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A Top-Down Proteomics Platform Coupling Serial Size Exclusion Chromatography and Fourier Transform Ion Cyclotron Resonance Mass Spectrometry Trisha Tucholski, Samantha Knott, Bifan Chen, Paige Pistono, Ziqing Lin, and Ying Ge Anal. Chem., Just Accepted Manuscript • DOI: 10.1021/acs.analchem.8b04082 • Publication Date (Web): 13 Feb 2019 Downloaded from http://pubs.acs.org on February 15, 2019

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Analytical Chemistry

A Top-Down Proteomics Platform Coupling Serial Size Exclusion Chromatography and Fourier Transform Ion Cyclotron Resonance Mass Spectrometry

Trisha Tucholski1,2, Samantha Knott1,2, Bifan Chen1,2, Paige Pistono3, Ziqing Lin4, Ying Ge1,2,4*

Department of Chemistry1, University of Wisconsin-Madison, Madison, WI, 53706; Human Proteomics Program2, University of Wisconsin, Madison, WI, 53705; Department of Biochemistry3, University of Wisconsin-Madison, Madison, WI, 53706; Department of Cell and Regenerative Biology3, University of Wisconsin-Madison, Madison, WI, 53705

*Correspondence: Prof. Ying Ge Department of Cell and Regenerative Biology Department of Chemistry University of Wisconsin-Madison 1111 Highland Ave., WIMR II 8551, Madison, WI 53705 Tel: 608-265-4744, Fax: 608-265-8745, E-mail: [email protected].

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Abstract Mass spectrometry (MS)-based top-down proteomics provides rich information about proteoforms arising from combinatorial amino acid sequence variations and post-translational modifications (PTMs). Fourier transform ion cyclotron resonance (FT-ICR) MS affords ultra-high resolving power and provides high-accuracy mass measurements, presenting a powerful tool for top-down MS characterization of proteoforms. However, detection and characterization of large proteins from complex mixtures remain challenging due to the exponential decrease in S:N with increasing molecular weight (MW) and co-eluting low-MW proteins; thus, size-based fractionation of complex protein mixtures prior to MS analysis is necessary. Here, we directly combine MS-compatible serial size exclusion chromatography (sSEC) fractionation with 12 T FTICR MS for targeted top-down characterization of proteins from complex mixtures extracted from the human and swine heart proteome. Benefiting from the ultra-high resolving power of FT-ICR, we isotopically resolved 31 distinct proteoforms (30-50 kDa) simultaneously in a single mass spectrum within a 100 m/z window. Notably, within a 5 m/z window, we obtained baseline isotopic resolution for 6 distinct large proteoforms (30-50 kDa). The ultra-high resolving power of FT-ICR MS combined with sSEC fractionation enabled targeted top-down analysis of large proteoforms (>30 kDa) from the human heart proteome without extensive chromatographic separation or protein purification. Further separation of proteoforms inside of the mass spectrometer (in-MS) allowed for isolation of individual proteoforms for targeted electron capture dissociation (ECD) for high sequence coverage. sSEC/FT-ICR ECD facilitated identification and sequence characterization of important metabolic enzymes. This platform, which facilitates deep interrogation of proteoform primary structure, is highly tunable, allows for adjustment of MS and MS/MS parameters in real-time, and can be utilized for a variety of complex protein mixtures. 3 ACS Paragon Plus Environment


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Introduction The ability to accurately measure intact protein mass prior to amino acid sequence characterization is a coveted facet of mass spectrometry (MS)-based top-down proteomics.1-3 Accurate intact mass measurements combined with the high-sequence coverage accessed by topdown proteomics provides rich information about the proteoforms which arise from a combination of genetic mutations, RNA-editing, alternative splicing events, and post-translational modifications (PTMs) of a single gene product.4-6 Thus, the top-down approach has become an indispensable tool for comprehensive characterization of proteoform primary structure to investigate important biological questions.7-14 With unmatched resolving power and high mass accuracy, Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) is well-suited to accurately measure the mass of large biomacromolecules and resolve complex MS/MS spectra, making it a powerful technique for topdown protein characterization.10,

15-20

FT-ICR mass spectrometers are compatible with a wide

variety of tandem MS (MS/MS) strategies, both energy- and electron- based, which can be used individually or in combination to obtain high sequence coverage.16, 19, 21-25 The high resolving power afforded by FT-ICR MS also allows for isotopic resolution of many protein components from complex mixtures without extensive chromatographic separation.26, 27 However, detection and characterization of large proteins remain challenging in top-down proteomics because of the exponential decay in S:N with increasing molecular weight (MW), making it difficult to detect larger proteins (30-200 kDa), especially in the presence of low-MW proteins (5-20 kDa).28 Hence, size-based fractionation, such as gel elution liquid fraction entrapment electrophoresis (GELFrEE), is commonly used at the front-end of top-down proteomics workflows to improve the analysis of high-MW proteins from complex mixtures.29-32 However, gel-based methods such as 4 ACS Paragon Plus Environment

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GELFrEE require the use of MS-incompatible detergents (e.g. SDS), necessitating additional detergent-removal steps prior to MS analysis. In contrast, size exclusion chromatography (SEC) is an attractive alternative for size-based separation because of its compatibility with MS-friendly solvents.33, 34 Recently, our group introduced serial (s)SEC, a high-resolution size-based separation strategy which combines SEC columns with different pore sizes in series to enhance fractionation power for complex mixtures across a wide MW range. sSEC employs an MS-compatible eluent (1% formic acid in water), making it highly compatible with top-down proteomics workflows.35 Herein, we sought to combine MS-compatible sSEC fractionation directly with the ultrahigh resolving power of FT-ICR MS for the top-down characterization of proteins without extensive purification or liquid chromatography. We fractionated cytosolic proteomes, extracted from human and swine heart tissue, by MS-compatible sSEC. Benefiting from the use of a highlyMS compatible sSEC eluent (1% formic acid (FA) in water), this platform requires little sample preparation between fractionation and top-down MS analysis. Direct infusion FT-ICR MS analysis of the sSEC fractions allowed for ultra-high resolution separation of ions inside of the mass spectrometer (in-MS). This permitted intact mass measurement of multiple species from a single spectrum and sequence characterization by MS/MS analysis (Scheme 1). From a single spectrum, we were able to detect 31 distinct proteoforms (30-50 kDa) within a 100 m/z window. Notably, in a 5 m/z window, we achieved baseline isotopic resolution for 6 distinct species. From the sSEC fractions, we identified large metabolic enzymes with good mass accuracy using FT-ICR MS. With this platform, we also isolated single proteoforms in-MS and performed electron capture dissociation (ECD) to obtain high sequence coverage for metabolic enzymes (>30 kDa). The versatility afforded by this sSEC/FT-ICR MS platform offers a valuable tool for top-down proteomics and for interrogation of proteoform primary structure. 5 ACS Paragon Plus Environment


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Scheme 1: A schematic representation of the sSEC/FT-ICR MS top-down proteomics workflow. 1) Offline sSEC fractionation of a protein mixture with automatic fraction collection, 2) FT-ICR MS analysis of sSEC fractions, 3) In-mass spectrometer (in-MS) separation of ions for MS or MS/MS analysis, 4) Measurement of intact mass for tentative protein identification, 5) MS/MS analysis for protein characterization.

Experimental Procedures Materials All chemicals and reagents were purchased from Sigma-Aldrich Inc. (St. Louis, MO, USA) unless otherwise noted. HPLC grade water and acetonitrile (ACN) were purchased from Fisher Scientific (Fair Lawn, NJ, USA). Amicon ultracentrifugal 10 kDa molecular weight cutoff (MWCO) filters were purchased from Millipore Sigma (Burlington, MA, USA). TGX Stain Free 8-16% gradient gels were purchased from Bio-Rad (Hercules, CA, USA). 6 ACS Paragon Plus Environment

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Extraction of the Soluble Heart Proteome Donor human heart tissue was obtained from the University of Wisconsin Hospital and Clinics according to the protocol approved by the Institutional Review Board at University of Wisconsin-Madison as reported previously.36 A detailed protein extraction procedure and list of reagents is provided in the Supporting Information. Briefly, heart tissue was homogenized in 4 volumes (mL/g tissue) of HEPES extraction buffer (pH=7.4) using an electric homogenizer to extract the cytosolic portion of the heart proteome. The resulting homogenate was centrifuged at 16,100 g for 15 min at 4 ºC. The supernatant was collected and the pellet was resuspended in HEPES extraction buffer and centrifuged at 16,100 g for 15 min at 4 ºC. The supernatants from both wash steps were combined, resulting in a protein extract with a total protein concentration of approximately 5.6 mg/mL.

Serial Size Exclusion Fractionation Heart protein extract was exchanged from HEPES extraction buffer to 1% FA in water (pH = 2) using ultracentrifugal 10 kDa MWCO filters prior to sSEC fractionation. A detailed procedure regarding buffer exchange is provided in the Supporting Information. sSEC fractionation was performed using an ACQUITY H-class UPLC system equipped with a UV detector and an automated fraction collector (Waters, Milford, MA, USA). A series of PolyHYDROXYETHYL A (PolyHEA) columns (9.4 x 200 mm, 3 µm) from PolyLC Inc. (Columbia, MD, USA) were assembled in order of decreasing pore sizes (1000 Å - 500 Å - 300 Å), as previously described.35 Proteins were eluted isocratically with 1% FA in water at a flow rate of 0.5 mL/min. Protein elution 7 ACS Paragon Plus Environment


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was monitored with UV detection at λ=280 nm. 150 µg of total protein (25 µL injection, 6 mg/mL) was loaded per sSEC run. Automatic fraction collection was performed based on the protein elution window. Twelve fractions were collected over 12 min (24-36 min). Fractions from 18 replicate injections were pooled and concentrated to a final volume of 100 µL using ultracentrifugal 10 kDa MWCO filters. Prior to FT-ICR MS, SDS-PAGE analysis was performed to evaluate the protein content and MW range for each fraction. For sSEC fractionation of soluble proteome extracted from swine heart tissue, the same procedure was followed, except 1000 Å 500 Å - 500 Å series was used. Further details regarding this fractionation are available in the Supporting Information.

FT-ICR MS Analysis Fractions collected and concentrated following sSEC fractionation were diluted with 0.1% FA in ACN (1:1 for sSEC fractions, 1:3 for unfractionated protein mixture) to aid nanoelectrospray ionization (nanoESI). Protein fractions were directly infused to the Bruker 12 Tesla SolariX FT-ICR mass spectrometer using an Advion TriVersa NanoMate with gas pressure and spray voltage set between 0.3 – 0.5 psi and 1.3 – 1.5 kV, respectively. In source energy of 70 V was applied at skimmer 1 to aid the desolvation of protein ions. For MS/MS experiments, collisionally activated dissociation (CAD) or ECD are used. A detailed list of MS and MS/MS parameters corresponding to data shown throughout manuscript can be found in the Supporting Information. FT-ICR mass spectra were calibrated externally using sodium trifluoracetic acid (1 mg/mL) in 50:50 water:ACN.


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Data Analysis MS and MS/MS data were analyzed using Bruker DataAnalysis (version 4.3.110) and inhouse developed MASH Suite Pro. First, data were externally calibrated using DataAnalysis Calibrate function. Mass lists were then extracted from raw Bruker .baf files in MASH Suite Pro using the Extract function (with THRASH deconvolution algorithm) in MASH Suite Pro with a quality fit factor of 60 and S:N of 3.37 TopPIC (version 1.1.1) search algorithm run against the human or swine Uniprot database was used to identify proteins from extracted mass lists.38 For all searches, a mass error tolerance of 15 ppm was used with 0.01 as an E-value cut-off. Matches were manually validated using MASH Suite Pro.

Results and Discussion sSEC Fractionation of the Heart Proteome We used a 1000-500-300 Å pore size series for fractionation of proteins extracted from the cytosolic proteome of human heart tissue (10-250 kDa). The combination of different pore sizes in series provided an extension of MW fractionation range and allows for high-resolution fractionation of complex mixtures.35 The protein elution time window and signal intensity for the sSEC runs were highly reproducible, evident from the overlay of replicate UV chromatograms (Figure S3). The UV chromatogram was used to determine the elution window for the proteins (12 min, Figure S4A) and automatic fraction collection was performed in 1-min intervals (12 total fractions) from the time proteins began eluting from the column series. We found that 1-min intervals provided efficient MW-fractionation of our specific mixture of cytosolic proteins extracted from heart tissue, based on SDS-PAGE visualization (Figure S4B). 9 ACS Paragon Plus Environment


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Visualization of the sSEC fractions with SDS-PAGE analysis showed a good distribution of protein size across the fractions (Figure S4B). Fractions 1-5 primarily contained larger proteins (75-200 kDa), which is conceivable since the largest components of a mixture have the least access to the column pore volume and elute first in SEC.39 Fraction 6 contained proteins mainly in the MW range of 50-75 kDa whereas fractions 7 and 8 contained primarily proteins between 25 - 50 kDa as indicated in the SDS-gel (Figure S4B). The absence of proteins less than 25 kDa in these sSEC fractions significantly improved MS detection of proteins within this size range (vide infra). Gel visualization showed that fraction 8 and 9 had similar composition between the ranges of 25 – 50 kDa, except that fraction 9 contained proteins less than 25 kDa. This difference in composition between fraction 8 and 9 may seem minor, however, we later showed that the presence of lowMW components significantly impacted FT-ICR MS analysis of the intermediate-MW protein components in fraction 9. Fraction 10 contained primarily lower MW proteins (

A Top-Down Proteomics Platform Coupling Serial ... - ACS Publications

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