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Cline EN, Alvarez C, Duan J, Patrie SM. Online μSEC 2-nRPLC-MS for Improved Sensitivity of Intact Protein Detection of IEF-Separated Nonhuman Primate Cerebrospinal Fluid Proteins. Anal Chem 2021; 93:16741-16750. [PMID: 34881887 PMCID: PMC10476446 DOI: 10.1021/acs.analchem.1c00396] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Proteoform-resolved information, obtained by top-down (TD) "intact protein" proteomics, is expected to contribute substantially to the understanding of molecular pathogenic mechanisms and, in turn, identify novel therapeutic and diagnostic targets. However, the robustness of mass spectrometry (MS) analysis of intact proteins in complex biological samples is hindered by the high dynamic range in protein concentration and mass, protein instability, and buffer complexity. Here, we describe an evolutionary step for intact protein investigations through the online implementation of tandem microflow size-exclusion chromatography with nanoflow reversed-phase liquid chromatography and MS (μSEC2-nRPLC-MS). Online serial high-/low-pass SEC filtration overcomes the aforementioned hurdles to intact proteomic analysis through automated sample desalting/cleanup and enrichment of target mass ranges (5-155 kDa) prior to nRPLC-MS. The coupling of μSEC to nRPLC is achieved through a novel injection volume control (IVC) strategy of inserting protein trap columns, pre- and post-μSEC columns, to enable injection of dilute samples in high volumes without loss of sensitivity or resolution. Critical characteristics of the approach are tested via rigorous investigations on samples of varied complexity and chemical background. Application of the platform to cerebrospinal fluid (CSF) prefractionated by OFFGEL isoelectric focusing drastically increases the number of intact mass tags (IMTs) detected within the target mass range (5-30 kDa) in comparison to one-dimensional nRPLC-MS with approximately 100× less CSF than previous OFFGEL studies. Furthermore, the modular design of the μSEC2-nRPLC-MS platform is robust and promises significant flexibility for large-scale TDMS analysis of diverse samples either directly or in concert with other multidimensional fractionation steps.
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Affiliation(s)
- Erika N Cline
- Department of Chemistry and the Proteomics Center of Excellence, Northwestern University, 2145 Sheridan Rd, Evanston, Illinois 60208, United States
| | - Carina Alvarez
- Department of Chemistry and the Proteomics Center of Excellence, Northwestern University, 2145 Sheridan Rd, Evanston, Illinois 60208, United States
| | - Jiana Duan
- Department of Chemistry and the Proteomics Center of Excellence, Northwestern University, 2145 Sheridan Rd, Evanston, Illinois 60208, United States
| | - Steven M Patrie
- Department of Chemistry and the Proteomics Center of Excellence, Northwestern University, 2145 Sheridan Rd, Evanston, Illinois 60208, United States
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Urade Y. Biochemical and Structural Characteristics, Gene Regulation, Physiological, Pathological and Clinical Features of Lipocalin-Type Prostaglandin D 2 Synthase as a Multifunctional Lipocalin. Front Physiol 2021; 12:718002. [PMID: 34744762 PMCID: PMC8569824 DOI: 10.3389/fphys.2021.718002] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 09/01/2021] [Indexed: 11/13/2022] Open
Abstract
Lipocalin-type prostaglandin (PG) D2 synthase (L-PGDS) catalyzes the isomerization of PGH2, a common precursor of the two series of PGs, to produce PGD2. PGD2 stimulates three distinct types of G protein-coupled receptors: (1) D type of prostanoid (DP) receptors involved in the regulation of sleep, pain, food intake, and others; (2) chemoattractant receptor-homologous molecule expressed on T helper type 2 cells (CRTH2) receptors, in myelination of peripheral nervous system, adipocyte differentiation, inhibition of hair follicle neogenesis, and others; and (3) F type of prostanoid (FP) receptors, in dexamethasone-induced cardioprotection. L-PGDS is the same protein as β-trace, a major protein in human cerebrospinal fluid (CSF). L-PGDS exists in the central nervous system and male genital organs of various mammals, and human heart; and is secreted into the CSF, seminal plasma, and plasma, respectively. L-PGDS binds retinoic acids and retinal with high affinities (Kd < 100 nM) and diverse small lipophilic substances, such as thyroids, gangliosides, bilirubin and biliverdin, heme, NAD(P)H, and PGD2, acting as an extracellular carrier of these substances. L-PGDS also binds amyloid β peptides, prevents their fibril formation, and disaggregates amyloid β fibrils, acting as a major amyloid β chaperone in human CSF. Here, I summarize the recent progress of the research on PGD2 and L-PGDS, in terms of its “molecular properties,” “cell culture studies,” “animal experiments,” and “clinical studies,” all of which should help to understand the pathophysiological role of L-PGDS and inspire the future research of this multifunctional lipocalin.
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Affiliation(s)
- Yoshihiro Urade
- Center for Supporting Pharmaceutical Education, Daiichi University of Pharmacy, Fukuoka, Japan.,Isotope Science Center, The University of Tokyo, Tokyo, Japan
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Corbett JR, Robinson DE, Patrie SM. Robustness and Ruggedness of Isoelectric Focusing and Superficially Porous Liquid Chromatography with Fourier Transform Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:346-354. [PMID: 33274937 PMCID: PMC10476448 DOI: 10.1021/jasms.0c00355] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
An investigation of a multidimensional proteomics workflow composed of off-gel isoelectric focusing (IEF) and superficially porous liquid chromatography (SPLC) with Fourier transform mass spectrometry (FTMS) was completed in order to assess various figures of merit associated with intact protein measurements. Triplicate analysis performed at both high and low FTMS resolutions on the E. coli proteome resulted in ∼900 redundant proteoforms from 3 to 95 kDa. Normalization of the chromatographic axis to identified proteoforms enabled reproducible physicochemical property measurements between proteome replicates with inter-replicate variances of ±3 ppm mass error for proteoforms <30 kDa, ±1.1 Da for proteins >30 kDa, ±12 s retention time error, and ±0.21 pI units. The results for E. coli and standard proteins revealed a correlation between pI precision and proteoform abundance with species detected in multiple IEF fractions exhibiting pI precisions less than the theoretical resolution of the off-gel system (±0.05 vs ±0.17, respectively). Evaluation of differentially modified proteoforms of standard proteins revealed that high sample loads (100s μgrams) change the IEF pH gradient profile, leading to sample broadening that facilitates resolution of charged post-translational modifications (e.g., phosphorylation, sialylation). Despite the impact of sample load on IEF resolution, results on standard proteins measured directly or after being spiked into E. coli demonstrated that the reproducibility of the workflow permitted recombination of the MS signal across IEF fractions in a manner supporting the evaluation of three label-free quantitation metrics for intact protein studies (proteoforms, proteoform ratios, and protein) over 102-103 sample amount with low femtomole detection limits.
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Affiliation(s)
- John R Corbett
- Department of Pathology, UT Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas 75390, United States
- Department of Bioengineering, UT Dallas, 800 West Campbell Road, Richardson, Texas 75080, United States
| | - Dana E Robinson
- Department of Pathology, UT Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas 75390, United States
| | - Steven M Patrie
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
- Department of Pathology, UT Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas 75390, United States
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Lee J, Perez L, Liu Y, Wang H, Hooley RJ, Zhong W. Separation of Methylated Histone Peptides via Host-Assisted Capillary Electrophoresis. Anal Chem 2018; 90:1881-1888. [PMID: 29286640 DOI: 10.1021/acs.analchem.7b03969] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Lysine methylation in protein is one important epigenetic mechanism that regulates diverse biological processes but is challenging to study due to the large variability in methylation levels and sites. Here, we show that supramolecular hosts such as calixarenes and cucurbiturils can be applied in the background electrolyte (BGE) of capillary electrophoresis (CE) for highly effective separation of post-translationally methylated histone peptides. The molecular recognition event causes a shift in the electrophoretic mobility of the peptide, allowing affinity measurement for binding between the synthetic receptor and various methylated lysine species. Successful separation of the H3 peptides carrying different methylation levels at the K9 position can be achieved using CX4 and CX6 as the BGE additives in CE, enabling monitoring of the activity of the histone lysine demethylase JMJD2E. This reveals the power of combining high resolution CE with synthetic hosts for study of protein methylation, and the method should be capable of analyzing complex biological samples for better understanding of the functions of histone methylation.
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Affiliation(s)
| | | | | | - Hua Wang
- Instrument Analysis Center, Yancheng Teachers University , Yancheng, Jiangsu 224007, China
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Plymire DA, Wing CE, Robinson DE, Patrie SM. Continuous Elution Proteoform Identification of Myelin Basic Protein by Superficially Porous Reversed-Phase Liquid Chromatography and Fourier Transform Mass Spectrometry. Anal Chem 2017; 89:12030-12038. [PMID: 29016107 DOI: 10.1021/acs.analchem.7b02426] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Myelin basic protein (MBP) plays an important structural and functional role in the neuronal myelin sheath. Translated MBP exhibits extreme microheterogeneity with numerous alternative splice variants (ASVs) and post-translational modifications (PTMs) reportedly tied to central nervous system maturation, myelin stability, and the pathobiology of various de- and dys-myelinating disorders. Conventional bioanalytical tools cannot efficiently examine ASV and PTM events simultaneously, which limits understanding of the role of MBP microheterogeneity in human physiology and disease. To address this need, we report on a top-down proteomics pipeline that combines superficially porous reversed-phase liquid chromatography (SPLC), Fourier transform mass spectrometry (FTMS), data-independent acquisition (DIA) with nozzle-skimmer dissociation (NSD), and aligned data processing resources to rapidly characterize abundant MBP proteoforms within murine tissue. The three-tier proteoform identification and characterization workflow resolved four known MBP ASVs and hundreds of differentially modified states from a single 90 min SPLC-FTMS run on ∼0.5 μg of material. This included 323 proteoforms for the 14.1 kDa ASV alone. We also identified two novel ASVs from an alternative transcriptional start site (ATSS) of the MBP gene as well as a never before characterized S-acylation event linking palmitic acid, oleic acid, and stearic acid at C78 of the 17.125 kDa ASV.
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Affiliation(s)
- Daniel A Plymire
- Department of Pathology, UT Southwestern Medical Center , 5323 Harry Hines Boulevard, Dallas, Texas 75390, United States
| | - Casey E Wing
- Department of Pathology, UT Southwestern Medical Center , 5323 Harry Hines Boulevard, Dallas, Texas 75390, United States
| | - Dana E Robinson
- Department of Pathology, UT Southwestern Medical Center , 5323 Harry Hines Boulevard, Dallas, Texas 75390, United States
| | - Steven M Patrie
- Department of Chemistry, Northwestern University , 2145 Sheridan Road, Evanston, Illinois 60208, United States.,Department of Pathology, UT Southwestern Medical Center , 5323 Harry Hines Boulevard, Dallas, Texas 75390, United States
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Patrie SM. Top-Down Mass Spectrometry: Proteomics to Proteoforms. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 919:171-200. [PMID: 27975217 DOI: 10.1007/978-3-319-41448-5_8] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
This chapter highlights many of the fundamental concepts and technologies in the field of top-down mass spectrometry (TDMS), and provides numerous examples of contributions that TD is making in biology, biophysics, and clinical investigations. TD workflows include variegated steps that may include non-specific or targeted preparative strategies, orthogonal liquid chromatography techniques, analyte ionization, mass analysis, tandem mass spectrometry (MS/MS) and informatics procedures. This diversity of experimental designs has evolved to manage the large dynamic range of protein expression and diverse physiochemical properties of proteins in proteome investigations, tackle proteoform microheterogeneity, as well as determine structure and composition of gas-phase proteins and protein assemblies.
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Affiliation(s)
- Steven M Patrie
- Computational and Systems Biology & Biomedical Engineering Graduate Programs, University of Texas Southwestern Medical Center, Dallas, TX, USA. .,Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, USA. .,Department of Bioengineering, University of Texas at Dallas, Richardson, TX, USA.
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Shining a spotlight on intact proteins. Proteomics 2014; 14:1125-7. [DOI: 10.1002/pmic.201470073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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