Determination of total sugar content in lignocellulosic hydrolysates by using a reaction headspace gas chromatographic technique

This paper investigates a new analytical technique for the quantitative detection of total sugar content in lignocellulosic hydrolysates by reaction headspace gas chromatography (HS-GC). By detecting the carbon dioxide (CO₂) generated from the reaction between sugars in lignocellulosic hydrolysates and potassium dichromate, the total sugar content in lignocellulosic hydrolysates can be quantified. The data illustrate that the conversion of sugars in lignocellulose hydrolysates can be achieved under the given conditions (at 90 °C for 30 min), the relative standard deviation of this HS-GC technique in the total sugar content determination was within 3.35%, and the measured total sugar content in 15 lignocellulose hydrolysate samples closely matched those measured by the reference spectrophotometric technique (relative differences <7.69%). The present technique is efficient, reliable and suitable to be used in the total sugar content quantification in lignocellulose hydrolysate related research and process control.     

Liquid chromatography tandem mass spectrometry method for the quantitative analysis of ceritinib in human plasma and its application to pharmacokinetic studies

Ceritinib is a highly selective inhibitor of an important cancer target, anaplastic lymphoma kinase (ALK). Because it is an investigational compound, there is a need to develop a robust and reliable analytical method for its quantitative determination in human plasma. Here, we report the validation of a liquid chromatography tandem mass spectrometry (LC-MS/MS) method for the rapid quantification of ceritinib in human plasma. The method consists of protein precipitation with acetonitrile, and salting-out assisted liquid-liquid extraction (SALLE) using a saturated solution of sodium chloride prior to analysis by LC-MS/MS with electrospray ionization (ESI) technique in positive mode. Samples were eluted at 0.800 mL min^?1 on Ascentis Express® C₁₈ column (50 mm?×?2.1 mm, 2.7 μm) with a mobile phase made of 0.1 % formic acid in water (A) and 0.1 % formic acid in acetonitrile (B). The method run time was 3.6 min and the low limit of quantification (LLOQ) was estimated at 1.00 ng mL^?1 when using 0.100 mL of human plasma. The assay was fully validated and the method exhibited sufficient specificity, accuracy, precision, and sensitivity. In addition, recovery data and matrix factor (MF) in normal and in hemolyzed plasmas were assessed, while incurred samples stability (ISS) for ceritinib was demonstrated for at least 21 months at a storage temperature of ?65 °C or below. The method was successfully applied to the measurement of ceritinib in clinical samples and the data obtained on incurred samples reanalysis (ISR) showed that our method was reliable and suitable to support the analysis of samples from the clinical studies.     

A novel quantification strategy of transferrin and albumin in human serum by species-unspecific isotope dilution laser ablation inductively coupled plasma mass spectrometry (ICP-MS)

Species-specific (SS) isotope dilution analysis with gel electrophoresis (GE)-laser ablation (LA)-ICP-MS is a promising technique for the quantification of particular metal-binding proteins in biological samples. However, unavailable isotopically enriched spike and metal losses in GE separation are main limitations for SS-isotope dilution PAGE-LA-ICP-MS. In this study, we report for the first time the absolute quantification of transferrin (Tf) and albumin (Alb) in human serum by non-denaturing (native) GE combined with species-unspecific isotope dilution mass spectrometry (IDMS). In order to achieve a homogeneous distribution of both protein and isotope-enriched spike (simulated isotope equilibration), immersing the protein strips with ³⁴S spike solution after gel electrophoresis was demonstrated to be an effective way of spike addition. Furthermore, effects of immersion time and ³⁴S spike concentration were investigated to obtain optimal conditions of the post-electrophoresis isotope dilution method. The relative mass of spike and ablated sample (m_sp/m_sam) in IDMS equation was calculated by standard Tf and Alb proteins, which could be applied to the quantification of Tf and Alb in ERM-DA470k/IFCC for method confirmation. The results were in agreement with the certified value with good precision and small uncertainty (1.5–3%). In this method, species-specific spike protein is not necessary and the integrity of the heteroatom-protein could be maintained in sample preparation process. Moreover, the application of species-unspecific isotope dilution GE-LA-ICP-MS has the potential to offer reliable, direct and simultaneous quantification of proteins after conventional 1D and 2D gel electrophoretic separations.     

Localized quantification of anhydrous calcium carbonate polymorphs using micro-Raman spectroscopy

Micro-Raman spectroscopy is a powerful technique for qualitative and quantitative analysis of different mineral mixtures. In this paper, micro-Raman spectroscopy was used for quantification in local regions (180 × 180 μm area) of ternary mixtures of the synthetic calcium carbonate (CaCO₃) polymorphs (vaterite, aragonite, calcite) as well as CaCO₃ formed during the carbonation of nanolime suspension. The obtained results of localized quantification were in agreement with the detected concentrations obtained from bulk quantitative phase analysis of X-ray powder diffraction patterns. The detection limits were found to be below 0.5 wt.% for each CaCO₃ polymorphs. Through the use of 2D mapping, localized quantification of CaCO₃ polymorphs can be achieved. This information could be potentially useful for conservation of valuable Cultural Heritage objects, as it might influence the consolidation treatment chosen.     

Characterization of green‐tissue protein extract from alfalfa (Medicago sativa) exploiting a 3‐D technique

There is a growing interest of pharmaceutical companies for plant‐based production systems. To facilitate the general acceptance of plants as bioreactors, the establishment of efficient downstream operations is critical. It has been proposed that a better understanding of the properties of the contaminant proteins can benefit downstream processing design and operation. The coupled application of 2‐DE with aqueous two‐phase partitioning has been suggested as a practical 3‐D method to characterize potential contaminant proteins from plant extracts. The application of this novel 3‐D approach to a complex protein extract from alfalfa (Medicago sativa) containing a model recombinant protein (human granulocyte colony stimulating factor (hG‐CSF)) resulted in the quantification of 55 protein spots. The 3‐D properties (M_r, pI, and K_p) obtained for 17 proteins comprising 69% of the alfalfa proteins, allowed the proposal of a prefractionation step as well as the identification of the target molecule (rG‐CSF) from bulk of alfalfa proteins. The information obtained from this experimental approach was useful for the identification of the potential contaminant proteins that will occur in alfalfa when this plant is used as a host for recombinant proteins. Additionally, this method will assist in the design of adequate purification strategies for recombinant proteins expressed in alfalfa green tissue.     

Quantification of genetically modified soya using strong anion exchange chromatography and time-of-flight mass spectrometry

Stable-isotope dimethyl labeling was applied to the quantification of genetically modified (GM) soya. The herbicide-resistant gene-related protein 5-enolpyruvylshikimate-3-phosphate synthase (CP4 EPSPS) was labeled using a dimethyl labeling reagent, formaldehyde-H₂ or -D₂. The identification and quantification of CP4 EPSPS was performed using matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS). The CP4 EPSPS protein was separated from high abundance proteins using strong anion exchange chromatography and sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Then, the tryptic peptides from the samples and reference were labeled with formaldehyde-H₂ and formaldehyde-D₂, respectively. The two labeled pools were mixed and analyzed using MALDI-MS. The data showed a good correlation between the peak ratio of the H- and D-labeled peptides and the GM soya percentages at 0.5, 1, 3, and 5 %, with R ² of 0.99. The labeling reagents are readily available. The labeling experiments and the detection procedures are simple. The approach is useful for the quantification of GM soya at a level as low as 0.5 %.     

Comparison of targeted peptide quantification assays for reductive dehalogenases by selective reaction monitoring (SRM) and precursor reaction monitoring (PRM)

Targeted absolute protein quantification yields valuable information about physiological adaptation of organisms and is thereby of high interest. Especially for this purpose, two proteomic mass spectrometry-based techniques namely selective reaction monitoring (SRM) and precursor reaction monitoring (PRM) are commonly applied. The objective of this study was to establish an optimal quantification assay for proteins with the focus on those involved in housekeeping functions and putative reductive dehalogenase proteins from the strictly anaerobic bacterium Dehalococcoides mccartyi strain CBDB1. This microbe is small and slow-growing; hence, it provides little biomass for comprehensive proteomic analysis. We therefore compared SRM and PRM techniques. Eleven peptides were successfully quantified by both methods. In addition, six peptides were solely quantified by SRM and four by PRM, respectively. Peptides were spiked into a background of Escherichia coli lysate and the majority of peptides were quantifiable down to 500 amol absolute on column by both methods. Peptide quantification in CBDB1 lysate resulted in the detection of 15 peptides using SRM and 14 peptides with the PRM assay. Resulting quantification of five dehalogenases revealed copy numbers of <10 to 115 protein molecules per cell indicating clear differences in abundance of RdhA proteins during growth on hexachlorobenzene. Our results indicated that both methods show comparable sensitivity and that the combination of the mass spectrometry assays resulted in higher peptide coverage and thus more reliable protein quantification.

A method combining SPITC and 18O labeling for simultaneous protein identification and relative quantification

The relative quantification and identification of proteins by matrix‐assisted laser desorption ionization time‐of‐flight MS is very important in /MS is very important in protein research and is usually conducted separately. Chemical N‐terminal derivatization with 4‐sulphophenyl isothiocyanate facilitates de novo sequencing analysis and accurate protein identification, while ¹⁸O labeling is simple, specific and widely applicable among the isotopic labeling methods used for relative quantification. In the present study, a method combining 4‐sulphophenyl isothiocyanate derivatization with ¹⁸O isotopic labeling was established to identify and quantify proteins simultaneously in one experiment. Reaction conditions were first optimized using a standard peptide (fibrin peptide) and tryptic peptides from the model protein (bovine serum albumin). Under the optimized conditions, these two independent labeling steps show good compatibility, and the linear relativity of quantification within the ten times dynamic range was stable as revealed by correlation coefficient analysis (R² value = 0.998); moreover, precursor peaks in MS/MS spectrum could provide accurate quantitative information, which is usually acquired from MS spectrum, enabling protein identification and quantification in a single MS/MS spectrum. Next, this method was applied to native peptides isolated from spider venoms. As expected, the de novo sequencing results of each peptide matched with the known sequence precisely, and the measured quantitative ratio of each peptide corresponded well with the theoretical ratio. Finally, complex protein mixtures of spider venoms from male and female species with unknown genome information were analyzed. Differentially expressed proteins were successfully identified, and their quantitative information was also accessed. Taken together, this protein identification and quantification method is simple, reliable and efficient, which has a good potential in the exploration of peptides/proteins from species with unknown genome. Copyright © 2014 John Wiley & Sons, Ltd.     

Quantitative Bulk and Trace Element X-Ray Mapping Using Multiple Detectors

X-ray mapping using energy dispersive spectroscopy or wavelength dispersive spectroscopy is a very popular characterisation tool for determining the elemental distribution in materials. Furthermore, quantitative X-ray mapping has become a very powerful technique enabling reliable quantitative results that can be an order of magnitude better than traditional analysis. Quantitative X-ray mapping is also far superior to regions of interest X-ray maps where low levels of an element or elemental overlaps are present. The one major drawback with X-ray mapping is the time required to obtain a high resolution X-ray map with good statistics at low levels of concentration. The use of multi-detectors, and just developed dual turret detectors for X-ray mapping, allows improvement in performance at low levels without compromising quantification quality and precision of traces, even in the presence of overlaps. However, for quantitative X-ray mapping to work properly, the characteristics of each detector must be accurately determined so that the final quantification of the individual detectors can be summed. To accomplish this effectively, the full spectrum at each pixel for each energy dispersive detector should be saved. As a final check for consistency between detectors, a technique was developed that involves assigning a different red-green-blue colour for each detector for the same element. By doing this, when we combine the three maps of the same element, we should obtain a grey scale map that indicates total correlation between the three detectors at the most critical final stage of quantification. To reduce contrast noise and further improve the quality of quantitative X-ray mapping images, a filter referred to as a “speckle filter” has been developed that allows the eye to see a more correct elemental concentration relationship.     

Detection and quantification of proteins and cells by use of elemental mass spectrometry: progress and challenges

Much progress has been made in identification of the proteins in proteomes, and quantification of these proteins has attracted much interest. In addition to popular tandem mass spectrometric methods based on soft ionization, inductively coupled plasma mass spectrometry (ICPMS), a typical example of mass spectrometry based on hard ionization, usually used for analysis of elements, has unique advantages in absolute quantification of proteins by determination of an element with a definite stoichiometry in a protein or attached to the protein. In this Trends article, we briefly describe state-of-the-art ICPMS-based methods for quantification of proteins, emphasizing protein-labeling and element-tagging strategies developed on the basis of chemically selective reactions and/or biospecific interactions. Recent progress from protein to cell quantification by use of ICPMS is also discussed, and the possibilities and challenges of ICPMS-based protein quantification for universal, selective, or targeted quantification of proteins and cells in a biological sample are also discussed critically. We believe ICPMS-based protein quantification will become ever more important in targeted quantitative proteomics and bioanalysis in the near future.

PCDD, PCDF, AND DL-PCB analysis in food: performance evaluation of the high-resolution gas chromatography/low-resolution tandem mass spectrometry technique using consensus-based samples

Due to safety concerns regarding dietary exposure to POPs, regulatory bodies are issuing detailed guidelines for testing for polychlorodibenzodioxins (PCDDs) and polychlorodibenzofurans (PCDFs) ('dioxins') and dioxin‐like (DL)‐PCBs in foods of animal origin. Determination of the aforesaid chemicals at regulatory levels requires highly selective and sensitive testing techniques. The new generation of low‐resolution mass spectrometers (triple quadrupoles) allows very low levels of quantification to be reached (in the order of tens of femtograms), thus suggesting a potential for their application in food and feed analysis. The performance of the low‐resolution tandem mass spectrometry (LRMS/MS) approach with triple quadrupoles was assessed on a qualified set of food samples from proficiency tests (PTs) and defense analysis. Accuracy was tested comparing the results with data from high‐resolution mass spectrometry (HRMS) and with consensus values from PTs. The cumulative TEQ results were characterized by deviations not exceeding 15% of PCDD + PCDF, DL‐PCB, and PCDD + PCDF + DL‐PCB (TEQ_TOT) reference consensus values (sample TEQ_TOT range, 2.29–25.1 pgWHO‐TEQ₉₇/g fat). Congener analytical variabilities did not influence significantly the WHO‐TEQ₉₇ outcome of the corresponding sample. This preliminary performance evaluation highlights the potential of LRMS/MS as a routine technique for quantitative analysis of PCDDs, PCDFs, and DL‐PCBs in food. Copyright © 2011 John Wiley & Sons, Ltd.     

Standard loading controls are not reliable for Western blot quantification across brain development or in pathological conditions

A frequently utilized method of data quantification in Western blot analysis is comparison of the protein of interest with a house keeping gene or control protein. Commonly used proteins include β‐actin, glyceraldehyde 3 phosphate dehydrogenase (GAPDH), and α‐tubulin. Various reliability issues have been raised when using this technique for data analysis—particularly when investigating protein expression changes during development and in disease states. In this study, we have demonstrated that β‐actin, GAPDH, and α‐tubulin are not appropriate controls in the study of development and hypoxic‐ischemic induced damage in the piglet brain. We have also shown that using an in‐house pooled standard, loaded on all blots is a reliable method for controlling interassay variability and data normalization in protein expression analysis.     

New technique for generating high concentrations of gaseous OH radicals in relative rate measurements

We have developed a technique for generating high concentrations of gaseous OH radicals in a reaction chamber. The technique, which involves the UV photolysis of O₃ in the presence of water vapor, was used in combination with the relative rate method to obtain rate constants for reactions of OH radicals with selected species. A key improvement of the technique is that an O₃/O₂ (3%) gas mixture is continuously introduced into the reaction chamber, during the UV irradiation period. An important feature is that a high concentration of OH radicals [(0.53–1.2) × 10¹¹ radicals cm^?3] can be produced during the irradiation in continuous, steady‐state experiment. Using the new technique in conjunction with the relative rate method, we obtained the rate constant for the reaction of CHF₃ (HFC‐23) with OH radicals, k₁. We obtained k₁(298 K) = (3.32 ± 0.20) × 10^?16 and determined the temperature dependence of k₁ to be (0.48 ± 0.13) × 10^?12 exp[?(2180 ± 100)/T] cm³ molecule^?1 s^?1 at 253–328 K using CHF₂CF₃ (HFC‐125) and CHF₂Cl (HCFC‐22) as reference compounds in CHF₃–reference–H₂O gas mixtures. The value of k₁ obtained in this study is in agreement with previous measurements of k₁. This result confirms that our technique for generating OH radicals is suitable for obtaining OH radical reaction rate constants of ～10^?16 cm³ molecule^?1 s^?1, provided the rate constants do not depend on pressure. In addition, it also needed to examine whether the reactions of sample and reference compound with O₃ interfere the measurement when selecting this technique. © 2003 Wiley Periodicals, Inc. Int J Chem Kinet 35: 317–325, 2003     

Optimization and application of microwave-assisted acid hydrolysis for rapid quantification of protein oxidation markers using LC-MS

Simple and efficient microwave-assisted acid hydrolysis (MAAH) of proteins was used for rapid quantification of α-aminoadipic semialdehyde (AAS) and γ-glutamic semialdehyde (GGS) as major protein oxidation markers. The precursor amino acid residues corresponding to AAS and GGS in oxidized proteins were derivatized by reductive amination with sodium cyanoborohydride (NaCNBH₃) and p-aminobenzoic acid (ABA) followed by MAAH to generate the marker derivatives AAS-ABA and GGS-ABA. The quantification was performed using electrospray ionization liquid chromatography-mass spectrometry (ESI LC-MS). The important parameters for hydrolysis were optimized, which include the temperature, the reaction time, the acid concentration and volume as well as the microwave power. Compared to the conventional acid hydrolysis of 18-24 h using 6-12 M HCl at 110 °C applied commonly in the literature and also in this work, MAAH of proteins can be completed as fast as in only 2-10 min and, additionally, with a 3-5 times higher yield of the final derivatization products. Furthermore, a better agreement between the ratio of the detected derivatization products and the theoretical yields from the studied protein has also been achieved, which indicates that MAAH may serve as a more reliable method of acid hydrolysis for this purpose than that with conventional thermal heating. The MAAH method is demonstrated to be a time-saving, reproducible and efficient technique for studying AAS and GGS as protein oxidation markers using LC-MS.     

The effect of low pH on the glycitein-BSA conjugate interaction with specific antiserum: competitive inhibition study using surface plasmon resonance technique

Competitive inhibition serological assay for detection of the phytoestrogen glycitein (Glyc) was developed using surface plasmon resonance (SPR) technique with protein conjugates and polyclonal antibodies initially designed for the enzyme-linked immunosorbent assays (ELISA). The efficiency of the approach to the quantification of the soy isoflavone glycitein in water was investigated using the competitive reaction of analyte (free Glyc)and immobilized Glyc-BSA-conjugate with polyclonal antibodies. It was shown that the efficiency to detect Glyc drastically depends on the pH level of the probe solution. With the decrease in pH from 7.4 to 4.0, (i) the affinity of the specific reaction increases and (ii) the level of unspecific sorption becomes saturated. Non-specific adsorption to a SPR sensor surface obscures the specific component and shaded specific response at higher pH (6.0-7.4) when used serum for the quantification of specific analytes. The standard curves obtained in acidic solutions (pH 4-5) indicate that the linear part of the dependence completely covers the range between detection limit (0.1 μg/ml) and Glyc solubility in water (0.9 μg/ml). The difference in SPR- and ELISA-based analytical protocols as well as the requirements for increasing the efficiency in quantitative SPR analysis using purified antibodies is discussed.     

Influence of measuring conditions on the quantification of spectroscopic signals in TA-FTIR-MS systems

Simultaneous thermal analysis (TA) and evolved gas analysis by mass spectrometry (MS) and/or Fourier transform infrared spectroscopy (FTIR) is a powerful hyphenated technique combining direct measurement of mass loss and sensitive spectroscopic analysis. In the present study the influence of several experimental parameters which may affect the quantification of FTIR signals have been studied using a combined TA-FTIR-MS system. Parameters studied include: sample mass (1-400 mg), carrier gas flow rate (25-200 mL min^-1), resolution of the FTIR spectrometer (1-32 cm^-1), and location of injection of the calibrating gas. MS analysis, which was not significantly affected by the experimental conditions, was used as a reference for assessing the accuracy of quantification by FTIR. The quantification of the spectroscopic signals was verified by the decomposition (NaHCO₃) or dehydration (CuSO₄·5H₂O) of compounds with well-known stoichiometry. The systematic study of the parametric sensitivity revealed that spectral resolution and carrier gas flow rate, which affect the acquisition time in the IR-cell, are key parameters that must be adjusted carefully for reliable quantification. The dependence of the reliability of quantification on these parameters is illustrated and conditions leading to proper quantification are discussed. As an example, for a standard spectral resolution of 4 cm^-1 and a FTIR gas cell volume of 8.7 mL, the carrier gas flow must be lower than 100 mL min^-1 for warranting accurate results (relative deviation <2%). The concentration range of analyzed species is limited but can be extended by proper selection of the wavenumber regions for molecules giving strong IR signals.     

cyc-DEP: Cyclic immunofluorescence profiling of particles collected using dielectrophoresis

Cancer is a highly heterogenous disease that requires precise detection tools and active surveillance methods. Liquid biopsy assays provide an agnostic way to follow the complex trajectory of cancer, providing better patient stratification tools for optimized treatment. Here, we present the development of a low-volume liquid biopsy assay called cyc-DEP (cyclic immunofluorescent imaging on dielectrophoretic chip) to profile biomarkers collected on a dielectrophoretic microfluidic chip platform. To enable on-chip cyclic imaging, we optimized a fluorophore quenching method and sequential rounds of on-chip staining with fluorescently conjugated primary antibodies. cyc-DEP allows for the quantification of a multiplex array of proteins using 25 µl of a patient plasma sample. We utilized nanoparticles from a prostate adenocarcinoma (LNCaP) cell line and a panel of six target proteins to develop our proof-of-concept technique. We then used cyc-DEP to quantify blood plasma levels of target proteins from healthy individuals, low-grade and high-grade prostate cancer patients (n = 3 each) in order to demonstrate that our platform is suitable for liquid biopsy analysis in its present form. To ensure accurate quantification of signal intensities and comparisons between different samples, we incorporated a signal intensity normalization method (fluorescent beads) and a custom signal intensity quantification algorithm that account for the distribution of signal across hundreds of collection regions on each chip. Our technique enabled a threefold improvement in multiplicity for detecting proteins associated with fluid samples, opening doors for early detection, and active surveillance through quantification of a multiplex array of biomarkers from low-volume liquid biopsies.     

PSAQ™ standards for accurate MS–based quantification of proteins: from the concept to biomedical applications

Absolute protein quantification, i.e. determining protein concentrations in biological samples, is essential to our understanding of biological and physiopathological phenomena. Protein quantification methods based on the use of antibodies are very effective and widely used. However, over the last ten years, absolute protein quantification by mass spectrometry has attracted considerable interest, particularly for the study of systems biology and as part of biomarker development. This interest is mainly linked to the high multiplexing capacity of MS analysis, and to the availability of stable‐isotope‐labelled standards for quantification. This article describes the details of how to produce, control the quality and use a specific type of standard: Protein Standard Absolute Quantification (PSAQ?) standards. These standards are whole isotopically labelled proteins, analogues of the proteins to be assayed. PSAQ standards can be added early during sample treatment, thus they can correct for protein losses during sample prefractionation and for incomplete sample digestion. Because of this, quantification of target proteins is very accurate and precise using these standards. To illustrate the advantages of the PSAQ method, and to contribute to the increase in its use, selected applications in the biomedical field are detailed here. Copyright © 2012 John Wiley & Sons, Ltd.     

The use of tryptic marker-peptides for the quantitative analysis of cystatin C

The use of marker-peptides, measured by LC-MS/MS, is investigated for the quantitative analysis of proteins. To that end, cystatin C is chosen as a model protein. It not only functions as a proof of concept protein but the growing interest in cystatin C as a new marker of kidney failure provides a practical application at the same time. The use of trypsin-based proteolysis, to obtain so-called marker-peptides, simplifies the quantification of a protein to the quantification of a single or a number of peptides. Reproducibility of the trypsin proteolysis procedure is vital and has been optimised. A number of the marker-peptides obtained are selected for LC-MS(/MS) analysis. They are completely separated by high-pressure LC allowing maximum selectivity and mass spectrometric multiple reaction monitoring sensitivity. By doing so, linear calibration curves can be obtained for cystatin C over two orders of magnitude. Experiments have been performed on a triple quadrupole mass spectrometer by single ion monitoring (maximum sensitivity) as well as by multiple reaction monitoring (maximum specificity).     

Degradation of misfolded proteins in neurodegenerative diseases: therapeutic targets and strategies

Mammalian cells remove misfolded proteins using various proteolytic systems, including the ubiquitin (Ub)-proteasome system (UPS), chaperone mediated autophagy (CMA) and macroautophagy. The majority of misfolded proteins are degraded by the UPS, in which Ub-conjugated substrates are deubiquitinated, unfolded and cleaved into small peptides when passing through the narrow chamber of the proteasome. The substrates that expose a specific degradation signal, the KFERQ sequence motif, can be delivered to and degraded in lysosomes via the CMA. Aggregation-prone substrates resistant to both the UPS and the CMA can be degraded by macroautophagy, in which cargoes are segregated into autophagosomes before degradation by lysosomal hydrolases. Although most misfolded and aggregated proteins in the human proteome can be degraded by cellular protein quality control, some native and mutant proteins prone to aggregation into β-sheet-enriched oligomers are resistant to all known proteolytic pathways and can thus grow into inclusion bodies or extracellular plaques. The accumulation of protease-resistant misfolded and aggregated proteins is a common mechanism underlying protein misfolding disorders, including neurodegenerative diseases such as Huntington''s disease (HD), Alzheimer''s disease (AD), Parkinson''s disease (PD), prion diseases and Amyotrophic Lateral Sclerosis (ALS). In this review, we provide an overview of the proteolytic pathways in neurons, with an emphasis on the UPS, CMA and macroautophagy, and discuss the role of protein quality control in the degradation of pathogenic proteins in neurodegenerative diseases. Additionally, we examine existing putative therapeutic strategies to efficiently remove cytotoxic proteins from degenerating neurons.