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Yeung D, Spicer V, Krokhin OV. Peptide retention time prediction for hydrophilic interaction liquid chromatography at acidic pH in formic-acid based eluents. J Chromatogr A 2024; 1736:465355. [PMID: 39260150 DOI: 10.1016/j.chroma.2024.465355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2024] [Revised: 09/05/2024] [Accepted: 09/06/2024] [Indexed: 09/13/2024]
Abstract
Peptide separation selectivity was evaluated for hydrophilic interaction liquid chromatography (HILIC) ZIC-HILIC, ZIC-cHILIC, and XBridge Amide sorbents using formic acid as eluent additive (pH 2.7). Sequence-specific retention prediction algorithms were trained using retention datasets of ∼30,000 peptides for each column. Our retention models were able to attain ∼0.98 R2-value and yielded retention coefficients that can be probed to understand peptide-stationary phase interaction. Overall, the hydrophilicity for these columns decreased when the mobile phase changed pH from 4.5 to 2.7, when using 0.1 % formic acid in the mobile phase. The acidic residues became protonated, and the resultant hydrophilic interaction is dampened at the lower pH, leaving only the basic residues as the primary hydrophilic interactors. Hence, peptides of increasing charge have higher retention. In this comparison between the three columns, ZIC-HILIC has the highest chromatographic resolution between groups of peptides of different charge. From the position-dependent retention coefficients for ZIC-HILIC at pH 2.7, we found that the amino acids at the terminal positions of the peptide modulate the basicity of the N-terminal amino group or the C-terminal Arg/Lys for tryptic peptides. With respect to the separation orthogonality between HILIC and acidic pH RPLC for two dimensional separations, the orthogonality values were lower at pH 2.7 than operating HILIC at pH 4.5 for the first dimension. We also demonstrate that ZIC-HILIC was able to distinguish citrullinated and deamidated peptides based on predicted retention values.
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Affiliation(s)
- Darien Yeung
- Manitoba Centre for Proteomics and Systems Biology, 799 JBRC, 715 McDermot Avenue, Winnipeg R3E 3P4, Canada; Department of Biochemistry and Medical Genetics, University of Manitoba, 336 BMSB, 745 Bannatyne Avenue, Winnipeg R3E 0J9, Canada
| | - Victor Spicer
- Manitoba Centre for Proteomics and Systems Biology, 799 JBRC, 715 McDermot Avenue, Winnipeg R3E 3P4, Canada
| | - Oleg V Krokhin
- Manitoba Centre for Proteomics and Systems Biology, 799 JBRC, 715 McDermot Avenue, Winnipeg R3E 3P4, Canada; Department of Biochemistry and Medical Genetics, University of Manitoba, 336 BMSB, 745 Bannatyne Avenue, Winnipeg R3E 0J9, Canada; Department of Chemistry, University of Manitoba, 360 Parker Building, 144 Dysart Road, Winnipeg R3T 2N2, Canada; Department of Internal Medicine, University of Manitoba, 799 JBRC, 715 McDermot Avenue, Winnipeg R3E 3P4, Canada.
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2
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Bottom-Up Proteomics: Advancements in Sample Preparation. Int J Mol Sci 2023; 24:ijms24065350. [PMID: 36982423 PMCID: PMC10049050 DOI: 10.3390/ijms24065350] [Citation(s) in RCA: 28] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 02/28/2023] [Accepted: 03/09/2023] [Indexed: 03/14/2023] Open
Abstract
Liquid chromatography–tandem mass spectrometry (LC–MS/MS)-based proteomics is a powerful technique for profiling proteomes of cells, tissues, and body fluids. Typical bottom-up proteomic workflows consist of the following three major steps: sample preparation, LC–MS/MS analysis, and data analysis. LC–MS/MS and data analysis techniques have been intensively developed, whereas sample preparation, a laborious process, remains a difficult task and the main challenge in different applications. Sample preparation is a crucial stage that affects the overall efficiency of a proteomic study; however, it is prone to errors and has low reproducibility and throughput. In-solution digestion and filter-aided sample preparation are the typical and widely used methods. In the past decade, novel methods to improve and facilitate the entire sample preparation process or integrate sample preparation and fractionation have been reported to reduce time, increase throughput, and improve reproducibility. In this review, we have outlined the current methods used for sample preparation in proteomics, including on-membrane digestion, bead-based digestion, immobilized enzymatic digestion, and suspension trapping. Additionally, we have summarized and discussed current devices and methods for integrating different steps of sample preparation and peptide fractionation.
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3
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Phlairaharn T, Ye Z, Krismer E, Pedersen AK, Pietzner M, Olsen JV, Schoof EM, Searle BC. Optimizing linear ion trap data independent acquisition towards single cell proteomics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.21.529444. [PMID: 36865114 PMCID: PMC9980145 DOI: 10.1101/2023.02.21.529444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/23/2023]
Abstract
A linear ion trap (LIT) is an affordable, robust mass spectrometer that proves fast scanning speed and high sensitivity, where its primary disadvantage is inferior mass accuracy compared to more commonly used time-of-flight (TOF) or orbitrap (OT) mass analyzers. Previous efforts to utilize the LIT for low-input proteomics analysis still rely on either built-in OTs for collecting precursor data or OT-based library generation. Here, we demonstrate the potential versatility of the LIT for low-input proteomics as a stand-alone mass analyzer for all mass spectrometry measurements, including library generation. To test this approach, we first optimized LIT data acquisition methods and performed library-free searches with and without entrapment peptides to evaluate both the detection and quantification accuracy. We then generated matrix-matched calibration curves to estimate the lower limit of quantification using only 10 ng of starting material. While LIT-MS1 measurements provided poor quantitative accuracy, LIT-MS2 measurements were quantitatively accurate down to 0.5 ng on column. Finally, we optimized a suitable strategy for spectral library generation from low-input material, which we used to analyze single-cell samples by LIT-DIA using LIT-based libraries generated from as few as 40 cells.
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4
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Mao Y, Su T, Lin T, Yang H, Zhao Y, Zhang Y, Dai X. Comprehensive Plasma N-Glycoproteome Profiling Based on EThcD-sceHCD-MS/MS. Front Chem 2022; 10:920009. [PMID: 35795219 PMCID: PMC9251008 DOI: 10.3389/fchem.2022.920009] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 05/09/2022] [Indexed: 01/05/2023] Open
Abstract
Glycoproteins are involved in a variety of biological processes. More than one-third of the plasma protein biomarkers of tumors approved by the FDA are glycoproteins, and could improve the diagnostic specificity and/or sensitivity. Therefore, it is of great significance to perform the systematic characterization of plasma N-glycoproteome. In previous studies, we developed an integrated method based on the combinatorial peptide ligand library (CPLL) and stepped collision energy/higher energy collisional dissociation (sceHCD) for comprehensive plasma N-glycoproteome profiling. Recently, we presented a new fragmentation method, EThcD-sceHCD, which outperformed sceHCD in the accuracy of identification. Herein, we integrated the combinatorial peptide ligand library (CPLL) into EThcD-sceHCD and compared the performance of different mass spectrometry dissociation methods (EThcD-sceHCD, EThcD, and sceHCD) in the intact N-glycopeptide analysis of prostate cancer plasma. The results illustrated that EThcD-sceHCD was better than EThcD and sceHCD in the number of identified intact N-glycopeptides (two-folds). A combination of sceHCD and EThcD-sceHCD methods can cover almost all glycoproteins (96.4%) and intact N-glycopeptides (93.6%), indicating good complementarity between the two. Our study has great potential for medium- and low-abundance plasma glycoprotein biomarker discovery.
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Affiliation(s)
- Yonghong Mao
- Institute of Thoracic Oncology, West China Hospital, Sichuan University, Chengdu, China
| | - Tao Su
- Institutes for Systems Genetics, West China Hospital, Sichuan University, Chengdu, China
| | - Tianhai Lin
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, China
| | - Hao Yang
- Institutes for Systems Genetics, West China Hospital, Sichuan University, Chengdu, China
| | - Yang Zhao
- Mass Spectrometry Engineering Technology Research Center, Center for Advanced Measurement Science, National Institute of Metrology, Beijing, China
- *Correspondence: Yang Zhao, ; Yong Zhang, ; Xinhua Dai,
| | - Yong Zhang
- Institutes for Systems Genetics, West China Hospital, Sichuan University, Chengdu, China
- *Correspondence: Yang Zhao, ; Yong Zhang, ; Xinhua Dai,
| | - Xinhua Dai
- Mass Spectrometry Engineering Technology Research Center, Center for Advanced Measurement Science, National Institute of Metrology, Beijing, China
- *Correspondence: Yang Zhao, ; Yong Zhang, ; Xinhua Dai,
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5
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Kohler I, Verhoeven M, Haselberg R, Gargano AF. Hydrophilic interaction chromatography – mass spectrometry for metabolomics and proteomics: state-of-the-art and current trends. Microchem J 2022. [DOI: 10.1016/j.microc.2021.106986] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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6
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Iannetta AA, Hicks LM. Maximizing Depth of PTM Coverage: Generating Robust MS Datasets for Computational Prediction Modeling. Methods Mol Biol 2022; 2499:1-41. [PMID: 35696073 DOI: 10.1007/978-1-0716-2317-6_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Post-translational modifications (PTMs) regulate complex biological processes through the modulation of protein activity, stability, and localization. Insights into the specific modification type and localization within a protein sequence can help ascertain functional significance. Computational models are increasingly demonstrated to offer a low-cost, high-throughput method for comprehensive PTM predictions. Algorithms are optimized using existing experimental PTM data, thus accurate prediction performance relies on the creation of robust datasets. Herein, advancements in mass spectrometry-based proteomics technologies to maximize PTM coverage are reviewed. Further, requisite experimental validation approaches for PTM predictions are explored to ensure that follow-up mechanistic studies are focused on accurate modification sites.
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Affiliation(s)
- Anthony A Iannetta
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Leslie M Hicks
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
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Walter TH, Alden BA, Berthelette K, Field JA, Lawrence NL, McLaughlin J, Patel AV. Characterization of a highly stable zwitterionic hydrophilic interaction chromatography stationary phase based on hybrid organic/inorganic particles. J Sep Sci 2021; 45:1389-1399. [PMID: 34937126 PMCID: PMC9487986 DOI: 10.1002/jssc.202100859] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 12/14/2021] [Accepted: 12/16/2021] [Indexed: 11/08/2022]
Abstract
We have characterized a sulfobetaine stationary phase based on 1.7 μm ethylene-bridged hybrid organic/inorganic particles, which is intended for use in hydrophilic interaction chromatography. The efficiency of columns packed with this material were determined as a function of flow rate, demonstrating a minimum reduced plate height of 2.4. The batch-to-batch reproducibility was assessed using the separation of a mixture of acids, bases and neutrals. We compared the retention and selectivity of the hybrid sulfobetaine stationary phase to that of several benchmark materials. The hybrid sulfobetaine material gave strong retention for polar neutrals and high selectivity for methyl groups, hydroxy groups and configurational isomers. Large differences in cation and anion retention were observed among the columns. We characterized the acid and base stability of the hybrid sulfobetaine stationary phase, using accelerated tests at pH 1.3 and 11.0, both at 70°C. The results support a recommended pH range of 2 to 10. We also investigated the performance of columns packed with this material for metal-sensitive analytes, comparing conventional stainless steel column hardware to hardware that incorporates hybrid surface technology to mitigate interactions with metal surfaces. Compared to the conventional columns, the hybrid surface technology columns showed greatly improved peak shape. This article is protected by copyright. All rights reserved.
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8
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Abstract
Mucin-domain glycoproteins comprise a class of proteins whose densely O-glycosylated mucin domains adopt a secondary structure with unique biophysical and biochemical properties. The canonical family of mucins is well-known to be involved in various diseases, especially cancer. Despite this, very little is known about the site-specific molecular structures and biological activities of mucins, in part because they are extremely challenging to study by mass spectrometry (MS). Here, we summarize recent advancements toward this goal, with a particular focus on mucin-domain glycoproteins as opposed to general O-glycoproteins. We summarize proteolytic digestion techniques, enrichment strategies, MS fragmentation, and intact analysis, as well as new bioinformatic platforms. In particular, we highlight mucin directed technologies such as mucin-selective proteases, tunable mucin platforms, and a mucinomics strategy to enrich mucin-domain glycoproteins from complex samples. Finally, we provide examples of targeted mucin-domain glycoproteomics that combine these techniques in comprehensive site-specific analyses of proteins. Overall, this Review summarizes the methods, challenges, and new opportunities associated with studying enigmatic mucin domains.
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Affiliation(s)
- Valentina Rangel-Angarita
- Department of Chemistry, Yale University, 275 Prospect Street, New Haven, Connecticut 06511, United States
| | - Stacy A. Malaker
- Department of Chemistry, Yale University, 275 Prospect Street, New Haven, Connecticut 06511, United States
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9
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Wang Y, Hao Z, Pan L. Evaluation of multiple hydrophilic interaction chromatography columns and surrogate matrix for arginine quantification in saliva by high-resolution mass spectrometry. J Sep Sci 2021; 44:3580-3593. [PMID: 34405941 DOI: 10.1002/jssc.202100361] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 08/15/2021] [Accepted: 08/15/2021] [Indexed: 02/05/2023]
Abstract
Arginine, a pivotal ingredient in many biochemical synthetic pathways, can be used as a biomarker for many oral care clinical applications. It is still a challenge to develop a sensitive and reliable chromatographic method to quantify arginine as a biomarker in saliva, with or without arginine product pretreatment. The current method solved two critical issues for arginine quantitation in human saliva. The first issue was how to optimize arginine peak shape. A hydrophilic interaction chromatography method based on the column selection, pH and pKa relationship, mobile phase ionic strength, organic solvent consideration, and temperature effects was developed. An optimized chromatographic condition for arginine quantitation in the saliva matrix was obtained. The second issue was how to build confidence in the use of a simple surrogate matrix methodology to replace the more complex traditional standard addition methodology. The surrogate matrix methodology we developed is applicable to the measurement of arginine as a potential non-invasive biomarker in human saliva. The method detection and quantification limit reached 2 and 6 ng/mL. The tailing factor was within the 0.9-1.1 range even though arginine had three pKa values at 2.18, 9.09, and 13.2.
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Affiliation(s)
- Yu Wang
- Cross Category Research and Innovation Department, Technology Center, Colgate-Palmolive Company, Piscataway, New Jersey, USA
| | - Zhigang Hao
- Cross Category Research and Innovation Department, Technology Center, Colgate-Palmolive Company, Piscataway, New Jersey, USA
| | - Long Pan
- Cross Category Research and Innovation Department, Technology Center, Colgate-Palmolive Company, Piscataway, New Jersey, USA
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10
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Fast determination of 16 circulating neurotransmitters and their metabolites in plasma samples of spontaneously hypertensive rats intervened with five different Uncaria. J Chromatogr B Analyt Technol Biomed Life Sci 2021; 1179:122856. [PMID: 34329893 DOI: 10.1016/j.jchromb.2021.122856] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2020] [Revised: 06/07/2021] [Accepted: 07/06/2021] [Indexed: 12/18/2022]
Abstract
This study aimed to establish a sensitive, reproducible, and rapid liquid chromatography method with tandem mass spectrometry detection to perform simultaneous quantitative analysis of 16 neurotransmitters and their metabolites in rat plasma, including levodopa, dopamine, norepinephrine, epinephrine, L-tryptophan, kynurenic acid, serotonin, melatonin, choline, acetylcholine, histamine, phenylethylamine, as well as excitatory (L-glutamic acid and L-aspartic acid) and inhibitory (γ-aminobutyric acid and L-glycine) neurotransmitters. These analytes were measured by ultra-high performance chromatography coupled with triple quadrupole mass spectrometry using a hydrophilic interaction chromatographic column (ethylene-bridged hybrid amide column). The internal standards of stable isotope labeling were used to improve the reliability of the results. Our method provided high linearity for all neurotransmitters (for all coefficients measured > 0.99), with inter- and intra-day accuracy from -14.82% to 17.49% and precision was between 0.89% and 17.70%. The method was subsequently verified in an animal study, where the intervention of five different Uncarias, the traditional Chinese medicine with hypotensive effects, was applied to the spontaneously hypertensive rats (SHRs). SHRs showed dysregulated plasma kynurenic acid, acetylcholine, and norepinephrine levels, and these neuroactive analytes were significantly restored by Uncaria treatment compared with the model group (SHR group). Compared with captopril, included as a positive control for its hypotensive effect, Uncaria had more effects on perturbing the levels of plasma neurotransmitters, which might indicate Uncaria's potential in treating symptoms related to the nervous system. These results suggested that the changes in the neurotransmitters and their metabolites in plasma may be related to the pathogenesis of hypertension. It also provided valuable information about the action mechanisms of Uncaria on its hypotensive effects.
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11
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Zheng R, Govorukhina N, Arrey TN, Pynn C, van der Zee A, Marko-Varga G, Bischoff R, Boychenko A. Online-2D NanoLC-MS for Crude Serum Proteome Profiling: Assessing Sample Preparation Impact on Proteome Composition. Anal Chem 2021; 93:9663-9668. [PMID: 34236853 DOI: 10.1021/acs.analchem.1c01291] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Although current LC-MS technology permits scientists to efficiently screen clinical samples in translational research, e.g., steroids, biogenic amines, and even plasma or serum proteomes, in a daily routine, maintaining the balance between throughput and analytical depth is still a limiting factor. A typical approach to enhance the proteome depth is employing offline two-dimensional (2D) fractionation techniques before reversed-phase nanoLC-MS/MS analysis (1D-nanoLC-MS). These additional sample preparation steps usually require extensive sample manipulation, which could result in sample alteration and sample loss. Here, we present and compare 1D-nanoLC-MS with an automated online-2D high-pH RP × low pH RP separation method for deep proteome profiling using a nanoLC system coupled to a high-resolution accurate-mass mass spectrometer. The proof-of-principle study permitted the identification of ca. 500 proteins with ∼10,000 peptides in 15 enzymatically digested crude serum samples collected from healthy donors in 3 laboratories across Europe. The developed method identified 60% more peptides in comparison with conventional 1D nanoLC-MS/MS analysis with ca. 4 times lower throughput while retaining the quantitative information. Serum sample preparation related changes were revealed by applying unsupervised classification techniques and, therefore, must be taken into account while planning multicentric biomarker discovery and validation studies. Overall, this novel method reduces sample complexity and boosts the number of peptide and protein identifications without the need for extra sample handling procedures for samples equivalent to less than 1 μL of blood, which expands the space for potential biomarker discovery by looking deeper into the composition of biofluids.
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Affiliation(s)
- Runsheng Zheng
- Thermo Fisher Scientific, Dornierstrasse 4, 82110 Germering, Germany
| | - Natalia Govorukhina
- Department of Analytical Biochemistry, University of Groningen, 9713 AV Groningen, The Netherlands
| | - Tabiwang N Arrey
- Thermo Fisher Scientific, Hanna-Kunath-Straße 11, 28199 Bremen, Germany
| | - Christopher Pynn
- Thermo Fisher Scientific, Dornierstrasse 4, 82110 Germering, Germany
| | - Ate van der Zee
- University Medical Centre Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands
| | - György Marko-Varga
- Clinical Protein Science and Imaging, Lund University, Box 117, S-22100 Lund, Sweden
| | - Rainer Bischoff
- Department of Analytical Biochemistry, University of Groningen, 9713 AV Groningen, The Netherlands
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12
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Abou Zeid L, Pell A, Tytus T, Delangle P, Bresson C. Separation of multiphosphorylated cyclopeptides and their positional isomers by hydrophilic interaction liquid chromatography (HILIC) coupled to electrospray ionization mass spectrometry (ESI-MS). J Chromatogr B Analyt Technol Biomed Life Sci 2021; 1177:122792. [PMID: 34102536 DOI: 10.1016/j.jchromb.2021.122792] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 05/17/2021] [Accepted: 05/19/2021] [Indexed: 10/21/2022]
Abstract
Peptides are efficient models used in different fields such as toxicology to study the interactions of several contaminants at the molecular scale, requiring the development of bio-analytical strategies. In this context, Hydrophilic interaction liquid chromatography (HILIC) coupled to electrospray ionization mass spectrometry (ESI-MS) was used to separate synthetic multiphosphorylated cyclopeptides and their positional isomers at physiological pH. We assessed (i) the selectivity of eleven HILIC columns, from different manufacturers and packed with diverse polar sorbents, and (ii) the effect of mobile phase composition on the separation selectivity. The best selectivity and baseline resolution were achieved with the columns grafted by neutral sorbents amide and diol. Furthermore, we investigated the HILIC retention mechanism of these peptides by examining the effect of the number of phosphorylated residues in the peptide scaffold on their retention. The peptide behavior followed the classical hydrophilic partitioning mechanism exclusively on amide and diol columns. This trend was not fully respected on bare and hybrid silica due to the attractive/repulsive interactions of the deprotonated surface silanol groups with the Arginine or Glutamate residues in the peptide scaffold according to the peptide sequence. The position of the phosphorylated amino acid in the peptide backbone also showed to have an impact on the retention, making possible the separation of positional isomers of these multiphosphorylated cyclic peptides using HILIC.
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Affiliation(s)
- Lana Abou Zeid
- Université Paris-Saclay, CEA, Service d'Etudes Analytiques et de Réactivité des Surfaces, F-91191 Gif-sur-Yvette, France; Sorbonne Université, F-75005 Paris, France.
| | - Albert Pell
- Université Paris-Saclay, CEA, Service d'Etudes Analytiques et de Réactivité des Surfaces, F-91191 Gif-sur-Yvette, France
| | - Théo Tytus
- Université Paris-Saclay, CEA, Service d'Etudes Analytiques et de Réactivité des Surfaces, F-91191 Gif-sur-Yvette, France
| | - Pascale Delangle
- Univ. Grenoble Alpes, CEA, CNRS, IRIG, SyMMES, 38 000 Grenoble, France
| | - Carole Bresson
- Université Paris-Saclay, CEA, Service d'Etudes Analytiques et de Réactivité des Surfaces, F-91191 Gif-sur-Yvette, France
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13
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Wang M, Shajahan A, Pepi LE, Azadi P, Zaia J. Glycoproteomic Sample Processing, LC-MS, and Data Analysis Using GlycReSoft. Curr Protoc 2021; 1:e84. [PMID: 33761173 DOI: 10.1002/cpz1.84] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Identification of N- and O-glycosylation on specific sites of proteins, along with glycan structural information, is necessary to determine the roles glycoproteins play in normal and pathologic cellular functions. Because such glycosylation is macro- and micro-heterogeneous and alters the dissociation behavior of glycopeptides, specific sample preparation, mass spectrometry, and data analysis techniques are required. Advanced tandem mass spectrometry-based glycoproteomics coupled with powerful data mining algorithms are key elements for characterization of protein glycosylation. This article includes the detailed, streamlined sample preparation method for liquid chromatography-mass spectrometry data acquisition and subsequent bioinformatics-based data annotation using the publicly available GlycReSoft program for highly efficient identification and quantification of glycoprotein glycosylation. © 2021 Wiley Periodicals LLC. Basic Protocol 1: Characterization of glycans and site occupancy on purified glycoprotein Support Protocol 1: In-gel digestion of glycoproteins Support Protocol 2: Detection of glycoproteins from cells/tissue through glycopeptide enrichment Basic Protocol 2: Acquisition of glycopeptides through high-resolution nano-LC-MS/MS Basic Protocol 3: Identification and quantification of glycopeptides using GlycReSoft.
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Affiliation(s)
- Meizhe Wang
- Department of Biochemistry, Boston University, Boston, Massachusetts
| | - Asif Shajahan
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia
| | - Lauren E Pepi
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia
| | - Parastoo Azadi
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia
| | - Joseph Zaia
- Department of Biochemistry, Boston University, Boston, Massachusetts.,Bioinformatics Program, Center for Biomedical Mass Spectrometry, Boston University, Boston, Massachusetts
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14
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Liu X, Jiang Y, Zhang F, Li Z, Yang B. Preparation and evaluation of a polymer-based sulfobetaine zwitterionic stationary phase. J Chromatogr A 2021; 1649:462229. [PMID: 34038779 DOI: 10.1016/j.chroma.2021.462229] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 04/24/2021] [Accepted: 04/29/2021] [Indexed: 10/21/2022]
Abstract
We describe a polymer-based sulfobetaine zwitterionic stationary phase for hydrophilic interaction liquid chromatography (HILIC). It was prepared by grafting acrylamide-type sulfobetaine monomer instead of common methacrylate-type sulfobetaine onto hydrolysed poly (glycidyl methacrylate-divinylbenzene) (GMA-DVB) microspheres via pendant double bonds of DVB. The phase has been characterized by elemental analysis, scanning electron micrograph and N2 adsorption-desorption experiment. It shows wider pH tolerance range (from 2 to 12) and excellent separation ability towards common strong polar analytes such as nucleosides and nucleic bases, water-soluble vitamins, amino acids, inorganic anions and cations. Notably, it exhibits negligible baseline noise level (~0.15 pA) under typical HILIC mobile phase. Excellent selectivity in separation of α- and β-anomers of reducing sugars and lactose/lactulose has also been observed.
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Affiliation(s)
- Xuefang Liu
- Engineering Research Center of Pharmaceutical Process Chemistry, Ministry of Education; School of Pharmacy, East China University of Science and Technology, 130 Meilong RD, Shanghai 200237, China
| | - Yu Jiang
- Engineering Research Center of Pharmaceutical Process Chemistry, Ministry of Education; School of Pharmacy, East China University of Science and Technology, 130 Meilong RD, Shanghai 200237, China
| | - Feifang Zhang
- Engineering Research Center of Pharmaceutical Process Chemistry, Ministry of Education; School of Pharmacy, East China University of Science and Technology, 130 Meilong RD, Shanghai 200237, China.
| | - Zongying Li
- Engineering Research Center of Pharmaceutical Process Chemistry, Ministry of Education; School of Pharmacy, East China University of Science and Technology, 130 Meilong RD, Shanghai 200237, China
| | - Bingcheng Yang
- Engineering Research Center of Pharmaceutical Process Chemistry, Ministry of Education; School of Pharmacy, East China University of Science and Technology, 130 Meilong RD, Shanghai 200237, China.
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15
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Wang M, Shajahan A, Pepi LE, Azadi P, Zaia J. Glycoproteomic Sample Processing, LC-MS, and Data Analysis Using GlycReSoft. Curr Protoc 2021. [PMID: 33761173 DOI: 10.1002/cpz1001.1084] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Identification of N- and O-glycosylation on specific sites of proteins, along with glycan structural information, is necessary to determine the roles glycoproteins play in normal and pathologic cellular functions. Because such glycosylation is macro- and micro-heterogeneous and alters the dissociation behavior of glycopeptides, specific sample preparation, mass spectrometry, and data analysis techniques are required. Advanced tandem mass spectrometry-based glycoproteomics coupled with powerful data mining algorithms are key elements for characterization of protein glycosylation. This article includes the detailed, streamlined sample preparation method for liquid chromatography-mass spectrometry data acquisition and subsequent bioinformatics-based data annotation using the publicly available GlycReSoft program for highly efficient identification and quantification of glycoprotein glycosylation. © 2021 Wiley Periodicals LLC. Basic Protocol 1: Characterization of glycans and site occupancy on purified glycoprotein Support Protocol 1: In-gel digestion of glycoproteins Support Protocol 2: Detection of glycoproteins from cells/tissue through glycopeptide enrichment Basic Protocol 2: Acquisition of glycopeptides through high-resolution nano-LC-MS/MS Basic Protocol 3: Identification and quantification of glycopeptides using GlycReSoft.
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Affiliation(s)
- Meizhe Wang
- Department of Biochemistry, Boston University, Boston, Massachusetts
| | - Asif Shajahan
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia
| | - Lauren E Pepi
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia
| | - Parastoo Azadi
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia
| | - Joseph Zaia
- Department of Biochemistry, Boston University, Boston, Massachusetts
- Bioinformatics Program, Center for Biomedical Mass Spectrometry, Boston University, Boston, Massachusetts
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16
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Construction of a microfluidic platform integrating online protein fractionation, denaturation, digestion, and peptide enrichment. Talanta 2021; 224:121810. [PMID: 33379035 DOI: 10.1016/j.talanta.2020.121810] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 10/19/2020] [Accepted: 10/23/2020] [Indexed: 11/22/2022]
Abstract
Microfluidic system with multi-functional integration of high-throughput protein/peptide separation ability has great potential for improving the identification capacity of biological samples in proteomics. In this paper, a sample treatment platform was constructed by integrating reversed phase chromatography, immobilized enzyme reactor (IMER) and imprinted monolith through a microfluidic chip to achieve the online proteins fractionation, denaturation, digestion and peptides enrichment. We firstly synthesized a poly-allyl phenoxyacetate (AP) monolith and a lysine-glycine-glycine (KGG) imprinted monolith separately, and investigated in detail their performance in fractionating proteins and extracting KGG from the protein digests of MCF-7 cell. The removal percentage of 94.6% for MCF-7 cell protein and the recovery of 90.8% for KGG were obtained. The number of proteins and peptides identified on this microfluidic platform was 2,004 and 8,797, respectively, which was 2.8-fold and 3.0-fold higher than that of untreatment sample. The time consumed by this platform for a sample treatment was about 9.6 h, less than that of conventional method (approximate 13.3 h). In addition, this platform can enrich some peptide fragments containing KGG based on imprinted monolith, which can be served for the identification of ubiquitin-modified proteomics. The successful construction of this integrated microfluidic platform provides a considerable and efficient technical tool for simultaneous identification of proteomics and post-translational modification proteomics information.
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17
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Mao Y, Zhao Y, Zhang Y, Yang H. In-depth characterization and comparison of the N-glycosylated proteome of two-dimensional- and three-dimensional-cultured breast cancer cells and xenografted tumors. PLoS One 2020; 15:e0243789. [PMID: 33301522 PMCID: PMC7728280 DOI: 10.1371/journal.pone.0243789] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 11/25/2020] [Indexed: 02/05/2023] Open
Abstract
Native intact N-glycopeptide analysis can provide access to the comprehensive characteristics of N-glycan occupancy, including N-glycosites, N-glycan compositions, and N-glycoproteins for complex samples. The sample pre-processing method used for the analysis of intact N-glycopeptides usually depends on the enrichment of low abundance N-glycopeptides from a tryptic peptide mixture using hydrophilic substances before LC-MS/MS detection. However, the number of identified intact N-glycopeptides remains inadequate to achieve an in-depth profile of the N-glycosylation landscape. Here, we optimized the sample preparation workflow prior to LC-MS/MS analysis by systematically comparing different analytical methods, including the use of different sources of trypsin, combinations of different proteases, and different enrichment materials. Finally, we found that the combination of Trypsin (B)/Lys-C digestion and zwitterionic HILIC (Zic-HILIC) enrichment significantly improved the mass spectrometric characterization of intact N-glycopeptides, increasing the number of identified intact N-glycopeptides and offering better analytical reproducibility. Furthermore, the optimized workflow was applied to the analysis of intact N-glycopeptides in two-dimensional (2D) and three-dimensional (3D)-cultured breast cancer cells in vitro and xenografted tumors in mice. These results indicated that the same breast cancer cells, when cultured in different microenvironments, can show different N-glycosylation patterns. This study also provides an interesting comparison of the N-glycoproteome of breast cancer cells cultured in different growth conditions, indicating the important role of N-glycosylated proteins in cancer cell growth and the choice of the cell culture model for studies in tumor biology and drug evaluation.
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Affiliation(s)
- Yonghong Mao
- Institute of Thoracic Oncology, West China Hospital, Sichuan University, Chengdu, China
- Department of Thoracic Surgery, West China Hospital, Sichuan University, Chengdu, China
| | - Yang Zhao
- Mass Spectrometry Engineering Technology Research Center, Center for Advanced Measurement Science, National Institute of Metrology, Beijing, China
| | - Yong Zhang
- Key Lab of Transplant Engineering and Immunology, MOH, West China Hospital, Sichuan University, Chengdu, China
- Institutes for Systems Genetics, West China Hospital, Sichuan University, Chengdu, China
- Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
- * E-mail: (YZ); (HY)
| | - Hao Yang
- Key Lab of Transplant Engineering and Immunology, MOH, West China Hospital, Sichuan University, Chengdu, China
- Institutes for Systems Genetics, West China Hospital, Sichuan University, Chengdu, China
- Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
- * E-mail: (YZ); (HY)
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18
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Zhao X, Zhang H, Zhou X, Wang L, Wan L, Wu R. One-pot hydrothermal cross-linking preparation of poly(vinylpyrrolidone) immobilized silica stationary phase for hydrophilic interaction chromatography. J Chromatogr A 2020; 1633:461656. [PMID: 33166745 DOI: 10.1016/j.chroma.2020.461656] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 09/27/2020] [Accepted: 10/23/2020] [Indexed: 11/29/2022]
Abstract
Hydrothermally cross-linked polyvinylpyrrolidone (PVP) immobilized SiO2 stationary phase (CPVP-Sil) was prepared via a green and facile one-pot method which was demonstrated for hydrophilic interaction liquid chromatography (HILIC) as well as reverse phase chromatography(RP). A water or organic solvent-insoluble permanent CPVP immobilizing on the silica particle surface can be formed simply by dipping silica particles into PVP solution and low temperature hydrothermal treatment. The cross-linked PVP network coating on SiO2 endow it ring lactam functional groups which exhibited excellent separation ability of polar compounds by a typical HILIC retention mechanism at higher organic solvent contents (>55% ACN) and additionally polyvinyl groups for separation of alkylbenzenes in RP mode(<25% ACN). A high column efficiency of about 7 × 104 plates per meter was obtained for the test catechol compound. Remarkably, the CPVP-Sil packing materials showed good stability in acid (at pH 3.5) or basic (at pH 9.5) conditions, with 5400-fold column volumes and 3500-fold column volumes respectively.
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Affiliation(s)
- Xingyun Zhao
- CAS Key laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hongyan Zhang
- CAS Key laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Xiaoyu Zhou
- CAS Key laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Li Wang
- CAS Key laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Lihong Wan
- CAS Key laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Ren'an Wu
- CAS Key laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China.
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19
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Zhao Y, Raidas S, Mao Y, Li N. Glycine additive facilitates site-specific glycosylation profiling of biopharmaceuticals by ion-pairing hydrophilic interaction chromatography mass spectrometry. Anal Bioanal Chem 2020; 413:1267-1277. [PMID: 33244686 DOI: 10.1007/s00216-020-03089-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 11/19/2020] [Accepted: 11/21/2020] [Indexed: 11/28/2022]
Abstract
Many biotherapeutics such as monoclonal antibodies (mAb) and Fc-domain fusion proteins contain heterogeneous glycan contents at one or multiple glycosylation site(s). Site-specific glycan profile characterization is critical for monitoring the quality of these molecules during different stages of drug development. Hydrophilic interaction chromatography (HILIC) as an orthogonal separation method to reversed-phase liquid chromatography (RPLC) can achieve better glycopeptide identification due to the effective separation between individual glycoforms as well as the separation of glycopeptides from high-abundance non-glycosylated peptides, which can be further improved by modifying the mobile phases with ion-pairing agents (IP-HILIC). However, an online IP-HILIC coupled to mass spectrometry (MS) detection may suffer from the suppression of mass spectrometry signal during electrospray ionization due to the trifluoroacetic acid (TFA), commonly used as an ion-pairing agent. Here, we reported an optimized experimental condition for IP-HILIC-MS where glycine is added in the TFA-containing mobile phases to enhance the MS detection sensitivity for glycopeptides up to ~ 50-fold by eliminating the ion-suppression effect of an ion-pairing agent while still retaining excellent separation capacity. We demonstrated that with enhanced detection sensitivity, IP-HILIC-MS can confidently identify an increased number of site-specific N-linked glycans for IgG1, and IgG4 mAbs as well as an Fc-domain fusion protein (containing five N-glycosylation sites) through MS/MS-based search in the data-dependent acquisition mode, meanwhile, achieve comparable quantitative results compared with the traditional methods. We also demonstrated that IP-HILIC-MS can be used to identify low-level O-glycosylation and non-consensus N-glycosylation on mAbs without any enrichment prior to LC-MS analysis. Graphical abstract.
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Affiliation(s)
- Yunlong Zhao
- Analytical Chemistry, Regeneron Pharmaceuticals, Inc., 777 Old Saw Mill River Road, Tarrytown, NY, 10591, USA
| | - Shivkumar Raidas
- Analytical Chemistry, Regeneron Pharmaceuticals, Inc., 777 Old Saw Mill River Road, Tarrytown, NY, 10591, USA
| | - Yuan Mao
- Analytical Chemistry, Regeneron Pharmaceuticals, Inc., 777 Old Saw Mill River Road, Tarrytown, NY, 10591, USA.
| | - Ning Li
- Analytical Chemistry, Regeneron Pharmaceuticals, Inc., 777 Old Saw Mill River Road, Tarrytown, NY, 10591, USA
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20
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Røst LM, Shafaei A, Fuchino K, Bruheim P. Zwitterionic HILIC tandem mass spectrometry with isotope dilution for rapid, sensitive and robust quantification of pyridine nucleotides in biological extracts. J Chromatogr B Analyt Technol Biomed Life Sci 2020; 1144:122078. [PMID: 32222674 DOI: 10.1016/j.jchromb.2020.122078] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Revised: 03/15/2020] [Accepted: 03/19/2020] [Indexed: 12/13/2022]
Abstract
The pyridine nucleotides nicotineamide adenine dinucleotide (NAD) and nicotineamide adenine dinucleotide phosphate (NADP) are conserved coenzymes across all domains of life, and are involved in more than 200 different hydride transfer reactions supporting essential catabolic and anabolic functions. The intracellular levels of these metabolites, and the ratio of their oxidized to reduced forms regulate an extensive network of reactions ranging beyond metabolism. Hence, monitoring their intracellular levels provides information about, but not limited to, the metabolic state of a cell or tissue. Interconversion between oxidized and reduced forms, varying pH liability and varying intracellular concentrations of the different species leaves absolute quantification of the pyridine nucleotides analytically challenging. These polar metabolites are poorly retained on conventional reverseed-phase stationary phases without ion-pair reagents that contaminates the LC-system. Herein we demonstrate that zwitterionic HILIC-tandem mass spectroemtry can be applied to successfully resolve the pyridine nucleotides in biological extracts in a fast, robust and highly sensitive way. The presented method applies isotope dilution to compensate potential loss of these labile metabolites and is validated for low, medium and high biomass samples of two popular biological model systems; Escherichia coli and the human cell line JJN-3. High stability and rapid sample preparation without solvent removal allows for long sequence runs, making this method ideal for high-throughput analysis of biological extracts.
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Affiliation(s)
- Lisa M Røst
- Department of Biotechnology and Food Science, Faculty of Natural Sciences, NTNU Norwegian University of Science and Technology, NO-7481 Trondheim, Norway
| | - Armaghan Shafaei
- Department of Biotechnology and Food Science, Faculty of Natural Sciences, NTNU Norwegian University of Science and Technology, NO-7481 Trondheim, Norway
| | - Katsuya Fuchino
- Department of Biotechnology and Food Science, Faculty of Natural Sciences, NTNU Norwegian University of Science and Technology, NO-7481 Trondheim, Norway
| | - Per Bruheim
- Department of Biotechnology and Food Science, Faculty of Natural Sciences, NTNU Norwegian University of Science and Technology, NO-7481 Trondheim, Norway.
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21
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Wang Q, Zhang Q, Huang H, Zhao P, Sun L, Peng K, Liu X, Ruan M, Shao H, Crommen J, Yu P, Jiang Z. Fabrication and application of zwitterionic phosphorylcholine functionalized monoliths with different hydrophilic crosslinkers in hydrophilic interaction chromatography. Anal Chim Acta 2020; 1101:222-229. [DOI: 10.1016/j.aca.2019.12.016] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 11/30/2019] [Accepted: 12/06/2019] [Indexed: 10/25/2022]
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22
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Vallaro M, Ermondi G, Caron G. Chromatographic HILIC indexes to characterize the lipophilicity of zwitterions. Eur J Pharm Sci 2020; 145:105232. [DOI: 10.1016/j.ejps.2020.105232] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 01/03/2020] [Accepted: 01/20/2020] [Indexed: 11/25/2022]
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23
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Review of Three-Dimensional Liquid Chromatography Platforms for Bottom-Up Proteomics. Int J Mol Sci 2020; 21:ijms21041524. [PMID: 32102244 PMCID: PMC7073195 DOI: 10.3390/ijms21041524] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 02/19/2020] [Accepted: 02/21/2020] [Indexed: 12/30/2022] Open
Abstract
Proteomics is a large-scale study of proteins, aiming at the description and characterization of all expressed proteins in biological systems. The expressed proteins are typically highly complex and large in abundance range. To fulfill high accuracy and sensitivity of proteome analysis, the hybrid platforms of multidimensional (MD) separations and mass spectrometry have provided the most powerful solution. Multidimensional separations provide enhanced peak capacity and reduce sample complexity, which enables mass spectrometry to analyze more proteins with high sensitivity. Although two-dimensional (2D) separations have been widely used since the early period of proteomics, three-dimensional (3D) separation was barely used by low reproducibility of separation, increased analysis time in mass spectrometry. With developments of novel microscale techniques such as nano-UPLC and improvements of mass spectrometry, the 3D separation becomes a reliable and practical selection. This review summarizes existing offline and online 3D-LC platforms developed for proteomics and their applications. In detail, setups and implementation of those systems as well as their advances are outlined. The performance of those platforms is also discussed and compared with the state-of-the-art 2D-LC. In addition, we provide some perspectives on the future developments and applications of 3D-LC in proteomics.
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24
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Yeung D, Klaassen N, Mizero B, Spicer V, Krokhin OV. Peptide retention time prediction in hydrophilic interaction liquid chromatography: Zwitter-ionic sulfoalkylbetaine and phosphorylcholine stationary phases. J Chromatogr A 2020; 1619:460909. [PMID: 32007221 DOI: 10.1016/j.chroma.2020.460909] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 01/17/2020] [Accepted: 01/21/2020] [Indexed: 01/01/2023]
Abstract
Peptide retention time prediction models have been developed for zwitter-ionic ZIC-HILIC and ZIC-cHILIC stationary phases (pH 4.5 eluents) using proteomics-derived retention datasets of ~30 thousand tryptic peptides each. Overall, hydrophilicity of these stationary phases was found to be similar to the previously studied Amide HILIC phase, but lower compared to bare silicas. Peptide retention is driven by interactions of all charged (hydrophilic) residues at pH 4.5 (Asp, Glu, Arg, Lys, His), but shows specificity according to orientation of functional groups in zwitter-ionic pair. Thus, ZIC-cHILIC exhibits an increased contribution of negatively charged Asp and Glu due to the distal positioning of positively charged quaternary amines on the stationary phase. These findings confirm that HILIC interactions are driven by both peptide distribution between water layer adsorbed on the stationary phase and by interactions specific to functional groups of the packing material. Sequence-Specific Retention Calculator HILIC models were optimized for these columns showing 0.967-0.976 R2-values between experimental and predicted retention values. ZIC-HILIC separations represent a good choice as a first dimension in 2D LC-MS of peptide mixtures with correlations between retention values of ZIC-HILIC against RPLC found at 0.197 (ZIC-HILIC) and 0.137 (ZIC-cHILIC) R2-values, confirming a good orthogonality.
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Affiliation(s)
- Darien Yeung
- Manitoba Centre for Proteomics and Systems Biology, 799 JBRC, 715 McDermot Avenue, Winnipeg, R3E 3P4, Canada; Department of Biochemistry and Medical Genetics, University of Manitoba, 336 BMSB, 745 Bannatyne Avenue, Winnipeg, R3E 0J9, Canada
| | - Nicole Klaassen
- Manitoba Centre for Proteomics and Systems Biology, 799 JBRC, 715 McDermot Avenue, Winnipeg, R3E 3P4, Canada; Department of Chemistry, University of Manitoba, 360 Parker Building, 144 Dysart Road, Winnipeg, R3T 2N2, Canada
| | - Benilde Mizero
- Manitoba Centre for Proteomics and Systems Biology, 799 JBRC, 715 McDermot Avenue, Winnipeg, R3E 3P4, Canada; Department of Chemistry, University of Manitoba, 360 Parker Building, 144 Dysart Road, Winnipeg, R3T 2N2, Canada
| | - Victor Spicer
- Manitoba Centre for Proteomics and Systems Biology, 799 JBRC, 715 McDermot Avenue, Winnipeg, R3E 3P4, Canada
| | - Oleg V Krokhin
- Manitoba Centre for Proteomics and Systems Biology, 799 JBRC, 715 McDermot Avenue, Winnipeg, R3E 3P4, Canada; Department of Biochemistry and Medical Genetics, University of Manitoba, 336 BMSB, 745 Bannatyne Avenue, Winnipeg, R3E 0J9, Canada; Department of Chemistry, University of Manitoba, 360 Parker Building, 144 Dysart Road, Winnipeg, R3T 2N2, Canada; Department of Internal Medicine, University of Manitoba, 799 JBRC, 715 McDermot Avenue, Winnipeg, R3E 3P4, Canada.
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25
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Retention behavior of ginsenosides in a sulfo-based high performance liquid chromatography column. J Chromatogr A 2020; 1610:460542. [PMID: 31558273 DOI: 10.1016/j.chroma.2019.460542] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 09/11/2019] [Accepted: 09/14/2019] [Indexed: 12/22/2022]
Abstract
We herein report the use of a sulfo-based column and hydrophilic interaction chromatography (HILIC) to separate 14 ginsenosides, namely Rb1, Rb2, Rb3, Rc, Rd, Rf, Re, Rg1, Rg2, Rg3, Rh1, Rh2, F2, and C-K. In addition to its rapid and efficient ability to separate these ginsenosides, the sulfo-based column exhibited a good relationship between the ginsenoside capacity factor (k') and molecular weight (Mw) and a strict elution order corresponding to the polarity (P) of the ginsenosides, as confirmed by thin layer chromatography.
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26
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Zhang Y, Jing H, Meng B, Qian X, Ying W. L-cysteine functionalized straticulate C 3N 4 for the selective enrichment of glycopeptides. J Chromatogr A 2019; 1610:460545. [PMID: 31551124 DOI: 10.1016/j.chroma.2019.460545] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 09/11/2019] [Accepted: 09/14/2019] [Indexed: 02/05/2023]
Abstract
The facile enrichment of glycopeptides or glycoproteins poses great challenges for glycoproteomic research. In this study, a novel hydrophilic material, named zwitterionic hydrophilic L-cysteine derivatized straticulate-C3N4 composites (LCAC), were synthesized and evaluated for the enrichment of N-glycopeptides. LCAC exhibited good biocompatibility, excellent hydrophilicity and selectivity, by virtue of the large surface of C3N4 and the zwitterionic property offered by cysteine. LCAC demonstrated excellent performance for N-glycopeptide enrichment with the sensitivity of 0.033 fmol/µL, selectivity of 1:100, and high recovery rate (∼85%). The performance of LCAC was demonstrated by the identification of 35 N-glycopeptides from IgG, as well as capturing 1809 human urine N-glycopeptides corresponding to 876 N-glycoproteins. Comparing the LCAC with our developed phenylboronic acid functionalized material showed a certain complementary due to the different binding mechanism. The simple production and enhanced hydrophilic properties make the material a promising choice for glycoproteomics researches.
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Affiliation(s)
- Yong Zhang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206, China; Key Lab of Transplant Engineering and Immunology, MOH, West China-Washington Mitochondria and Metabolism Research Center, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Hongyu Jing
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206, China
| | - Bo Meng
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206, China
| | - Xiaohong Qian
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206, China
| | - Wantao Ying
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206, China.
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27
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Zhang W, Zhang Y, Zhang Y, Lan C, Miao Y, Deng Z, Ba X, Zhao W, Zhang S. Tetra-proline modified calix[4]arene bonded silica gel: A novel stationary phase for hydrophilic interaction liquid chromatography. Talanta 2019; 193:56-63. [DOI: 10.1016/j.talanta.2018.09.083] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Revised: 08/30/2018] [Accepted: 09/23/2018] [Indexed: 12/01/2022]
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28
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Tanase M, Bacalum E, David V. Variability of temperature dependences of the retention of strongly polar compounds under ZIC-HILIC liquid chromatographic mechanism. SEPARATION SCIENCE PLUS 2019. [DOI: 10.1002/sscp.201800144] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Maria Tanase
- University of Bucharest, ; Faculty of Chemistry; Department of Analytical Chemistry; Bucharest Romania
| | - Elena Bacalum
- Research Institute - ICUB; Blvd. M. Kogalniceanu; University of Bucharest; Bucharest Romania
| | - Victor David
- University of Bucharest, ; Faculty of Chemistry; Department of Analytical Chemistry; Bucharest Romania
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29
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Xue Y, Xie J, Fang P, Yao J, Yan G, Shen H, Yang P. Study on behaviors and performances of universal N-glycopeptide enrichment methods. Analyst 2019; 143:1870-1880. [PMID: 29557479 DOI: 10.1039/c7an02062g] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Glycosylation is a crucial process in protein biosynthesis. However, the analysis of glycopeptides through MS remains challenging due to the microheterogeneity and macroheterogeneity of the glycoprotein. Selective enrichment of glycopeptides from complex samples prior to MS analysis is essential for successful glycoproteome research. In this work, we systematically investigated the behaviors and performances of boronic acid chemistry, ZIC-HILIC, and PGC of glycopeptide enrichment to promote understanding of these methods. We also optimized boronic acid chemistry and ZIC-HILIC enrichment methods and applied them to enrich glycopeptides from mouse liver. The intact N-glycopeptides were interpreted using the in-house analysis software pGlyco 2.0. We found that boronic acid chemistry in this study preferred to capture glycopeptides with high mannose glycans, ZIC-HILIC enriched most N-glycopeptides and did not show significant preference during enrichment and PGC was not suitable for separating glycopeptides with a long amino acid sequence. We performed a detailed study on the behaviors and performances of boronic acid chemistry, ZIC-HILIC, and PGC enrichment methods and provide a better understanding of enrichment methods for further glycoproteomics research.
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Affiliation(s)
- Yu Xue
- Department of Chemistry, Fudan University, Shanghai, 200433, P.R. China
| | - Juanjuan Xie
- Minhang Hospital and Institutes of Biomedical Sciences, Fudan University, Shanghai, 201199, P.R. China.
| | - Pan Fang
- Minhang Hospital and Institutes of Biomedical Sciences, Fudan University, Shanghai, 201199, P.R. China.
| | - Jun Yao
- Minhang Hospital and Institutes of Biomedical Sciences, Fudan University, Shanghai, 201199, P.R. China.
| | - Guoquan Yan
- Department of Chemistry, Fudan University, Shanghai, 200433, P.R. China
| | - Huali Shen
- Minhang Hospital and Institutes of Biomedical Sciences, Fudan University, Shanghai, 201199, P.R. China. and Department of Systems Biology for Medicine and School of Basic Medical Sciences, Fudan University, Shanghai, 200032, P.R. China
| | - Pengyuan Yang
- Department of Chemistry, Fudan University, Shanghai, 200433, P.R. China and Minhang Hospital and Institutes of Biomedical Sciences, Fudan University, Shanghai, 201199, P.R. China.
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30
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Zhang M, Gong L, Liu G, Kang J. Preparation of a monolithic column with a mixed-mode stationary phase of reversed-phase/hydrophilic interaction for capillary liquid chromatography. J Sep Sci 2019; 42:662-669. [DOI: 10.1002/jssc.201800826] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Revised: 11/02/2018] [Accepted: 11/02/2018] [Indexed: 11/06/2022]
Affiliation(s)
- Meng Zhang
- State Key Laboratory of Bioorganic and Natural Products Chemistry; Center for Excellence in Molecular Synthesis; Shanghai Institute of Organic Chemistry; University of Chinese Academy of Sciences; Shanghai P. R. China
- School of physical science and technology; ShanghaiTech University; Shanghai P. R. China
| | - Li Gong
- State Key Laboratory of Bioorganic and Natural Products Chemistry; Center for Excellence in Molecular Synthesis; Shanghai Institute of Organic Chemistry; University of Chinese Academy of Sciences; Shanghai P. R. China
| | - Guizhen Liu
- State Key Laboratory of Bioorganic and Natural Products Chemistry; Center for Excellence in Molecular Synthesis; Shanghai Institute of Organic Chemistry; University of Chinese Academy of Sciences; Shanghai P. R. China
- School of physical science and technology; ShanghaiTech University; Shanghai P. R. China
| | - Jingwu Kang
- State Key Laboratory of Bioorganic and Natural Products Chemistry; Center for Excellence in Molecular Synthesis; Shanghai Institute of Organic Chemistry; University of Chinese Academy of Sciences; Shanghai P. R. China
- School of physical science and technology; ShanghaiTech University; Shanghai P. R. China
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Žuvela P, Skoczylas M, Jay Liu J, Ba Czek T, Kaliszan R, Wong MW, Buszewski B, Héberger K. Column Characterization and Selection Systems in Reversed-Phase High-Performance Liquid Chromatography. Chem Rev 2019; 119:3674-3729. [PMID: 30604951 DOI: 10.1021/acs.chemrev.8b00246] [Citation(s) in RCA: 143] [Impact Index Per Article: 28.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Reversed-phase high-performance liquid chromatography (RP-HPLC) is the most popular chromatographic mode, accounting for more than 90% of all separations. HPLC itself owes its immense popularity to it being relatively simple and inexpensive, with the equipment being reliable and easy to operate. Due to extensive automation, it can be run virtually unattended with multiple samples at various separation conditions, even by relatively low-skilled personnel. Currently, there are >600 RP-HPLC columns available to end users for purchase, some of which exhibit very large differences in selectivity and production quality. Often, two similar RP-HPLC columns are not equally suitable for the requisite separation, and to date, there is no universal RP-HPLC column covering a variety of analytes. This forces analytical laboratories to keep a multitude of diverse columns. Therefore, column selection is a crucial segment of RP-HPLC method development, especially since sample complexity is constantly increasing. Rationally choosing an appropriate column is complicated. In addition to the differences in the primary intermolecular interactions with analytes of the dispersive (London) type, individual columns can also exhibit a unique character owing to specific polar, hydrogen bond, and electron pair donor-acceptor interactions. They can also vary depending on the type of packing, amount and type of residual silanols, "end-capping", bonding density of ligands, and pore size, among others. Consequently, the chromatographic performance of RP-HPLC systems is often considerably altered depending on the selected column. Although a wide spectrum of knowledge is available on this important subject, there is still a lack of a comprehensive review for an objective comparison and/or selection of chromatographic columns. We aim for this review to be a comprehensive, authoritative, critical, and easily readable monograph of the most relevant publications regarding column selection and characterization in RP-HPLC covering the past four decades. Future perspectives, which involve the integration of state-of-the-art molecular simulations (molecular dynamics or Monte Carlo) with minimal experiments, aimed at nearly "experiment-free" column selection methodology, are proposed.
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Affiliation(s)
- Petar Žuvela
- Department of Chemistry , National University of Singapore , Singapore 117543 , Singapore
| | - Magdalena Skoczylas
- Department of Environmental Chemistry and Bioanalytics, Center for Modern Interdisciplinary Technologies , Nicolaus Copernicus University , Wileńska 4 , 87-100 Toruń , Poland
| | - J Jay Liu
- Department of Chemical Engineering , Pukyong National University , 365 Sinseon-ro , Nam-gu, 48-513 Busan , Korea
| | | | | | - Ming Wah Wong
- Department of Chemistry , National University of Singapore , Singapore 117543 , Singapore
| | - Bogusław Buszewski
- Department of Environmental Chemistry and Bioanalytics, Center for Modern Interdisciplinary Technologies , Nicolaus Copernicus University , Wileńska 4 , 87-100 Toruń , Poland
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Swarge BN, Roseboom W, Zheng L, Abhyankar WR, Brul S, de Koster CG, de Koning LJ. "One-Pot" Sample Processing Method for Proteome-Wide Analysis of Microbial Cells and Spores. Proteomics Clin Appl 2018; 12:e1700169. [PMID: 29484825 PMCID: PMC6174930 DOI: 10.1002/prca.201700169] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Revised: 01/22/2018] [Indexed: 11/15/2022]
Abstract
PURPOSE Bacterial endospores, the transmissible forms of pathogenic bacilli and clostridia, are heterogeneous multilayered structures composed of proteins. These proteins protect the spores against a variety of stresses, thus helping spore survival, and assist in germination, by interacting with the environment to form vegetative cells. Owing to the complexity, insolubility, and dynamic nature of spore proteins, it has been difficult to obtain their comprehensive protein profiles. EXPERIMENTAL DESIGN The intact spores of Bacillus subtilis, Bacillus cereus, and Peptoclostridium difficile and their vegetative counterparts were disrupted by bead beating in 6 m urea under reductive conditions. The heterogeneous mixture was then double digested with LysC and trypsin. Next, the peptide mixture was pre-fractionated with zwitterionic hydrophilic interaction liquid chromatography (ZIC-HILIC) followed by reverse-phase LC-FT-MS analysis of the fractions. RESULTS "One-pot" method is a simple, robust method that yields identification of >1000 proteins with high confidence, across all spore layers from B. subtilis, B. cereus, and P. difficile. CONCLUSIONS AND MEDICAL RELEVANCE This method can be employed for proteome-wide analysis of non-spore-forming as well as spore-forming pathogens. Analysis of spore protein profile will help to understand the sporulation and germination processes and to distinguish immunogenic protein markers.
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Affiliation(s)
- Bhagyashree Nandakishor Swarge
- Department of Mass Spectrometry of Bio macromolecules, University of Amsterdam, Amsterdam, The Netherlands
- Department of Molecular Biology and Microbial Food Safety, Swammerdam Institutes of Life Sciences, University of Amsterdam, The Netherlands
| | - Winfried Roseboom
- Department of Mass Spectrometry of Bio macromolecules, University of Amsterdam, Amsterdam, The Netherlands
| | - Linli Zheng
- Department of Mass Spectrometry of Bio macromolecules, University of Amsterdam, Amsterdam, The Netherlands
- Department of Molecular Biology and Microbial Food Safety, Swammerdam Institutes of Life Sciences, University of Amsterdam, The Netherlands
| | - Wishwas R Abhyankar
- Department of Mass Spectrometry of Bio macromolecules, University of Amsterdam, Amsterdam, The Netherlands
- Department of Molecular Biology and Microbial Food Safety, Swammerdam Institutes of Life Sciences, University of Amsterdam, The Netherlands
| | - Stanley Brul
- Department of Molecular Biology and Microbial Food Safety, Swammerdam Institutes of Life Sciences, University of Amsterdam, The Netherlands
| | - Chris G de Koster
- Department of Mass Spectrometry of Bio macromolecules, University of Amsterdam, Amsterdam, The Netherlands
| | - Leo J de Koning
- Department of Mass Spectrometry of Bio macromolecules, University of Amsterdam, Amsterdam, The Netherlands
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Ermondi G, Vallaro M, Camacho-Leal M, Potter T, Visentin S, Caron G. Charged cyclic hexapeptides: Updating molecular descriptors for permeability purposes. Eur J Pharm Sci 2018; 122:85-93. [DOI: 10.1016/j.ejps.2018.06.021] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Revised: 06/16/2018] [Accepted: 06/19/2018] [Indexed: 10/28/2022]
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Núñez C, Chantada-Vázquez MDP, Bravo SB, Vázquez-Estévez S. Novel functionalized nanomaterials for the effective enrichment of proteins and peptides with post-translational modifications. J Proteomics 2018; 181:170-189. [DOI: 10.1016/j.jprot.2018.04.017] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Revised: 04/02/2018] [Accepted: 04/09/2018] [Indexed: 02/07/2023]
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Guo ZY, Hai X, Wang YT, Shu Y, Chen XW, Wang JH. Core–Corona Magnetic Nanospheres Functionalized with Zwitterionic Polymer Ionic Liquid for Highly Selective Isolation of Glycoprotein. Biomacromolecules 2017; 19:53-61. [DOI: 10.1021/acs.biomac.7b01231] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Zhi-Yong Guo
- Research
Center for Analytical Sciences, Department of Chemistry, College of
Sciences, Northeastern University, Box 332, Shenyang 110819, China
| | - Xin Hai
- Research
Center for Analytical Sciences, Department of Chemistry, College of
Sciences, Northeastern University, Box 332, Shenyang 110819, China
| | - Yi-Ting Wang
- Research
Center for Analytical Sciences, Department of Chemistry, College of
Sciences, Northeastern University, Box 332, Shenyang 110819, China
| | - Yang Shu
- Institute
of Biotechnology, College of Life and Health Sciences, Northeastern University, Box H006, Shenyang 110169, China
| | - Xu-Wei Chen
- Research
Center for Analytical Sciences, Department of Chemistry, College of
Sciences, Northeastern University, Box 332, Shenyang 110819, China
| | - Jian-Hua Wang
- Research
Center for Analytical Sciences, Department of Chemistry, College of
Sciences, Northeastern University, Box 332, Shenyang 110819, China
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Behrens AJ, Struwe WB, Crispin M. Glycosylation profiling to evaluate glycoprotein immunogens against HIV-1. Expert Rev Proteomics 2017; 14:881-890. [PMID: 28870097 DOI: 10.1080/14789450.2017.1376658] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
INTRODUCTION Much of the efforts to develop a vaccine against the human immunodeficiency virus (HIV) have focused on the design of recombinant mimics of the viral attachment glycoprotein (Env). The leading immunogens exhibit native-like antigenic properties and are being investigated for their ability to induce broadly neutralizing antibodies (bNAbs). Understanding the relative abundance of glycans at particular glycosylation sites on these immunogens is important as most bNAbs have evolved to recognize or evade the dense coat of glycans that masks much of the protein surface. Understanding the glycan structures on candidate immunogens enables triaging between native-like conformations and immunogens lacking key structural features as steric constraints limit glycan processing. The sensitivity of the processing state of a particular glycan to its structural environment has led to the need for quantitative glycan profiling and site-specific analysis to probe the structural integrity of immunogens. Areas covered: We review analytical methodologies for HIV immunogen evaluation and discuss how these studies have led to a greater understanding of the structural constraints that control the glycosylation state of the HIV attachment and fusion spike. Expert commentary: Total composition and site-specific glycosylation profiling are emerging as standard methods in the evaluation of Env-based immunogen candidates.
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Affiliation(s)
- Anna-Janina Behrens
- a Oxford Glycobiology Institute, Department of Biochemistry , University of Oxford , Oxford , UK
| | - Weston B Struwe
- a Oxford Glycobiology Institute, Department of Biochemistry , University of Oxford , Oxford , UK
| | - Max Crispin
- a Oxford Glycobiology Institute, Department of Biochemistry , University of Oxford , Oxford , UK.,b Department of Immunology and Microbial Science , The Scripps Research Institute , La Jolla , CA , USA.,c Centre for Biological Sciences and Institute for Life Sciences , University of Southampton , Southampton SO17 1BJ , UK
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Yu P, Petzoldt S, Wilhelm M, Zolg DP, Zheng R, Sun X, Liu X, Schneider G, Huhmer A, Kuster B. Trimodal Mixed Mode Chromatography That Enables Efficient Offline Two-Dimensional Peptide Fractionation for Proteome Analysis. Anal Chem 2017; 89:8884-8891. [DOI: 10.1021/acs.analchem.7b01356] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Peng Yu
- Technical University of Munich, D-85354 Freising, Germany
| | - Svenja Petzoldt
- Technical University of Munich, D-85354 Freising, Germany
- German Cancer Consortium (DKTK), 80336 Munich, Germany
- German Cancer Center (DKFZ), D-69120 Heidelberg, Germany
| | | | | | - Runsheng Zheng
- Technical University of Munich, D-85354 Freising, Germany
| | - Xuefei Sun
- Thermo Fisher Scientific, Sunnyvale, California 94085, United States
| | - Xiaodong Liu
- Thermo Fisher Scientific, Sunnyvale, California 94085, United States
| | - Günter Schneider
- Department
of Medicine II, Klinikum rechts der Isar, Technical University of Munich, D-81675 Munich, Germany
| | - Andreas Huhmer
- Thermo Fisher Scientific, San Jose, California 95134, United States
| | - Bernhard Kuster
- Technical University of Munich, D-85354 Freising, Germany
- German Cancer Consortium (DKTK), 80336 Munich, Germany
- German Cancer Center (DKFZ), D-69120 Heidelberg, Germany
- Center for Integrated Protein Science Munich, 85354 Freising, Germany
- Bavarian Center for Biomolecular Mass Spectrometry, 85354 Freising, Germany
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Wang Y, Wang J, Gao M, Zhang X. Functional dual hydrophilic dendrimer-modified metal-organic framework for the selective enrichment of N-glycopeptides. Proteomics 2017; 17:e1700005. [PMID: 28390088 DOI: 10.1002/pmic.201700005] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Revised: 03/06/2017] [Accepted: 04/06/2017] [Indexed: 01/03/2023]
Abstract
Analysis of protein glycosylation remains a significant challenge due to the low abundance of glycoproteins or N-glycopeptides. Here we have synthesized an amino-functionalized metal-organic framework (MOF) MIL-101(Cr)-NH2 whose surface is grafted with a hydrophilic dendrimer poly(amidoamine) (PAMAM) for N-glycopeptide enrichment based on the hydrophilic interactions. The selected substrate MOF MIL-101(Cr) owns high surface area which provides nice support for peptide adsorption. In addition, the MOF displayed a good hydrophilic property after being modified with amino groups. Most importantly, the grafted hydrophilic dendrimer PAMAM was firstly applied in the postsynthetic modification of MOFs. And this functionalization route using macromolecular dendrimer opens a new perspective in MOFs design. Owing to its long dendritic chains and abundant amino groups, our material displayed dual hydrophilic property. In the enrichment of standard glycoprotein HRP digestion, the functional MOF material was shown to have low detection limit (1 fmol/μL) and good selectivity when the concentration of nonglycopeptides was 100 fold higher than the target N-glycopeptides. All the results proved that MIL-101(Cr)-NH2 @PAMAM has great potential in the glycoproteome analysis.
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Affiliation(s)
- Yanan Wang
- Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai, P. R. China
| | - Jiaxi Wang
- Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai, P. R. China
| | - Mingxia Gao
- Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai, P. R. China
| | - Xiangmin Zhang
- Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai, P. R. China
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Wang X, Bo C, Wang C, Wei Y. Controllable preparation of a hydrophilic/ion-exchange mixed-mode stationary phase by surface-initiated atom transfer radical polymerization using a mixture of two functional monomers. J Sep Sci 2017; 40:1861-1868. [PMID: 28247469 DOI: 10.1002/jssc.201601292] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Revised: 02/08/2017] [Accepted: 02/19/2017] [Indexed: 11/06/2022]
Abstract
Mixed-mode chromatographic stationary phases require functionalization with at least two functional groups to yield multiple interactions with analytes. Departing from reported methods, a mixture of two different monomers, glycidyl methacrylate and 2-dimethylaminoethylmethacrylate, was grafted onto the surface of silica by a one-step surface-initiated atom transfer radical polymerization to prepare a novel hydrophilic interaction/anion-exchange mixed-mode chromatographic stationary phase. The grafted amounts of functional groups were controlled via varying the ratio of monomers in the polymerization system. The influences of water content, salt concentration and pH in the mobile phase were investigated to illustrate the mixed interaction between the stationary phase and analytes. The retention of various solutes on three columns, especially acidic and basic solutes, showed an obvious dependence on the ratio of the two monomers in the polymerization system. The results indicated that the strategy proposed in this work was beneficial to develop various types of mixed-mode chromatographic stationary phases with adjustable selectivity to meet the needs of complex samples. Finally, the column was successfully employed in the isolation of melamine in liquid milk.
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Affiliation(s)
- Xiaomeng Wang
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, Key Laboratory of Modern Separation Science in Shaanxi Province, College of Chemistry and Materials Science, Northwest University, Xi'an, P.R. China
| | - Chunmiao Bo
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, Key Laboratory of Modern Separation Science in Shaanxi Province, College of Chemistry and Materials Science, Northwest University, Xi'an, P.R. China
| | - Chaozhan Wang
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, Key Laboratory of Modern Separation Science in Shaanxi Province, College of Chemistry and Materials Science, Northwest University, Xi'an, P.R. China
| | - Yinmao Wei
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, Key Laboratory of Modern Separation Science in Shaanxi Province, College of Chemistry and Materials Science, Northwest University, Xi'an, P.R. China
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40
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Improving Proteome Coverage by Reducing Sample Complexity via Chromatography. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 919:83-143. [DOI: 10.1007/978-3-319-41448-5_5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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41
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Synthesis and evaluation of sulfobetaine zwitterionic polymer bonded stationary phase. Talanta 2016; 161:860-866. [DOI: 10.1016/j.talanta.2016.09.003] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Revised: 08/30/2016] [Accepted: 09/03/2016] [Indexed: 11/16/2022]
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Li H, Liu C, Wang Q, Zhou H, Jiang Z. The effect of charged groups on hydrophilic monolithic stationary phases on their chromatographic properties. J Chromatogr A 2016; 1469:77-87. [PMID: 27692647 DOI: 10.1016/j.chroma.2016.09.059] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2016] [Revised: 09/21/2016] [Accepted: 09/24/2016] [Indexed: 01/03/2023]
Abstract
In order to investigate the effect of charged groups present in hydrophilic monolithic stationary phases on their chromatographic properties, three charged hydrophilic monomers, i.e. N,N-dimethyl-N-acryloyloxyethyl-N-(3-sulfopropyl)ammonium betaine (SPDA), [2-(acryloyloxy)ethyl]trimethylammonium chloride (AETA), and 3-sulfopropyl acrylate potassium salt (SPA) were co-polymerized with the crosslinker N,N'-methylenebisacrylamide (MBA), respectively. The physicochemical properties of the three resulting charged hydrophilic monolithic columns were evaluated using scanning electron microscopy, ζ-potential analysis and micro-HPLC. High column efficiency was obtained on the three monolithic columns at a linear velocity of 1mm/s using thiourea as test compound. Comparative characterization of the three charged HILIC phases was then carried out using a set of model compounds, including nucleobases, nucleosides, benzoic acid derivatives, phenols, β-blockers and small peptides. Depending on the combination of stationary phase/mobile phase/solute, both hydrophilic interaction and other potential secondary interactions, including electrostatic interaction, hydrogen-bonding interaction, molecular shape selectivity, could contribute to the over-all retention of the analytes. Because of the strong electrostatic interaction provided by the quaternary ammonium groups in the poly (AETA-co-MBA) monolith, this cationic HILIC monolith exhibited the strongest retention for benzoic acid derivatives and small peptides with distorted peak shapes and the weakest retention for basic β-blockers. The sulfonyl groups on the poly (SPA-co-MBA) hydrophilic monolith could provide strong electrostatic attraction and hydrogen bonding for positively charged analytes and hydrogen-donor/acceptor containing analytes, respectively. Therefore, basic drugs, nucleobases and nucleotides exhibited the strongest retention on this anionic monolith. Because of the weak but distinct cation exchange properties of the zwitterionic poly (SPDA-co-MBA) hydrophilic monolith, it exhibited the best separation for most test analytes (including phenols, β-blockers and small peptides) in terms of selectivity, peak shape and analysis time. The poly (AETA-co-MBA) hydrophilic monolithic column provides the best separation of nucleobases and nucleosides. These results could guide the selection and application of these charged HILIC monoliths in the future.
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Affiliation(s)
- Haibin Li
- Institute of Pharmaceutical Analysis, College of Pharmacy, Jinan University, Guangzhou, Guangdong, 510632, China
| | - Chusheng Liu
- Institute of Pharmaceutical Analysis, College of Pharmacy, Jinan University, Guangzhou, Guangdong, 510632, China
| | - Qiqin Wang
- Institute of Pharmaceutical Analysis, College of Pharmacy, Jinan University, Guangzhou, Guangdong, 510632, China
| | - Haibo Zhou
- Institute of Pharmaceutical Analysis, College of Pharmacy, Jinan University, Guangzhou, Guangdong, 510632, China.
| | - Zhengjin Jiang
- Institute of Pharmaceutical Analysis, College of Pharmacy, Jinan University, Guangzhou, Guangdong, 510632, China.
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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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Wu R, Li L, Deng C. Highly efficient and selective enrichment of glycopeptides using easily synthesized magG/PDA/Au/l-Cys composites. Proteomics 2016; 16:1311-20. [DOI: 10.1002/pmic.201500383] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2015] [Revised: 01/26/2016] [Accepted: 02/10/2016] [Indexed: 01/01/2023]
Affiliation(s)
- Runqing Wu
- Department of Chemistry; Fudan University; Shanghai China
| | - Lanting Li
- Department of Chemistry; Fudan University; Shanghai China
| | - Chunhui Deng
- Department of Chemistry and Institutes of Biomedical Sciences; Collaborative Innovation Center of Genetics and Development, Fudan University; Shanghai P. R. China
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Ermondi G, Catalano F, Vallaro M, Ermondi I, Leal MC, Rinaldi L, Visentin S, Caron G. Lipophilicity of amyloid β-peptide 12–28 and 25–35 to unravel their ability to promote hydrophobic and electrostatic interactions. Int J Pharm 2015; 495:179-185. [DOI: 10.1016/j.ijpharm.2015.08.075] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Revised: 08/21/2015] [Accepted: 08/22/2015] [Indexed: 12/30/2022]
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46
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Recent advances in the application of hydrophilic interaction chromatography for the analysis of biological matrices. Bioanalysis 2015; 7:2927-45. [DOI: 10.4155/bio.15.200] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Hydrophilic interaction chromatography (HILIC) is being increasingly used for the analysis of hydrophilic compounds in biological matrices. The complexity of biological samples demands adequate sample preparation procedures, specifically adjusted for HILIC analyses. Currently, most bioanalytical assays are performed on bare silica and ZIC-HILIC columns. Trends in HILIC for bioanalysis include smaller particle sizes and miniaturization of the analytical column. For complex biological samples, multidimensional techniques can separate and identify more compounds than 1D separations. The high volatility of the mobile phase, the added separation power and high sensitivity make MS the detection method of choice for bioanalysis using HILIC, although other detectors such as evaporative light scattering detection, charged aerosol detection and nuclear magnetic resonance have been reported.
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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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48
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Raju SPK, Narayanam M, Kumar BK, Tejaswee S, Singh S. Validated Stability-Indicating Method for Alendronate Sodium Employing Zwitterionic Hydrophilic Interaction Chromatography Coupled with Charged Aerosol Detection. Chromatographia 2015. [DOI: 10.1007/s10337-015-2941-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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49
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Zhu Z, Desaire H. Carbohydrates on Proteins: Site-Specific Glycosylation Analysis by Mass Spectrometry. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2015; 8:463-483. [PMID: 26070719 DOI: 10.1146/annurev-anchem-071114-040240] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Glycosylation on proteins adds complexity and versatility to these biologically vital macromolecules. To unveil the structure-function relationship of glycoproteins, glycopeptide-centric analysis using mass spectrometry (MS) has become a method of choice because the glycan is preserved on the glycosylation site and site-specific glycosylation profiles of proteins can be readily determined. However, glycopeptide analysis is still challenging given that glycopeptides are usually low in abundance and relatively difficult to detect and the resulting data require expertise to analyze. Viewing the urgent need to address these challenges, emerging methods and techniques are being developed with the goal of analyzing glycopeptides in a sensitive, comprehensive, and high-throughput manner. In this review, we discuss recent advances in glycoprotein and glycopeptide analysis, with topics covering sample preparation, analytical separation, MS and tandem MS techniques, as well as data interpretation and automation.
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Affiliation(s)
- Zhikai Zhu
- Ralph N. Adams Institute for Bioanalytical Chemistry, Department of Chemistry, University of Kansas, Lawrence, Kansas 66047;
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50
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Simultaneous analysis of multiple neurotransmitters by hydrophilic interaction liquid chromatography coupled to tandem mass spectrometry. J Chromatogr A 2015; 1395:79-87. [DOI: 10.1016/j.chroma.2015.03.056] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2014] [Revised: 03/18/2015] [Accepted: 03/23/2015] [Indexed: 11/23/2022]
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