Organic Solvent-Based Protein Precipitation for Robust Proteome Purification Ahead of Mass Spectrometry
Summary
The present protocol describes solvent-based protein precipitation under controlled conditions for robust and rapid recovery and purification of proteome samples prior to mass spectrometry.
Abstract
While multiple advances in mass spectrometry (MS) instruments have improved qualitative and quantitative proteome analysis, more reliable front-end approaches to isolate, enrich, and process proteins ahead of MS are critical for successful proteome characterization. Low, inconsistent protein recovery and residual impurities such as surfactants are detrimental to MS analysis. Protein precipitation is often considered unreliable, time-consuming, and technically challenging to perform compared to other sample preparation strategies. These concerns are overcome by employing optimal protein precipitation protocols. For acetone precipitation, the combination of specific salts, temperature control, solvent composition, and precipitation time is critical, while the efficiency of chloroform/methanol/water precipitation depends on proper pipetting and vial manipulation. Alternatively, these precipitation protocols are streamlined and semi-automated within a disposable spin cartridge. The expected outcomes of solvent-based protein precipitation in the conventional format and using a disposable, two-stage filtration and extraction cartridge are illustrated in this work. This includes the detailed characterization of proteomic mixtures by bottom-up LC-MS/MS analysis. The superior performance of SDS-based workflows is also demonstrated relative to non-contaminated protein.
Introduction
Proteome analysis by mass spectrometry has become increasingly rigorous, owing to the enhanced sensitivity, resolution, scan speed, and versatility of modern MS instruments. MS advances contribute to greater protein identification efficiency and more precise quantitation1,2,3,4,5. With improved MS instrumentation, researchers demand a correspondingly consistent front-end sample preparation strategy capable of quantitative recovery of high-purity proteins in minimal time across all stages of the workflow6,7,8,9,10,11. To accurately reflect the proteome status of a biological system, proteins must be isolated from the native sample matrix in an efficient and unbiased fashion. To this end, including a denaturing surfactant, such as sodium dodecyl sulfate (SDS), ensures efficient protein extraction and solubilization12. However, SDS strongly interferes with electrospray ionization, causing severe MS signal suppression if not properly eliminated13.
Various SDS depletion strategies are available for subsequent proteome analysis, such as the retention of proteins above a molecular weight cutoff filter contained within disposable spin cartridges14,15,16. The filter-aided sample preparation method (FASP) is favored as it effectively depletes SDS below 10 ppm, facilitating optimal MS. However, protein recovery with FASP is variable, which prompted the exploration of other techniques. Chromatographic approaches that selectively capture protein (or surfactant) have evolved into various convenient cartridges or bead-based formats17,18,19,20,21. Given these simple and (ideally) consistent strategies to protein purification, the classical approach of protein precipitation with organic solvents is often overlooked as a promising approach to protein isolation. While solvent precipitation is shown to deplete SDS below critical levels successfully, protein recovery has been a longstanding concern of this approach. Multiple groups have observed a protein recovery bias, with unacceptably low precipitation yields as a function of protein concentration, molecular weight, and hydrophobicity22,23. Due to the diversity of precipitation protocols reported in the literature, standardized precipitation conditions were developed. In 2013, Crowell et al. first reported the dependence of ionic strength on the precipitation efficiency of proteins in 80% acetone24. For all proteins examined, the addition of up to 30 mM sodium chloride was shown to be essential to maximize yields (up to 100% recovery). More recently, Nickerson et al. showed that the combination of even higher ionic strength (up to 100 mM) with elevated temperature (20 °C) during acetone precipitation gave near quantitative recovery in 2-5 min25. A slight drop in the recovery of low molecular weight (LMW) proteins was observed. Therefore, a subsequent report by Baghalabadi et al. demonstrated the successful recovery of LMW proteins and peptides (≤5 kDa) by combining specific salts, particularly zinc sulfate, with a higher level of organic solvent (97% acetone)26.
While refining the precipitation protocol lends a more reliable protein purification strategy for MS-based proteomics, the success of conventional precipitation relies heavily on user technique. A primary goal of this work is to present a robust precipitation strategy that facilitates the isolation of the protein pellet from the contaminating supernatant. A disposable filtration cartridge was developed to eliminate pipetting by isolating aggregated protein above a porous PTFE membrane filter27. MS-interfering components in the supernatant are effectively removed in a short, low-speed centrifugation step. The disposable filter cartridge also offers an interchangeable SPE cartridge, which facilitates subsequent sample clean-up following resolubilization and optional protein digestion, ahead of mass spectrometry.
A series of recommended proteome precipitation workflows are presented here, including modified acetone and chloroform/methanol/water28 protocols, in a conventional (vial-based) and a semi-automated format in a disposable two-state filtration and extraction cartridge. The resulting protein recoveries and SDS depletion efficiencies are highlighted, together with bottom-up LC-MS/MS proteome coverage, to demonstrate the expected outcome from each protocol. The practical benefits and drawbacks associated with each approach are discussed.
Protocol
Representative Results
Discussion
Optimal MS characterization is achieved when residual SDS is depleted below 10 ppm. While alternative approaches, such as FASP and on-bead digestion, offer quantitative SDS depletion with variable recovery31,32,33, the primary objective of precipitation is to maximize purity and yield simultaneously. This depends on effectively isolating the supernatant (containing the SDS) without disturbing the protein pellet. With vial-based …
Divulgations
The authors have nothing to disclose.
Acknowledgements
This work was funded by the Natural Sciences and Engineering Research Council of Canada. The authors thank Bioinformatics Solutions Inc. (Waterloo, Canada) and SPARC BioCentre (Molecular Analysis) at the Hospital for Sick Children (Toronto, Canada) for their contributions to the acquisition of MS data.
Materials
| Acetone | Fisher Scientific | AC177170010 | ≤0.002 % aldehyde |
| Acetonitrile | Fisher Scientific | A998-4 | HPLC grade |
| Ammonium Bicarbonate | Millipore Sigma | A6141-1KG | solid |
| Beta mercaptoethanol | Millipore Sigma | M3148-25ML | Molecular biology grade |
| Bromophenol blue | Millipore Sigma | B8026-5G | Bromophenol blue sodium salt |
| Chloroform | Fisher Scientific | C298-400 | Chloroform |
| Formic Acid | Honeywell | 56302 | Eluent additive for LC-MS |
| Fusion Lumos Mass Spectrometer | ThermoFisher Scientific | for analysis of standard protein mixture | |
| Glycerol | Millipore Sigma | 356352-1L-M | For molecular biology, > 99% |
| Isopropanol | Fisher Scientific | A4641 | HPLC grade |
| Methanol | Fisher Scientific | A452SK-4 | HPLC grade |
| Microcentrifuge | Fisher Scientific | 75-400-102 | up to 21,000 xg |
| Microcentrifuge Tube (1.5 mL) | Fisher Scientific | 05-408-130 | tapered bottom |
| Microcentrifuge Tube (2 mL) | Fisher Scientific | 02-681-321 | rounded bottom |
| Micropipette Tips (0.1-10 μL) | Fisher Scientific | 21-197-28 | Universal pipet tip, non-sterile |
| Micropipette Tips (1-200 μL) | Fisher Scientific | 07-200-302 | Universal pipet tip, non-sterile |
| Micropipette Tips (200-1000 μL) | Fisher Scientific | 07-200-303 | Universal pipet tip, non-sterile |
| Micropipettes | Fisher Scientific | 13-710-903 | Micropipet Trio pack |
| Pepsin | Millipore Sigma | P0525000 | Lyophilized powder, >3200 units/ mg |
| ProTrap XG | Proteoform Scientific | PXG-0002 | 50 complete units per box |
| Sodium Chloride | Millipore Sigma | S9888-1KG | ACS reagent, >99 % |
| Sodium Dodecyl Sulfate | ThermoFisher Scientific | 28312 | powdered solid |
| timsTOF Pro Mass Spectrometer | Bruker | for analysis of liver proteome extract | |
| Trifluoroacetic Acid | ThermoFisher Scientific | L06374.AP | 99% |
| Tris | Fisher Scientific | BP152-500 | Molecular biology grade |
| Trypsin | Millipore Sigma | 9002-07-7 | From bovine pancreas, TPCK-treated |
| Urea | Bio-Rad | 1610731 | solid |
| Water (deionized) | Sartorius Arium Mini Water Purification System | 76307-662 | Type 1 ultrapure (18.2 MΩ cm) |
| Zinc Sulfate | Millipore Sigma | 307491-100G | solid |
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