] [Revised: 07/02/2022] [Accepted: 07/03/2022] [Indexed: 02/04/2023] Open
Abstract
Proteomics is one of the most significant methodologies to better understand the molecular pathways involved in diseases and to improve their diagnosis, treatment and follow-up. The investigation of the proteome of complex organisms is challenging from an analytical point of view, because of the large number of proteins present in a wide range of concentrations. In this study, nanofluidic chromatography, using a micropillar array column, was coupled to drift-tube ion mobility and time-of-flight mass spectrometry to identify as many proteins as possible in a protein digest standard of HeLa cells. Several chromatographic parameters were optimized. The high interest of drift-tube ion mobility to increase the number of identifications and to separate isobaric coeluting peptides was demonstrated. Multiplexed drift-tube ion mobility spectrometry was also investigated, to increase the sensitivity in proteomics studies. This innovative proteomics platform will be useful for analyzing patient samples to better understand unresolved disorders.
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15
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Dong C, Donnarumma F, Murray KK. Infrared Laser Ablation Microsampling for Small Volume Proteomics. J Am Soc Mass Spectrom 2022; 33:1003-1010. [PMID: 35536596 DOI: 10.1021/jasms.2c00063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Infrared (IR) laser ablation was used to remove localized tissue regions from which proteins were extracted and processed with a low volume sample preparation workflow for bottom-up proteomics by liquid chromatography tandem mass spectrometry (LC-MS/MS). A polytetrafluoroethylene (PTFE) coated glass slide with 2 mm diameter microwells was used to capture ablated rat brain tissue for in situ protein digestion with submicroliter solution volumes. The resulting peptides were analyzed with LC-MS/MS for protein identification and label-free quantification. The method was used to identify an average of 600, 1350, and 1900 proteins from ablation areas of 0.01, 0.04, and 0.1 mm2, respectively, from a 50 μm thick rat brain tissue section. Differential proteomics of 0.01 mm2 regions captured from cerebral cortex and corpus callosum was accomplished to demonstrate the capabilities of the approach.
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Affiliation(s)
- Chao Dong
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, United States
| | - Fabrizio Donnarumma
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, United States
| | - Kermit K Murray
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, United States
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