Detection of the tuberculosis biomarker mannose-capped lipoarabinomannan in human serum: Impact of sample pretreatment with perchloric acid

The development of an accurate and rapid diagnostic test for tuberculosis (TB) to use at point of need is vital to efforts aimed at reducing the global burden from this disease. This paper builds on our previous studies of mannose-capped lipoarabinomannan (ManLAM) as a serum biomarker for active TB infection by means of a heterogeneous immunoassay. That work found that complexation with components in serum (e.g., proteins) sterically hindered the capture and/or labeling of ManLAM in an immunoassay at levels <10 ng mL-1, compromising the clinical utility of this biomarker for detection of active TB infection. We also showed that the acidification of ManLAM-containing serum samples with perchloric acid improved the detectability of ManLAM by 250× by complex disruption when compared to measurements of untreated serum. The present study examined what effects the PCA treatment of serum samples may have on the recovery and structural integrity of ManLAM, owing to its potential susceptibility to acid hydrolysis. Recovery was assessed with an enzyme-linked immunosorbent assay (ELISA). The possible impact of acid hydrolysis on the ManLAM structure was investigated by gas chromatography-mass spectrometry and carbohydrate chemical degradation methods. The ELISA study indicated that while the signal strength for ManLAM in the serum spike-in experiments was significantly stronger after PCA pretreatment when compared to untreated human serum, it was only ∼20% of the ManLAM measured in physiological buffer. This loss in detectability was shown by structural analysis to arise mainly from the acid-induced degradation of the arabinan domains of ManLAM that are targeted by antibodies used for antigen capture and/or tagging. The implications of these findings in terms of the detection of this important biomarker for TB are also discussed.

Proteomic analysis of pancreatic secretory trypsin inhibitor/tumor-associated trypsin inhibitor from urine of patients with pancreatitis or prostate cancer

The development of proteomic methods, especially mass spectrometry, has brought new possibilities to tumor marker research. Pancreatic secretory trypsin inhibitor (PSTI), a common known biomarker for various malignancies, occurs on genetic variants that we are able to detect at the protein level with proteomic techniques using immunoaffinity capture prior to liquid chromatography-mass spectrometry (LC-MS). We also show that PSTI can be detected in urine from cancer patients using a two-step peptide enrichment technique and LC-MS. These results show that tumor-associated peptides can be detected in urine by proteomic techniques.

Solution-state nuclear magnetic resonance spectroscopy and protein folding

A protein undergoes a variety of structural changes during its folding and misfolding and a knowledge of its behaviour is key to understanding the molecular details of these events. Solution-state NMR spectroscopy is unique in that it can provide both structural and dynamical information at both high-resolution and at a residue-specific level, and is particularly useful in the study of dynamic systems. In this chapter, we describe NMR strategies and how they are applied in the study of protein folding and misfolding.

Metabolites secreted by human atherothrombotic aneurysm

One of the possibilities to study abdominal aortic aneurysm (AAA) biomarkers is to use -aneurysm biopsies of dilated arteries or intraluminal thrombus (ILT) for explant cultures. Those metabolites secreted into the culture medium are concentrated in comparison to plasma and free from other interferences that can appear in it, allowing an easier harvesting. Liquid chromatography coupled to quadrupole time-of-flight mass spectrometry detector (LC-QTOF-MS) with an electrospray (ESI) interface has a broad applicability to detect metabolites of all classes with high sensitivity and mass accuracy. Therefore, an LC-QTOF-MS-based metabolomics approach was chosen to select and identify metabolites that could be useful as diagnostic/prognostic markers of AAA. This chapter describes the methodology for the differential analysis of AAA metabolites in secretomes. It gives experimental details on basic steps such as sample preparation, protein precipitation, and analysis of the samples by LC-MS. A description for quality control of the methodology, raw data processing, as well as selection and identification of differentiating -metabolites are also presented in this chapter.

(1)H NMR Metabolomic Footprinting Analysis for the In Vitro Screening of Potential Chemopreventive Agents

Metabolomics is the quantification and analysis of the concentration profiles of low-molecular-weight compounds present in biological samples. In particular metabolic footprinting analysis, based on the monitoring of metabolites consumed from and secreted into the growth medium, is a valuable tool for the study of pharmacological and toxicological effects of drugs. Mass spectrometry and nuclear magnetic resonance (NMR) are the two main complementary techniques used in this field. Although less sensitive, NMR gives a direct fingerprint of the system, and the spectra obtained contain metabolic information that can be distilled by chemometric techniques. In this chapter, we present how metabolomic footprinting can be used to assess in vitro a potential chemopreventive molecule as metformin.

Autophagosomal proteome analysis by protein correlation profiling-SILAC

Autophagy is one of the two major degradation pathways within eukaryotic cells. Nevertheless, little is known about the protein composition of autophagosomes, the vesicles shuttling proteins to lysosomes for degradation. Protein correlation profiling in combination with stable isotope labeling by amino acids in cell culture is a stringent method to investigate the dynamics of the autophagosomal proteome. It enables the discrimination between autophagosomal and co-purifying proteins identifying organellar candidate proteins for further investigation.

GdClean: removal of Gadolinium contamination in mass cytometry data

MOTIVATION

Mass cytometry (Cytometry by Time-Of-Flight, CyTOF) is a single-cell technology that is able to quantify multiplex biomarker expressions and is commonly used in basic life science and translational research. However, the widely used Gadolinium (Gd)-based contrast agents (GBCAs) in magnetic resonance imaging (MRI) scanning in clinical practice can lead to signal contamination on the Gd channels in the CyTOF analysis. This Gd contamination greatly affects the characterization of the real signal from Gd-isotope-conjugated antibodies, severely impairing the CyTOF data quality and ruining downstream single-cell data interpretation.

RESULTS

We first in-depth characterized the signals of Gd isotopes from a control sample that was not stained with Gd-labeled antibodies but was contaminated by Gd isotopes from GBCAs, and revealed the collinear intensity relationship across Gd contamination signals. We also found that the intensity ratios of detected Gd contamination signals to the reference Gd signal were highly correlated with the natural abundance ratios of corresponding Gd isotopes. We then developed a computational method named by GdClean to remove the Gd contamination signal at the single-cell level in the CyTOF data. We further demonstrated that the GdClean effectively cleaned up the Gd contamination signal while preserving the real Gd-labeled antibodies signal in Gd channels. All of these shed lights on the promising applications of the GdClean method in preprocessing CyTOF datasets for revealing the true single-cell information.

AVAILABILITY AND IMPLEMENTATION

The R package GdClean is available on GitHub at https://github.com/JunweiLiu0208/GdClean.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Influence of sample preservation on endotoxin measurement in water

Appropriate preservation of a range of water types prior to analysis for endotoxin was investigated, including sample storage and addition of sodium thiosulphate. Biologically active endotoxin in water samples was assayed using a chromogenic Limulus Amoebocyte Lysate (LAL) assay. Statistical analysis of measured mean endotoxin levels obtained for samples with and without sodium thiosulphate showed no significant difference in results. There was a 44% mean decline in the concentration of detectable endotoxin in water samples stored at -80 degrees C for 4 weeks compared with samples stored at 4 degrees C and analysed within 24 hours. Freezing of water samples at -80 degrees C in pyrogen-free containers for 4 weeks or longer, then thawing may lead to considerable endotoxin loss; however the addition of sodium thiosulphate to water samples interferes minimally with the LAL assay. These results provide methodological information that can be used to assist researchers in future water endotoxin monitoring studies. The validation and standardisation of water sample preservation protocols are necessary, given the likely increase in the quantification of endotoxin levels in a variety of water sources and the use of such results for health effect determinations.

Applying SILAC for the differential analysis of protein complexes

Pull-downs based on tag fusion proteins as well as immunoprecipitations (IP) are widely used methods to analyze protein interactions. Selectivity and specificity of both methods are compromised by nonspecific binding to the capture agent or carrier beads thereby generating false positives. Here, we provide a method combining stable isotope labeling of amino acids in cell culture (SILAC) with affinity purification, coupled to quantitative tandem mass spectrometry. It permits the analysis of protein interactions with high sensitivity, while being able to discriminate contaminants and nonspecific binders. Besides pruning out contaminants, high-resolution MS data combined with quantitative proteomics software allow the comparative analysis of protein interaction patterns of different protein variants, for example mutated versus normal protein variant or of regulatory changes in a given protein complex due to different states of activity.

Matrix-enhanced surface-assisted laser desorption/ionization mass spectrometry (ME-SALDI-MS) for mass spectrometry imaging of small molecules

Surface-assisted laser desorption/ionization mass spectrometry (SALDI-MS), a parallel technique to matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS), utilizes inorganic particles or porous surfaces to aid in the desorption/ionization of low-molecular-weight (MW) analytes. As a matrix-free and "soft" LDI approach, SALDI offers the benefit of reduced background noise in the low MW range, allowing for easier detection of biologically significant small MW species. Despite the inherent advantages of SALDI-MS, it has not reached comparable sensitivity levels to MALDI-MS. In relation to mass spectrometry imaging (MSI), intense efforts have been made in order to improve sensitivity and versatility of SALDI-MSI. We describe herein a detailed protocol that utilizes a hybrid LDI method, matrix-enhanced SALDI-MS (ME-SALDI MS), to detect and image low MW species in an imaging mode.

[Methods of microorganism immobilization for dynamic atomic-force studies (review)]

Atomic-force microscopy (AFM) is an efficient method for studying the surface ultrastructure and nanomechanical properties of biological objects (including microorganisms). A correctly selected method of microorganism immobilization (that provides a strong attachment of cells on the surface of a biologically inert substrate and the preservation of their native properties) is an important condition of AFM scanning in a liquid medium. Comparative characteristics of methods of microorganism immobilization (that are applied in dynamic AFM studies) are given in the review. Technologies of mechanical retention and chemical binding of cells to a substrate, as well as protein and immunospecific adsorption, are considered.

On-line desalting of crude oil in the source region of a Fourier transform ion cyclotron resonance mass spectrometer

The presence of dissolved metal ions in waters associated with crude oils has many negative implications for the transport, processing, and refining of petroleum. In addition, mass spectrometric analysis of sodium containing crude oil samples suffers from ionization suppression, unwanted adduct formation, and an increase in the complexity of data analysis. Here, we describe a method for the reduction/elimination of these adverse effects by modification of the source region gas-inlet system of a 12 T Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometer. Several acids were examined as part of this study, with the most suitable for on-line desalting found to have both high vapor pressure and low pK(a); 12.1 M HCl showed the strongest desalting effect for crude oil samples with a sodium removal index (SRI) of 88%-100% ± 7% for the NaOS compound class. In comparison, a SRI of only 38% ± 9% was observed for a H₂O/toluene solution-phase extraction of oil 1. These results clearly demonstrate the increased efficacy of pseudo-vapor phase desalting with the additional advantages that initial sample solution conditions are preserved and no sample preparation is required prior to analysis.

Mapping of phosphorylation sites by LC-MS/MS

Reversible protein phosphorylation ranks among the most important post-translational modifications that occurs in the cell. It is therefore highly relevant to elucidate the phosphorylation states of a given biological system, albeit challenging. Most notably the often low stoichiometry of phosphorylation is inherently incompatible with standard LC-MS analysis of a complex protein digest mixture, primarily due to the relative low dynamic range of current mass analyzers. Therefore a need for specific enrichment of phosphorylated peptides or proteins exists. Significant progress surrounding the biochemical analysis of reversible protein phosphorylation in the past years has led to the development of several new techniques to isolate or enrich phosphopeptides, particularly in large-scale analyses. This chapter deals with three such examples.

Native DIGE of fluorescent plant protein complexes

CyDye labeling and DIGE have not only been proven to work for soluble proteins but also at the level of whole membrane protein complexes. After complex solubilization and CyDye labeling, proteins can be separated by native PAGE which is often combined with SDS PAGE in a subsequent step. By this combination, sizes of complexes as well as their subunit composition can be compared after mixing samples from different physiological states. Plants interact specifically with light via protein-bound pigments. This can be used in combination with CyDye technology to extend the "classical" approach in plant research. As an example, chlorophyll can be excited for fluorescent scanning at the Cy5 excitation wavelength. This property can be used to identify pigment-binding plant complexes and complex subunits isolated from plastid membranes. In this protocol, we present a combination of the conventional CyDye labeling technique with 2D native/SDS PAGE and parallel scanning for CyDyes and fluorescence from endogenous bound chlorophyll for identification of pigment-binding complexes and complex subunits.

Sample Preparation of Secreted Mammalian Host Cell Proteins and Their Characterization by Two-Dimensional Electrophoresis and Western Blotting

The manufacturing and purification of therapeutic recombinant proteins expressed by cultivated mammalian cells into the cell culture medium leaves the potential for contamination by host cell proteins (HCPs). Validation and quality control testing of any therapeutic protein needs to include a test to show that HCP contamination is at a minimal level. The presence of residual mammalian HCPs during purification and in the final drug product is typically determined using enzyme linked immunosorbent assay (ELISA), which is regarded as the gold standard. The complexity and heterogeneity of HCPs, which include proteins with significant differences in molecular weight (MW), isoelectric point (pI) and hydrophobicity, poses a challenge to detection and quantitation. Two-dimensional gel electrophoresis (2-DE) is one of the most powerful technologies for studying complex protein profiles and is a valuable analytical method in biologics manufacturing. In the purification process, it is very important to know the nature and composition of HCPs, and this information can be used in a rational process design in order to minimize HCPs from the product. Additionally, 2-DE in combination with western blotting can support ELISA development and quality control for the comprehensive immunochemical detection of HCPs by estimating the recognition capacity of the polyclonal serum used in those assays. Here, we present a standardized 2-DE western blotting protocol which takes into account the latest developments in sample preparation of HCPs, protein electrophoresis, protein transfer, immunostaining, and imaging.

Bead-Based Multiplex Immunoassays: Procedures, Tips, and Tricks

Multiplex immunoassays enable the measurement of multiple proteins in a small volume of sample in a single well, enhancing discovery and profiling of multiple biomarkers when compared to singleplex immunoassays. In order to ensure optimal results are generated, it is important to know what critical actions and assay steps can adversely affect results. This chapter covers best practices for sample collection and storage, to important considerations during the assay run, and ways to ensure optimal data generation and efficient data analysis. When these practices are applied, the potential to generate actionable and quality results accelerates the research and discovery process.

Quantification of protein kinase activities by LC-MS

Measuring the enzymatic activity of protein kinases in cell and tissue extracts represents a difficult task owing to the complex regulation and dynamics of such enzymes. Here we describe a sensitive and specific approach for the quantitative analysis of PI3K-dependent protein kinase activity based on the mass spectrometry measurement of reaction products. The principle of this method can be applied to develop other kinase assays and thus should contribute to the understanding of processes controlled by protein kinases. Because of the enhanced sensitivity of this technique, it may be applied to the multiplex measurement of pathway activities when sample amounts are limiting.

A Prototype Ice-Melting Probe for Collecting Biological Samples from Cryogenic Ice at Low Pressure

In the Solar System, the surface of an icy moon is composed of irregular ice formations at cryogenic temperatures (<200 K), with an oxidized surface layer and a tenuous atmosphere at very low pressure (<10^-6 atm). A lander mission, whose aim is to collect and analyze biological samples from the surface ice, must contain a device that collects samples without refreezing liquid and without sublimation of ice. In addition, if the samples are biological in nature, then precautions must be taken to ensure the samples do not overheat or mix with the oxidized layer. To achieve these conditions, the collector must maintain temperatures close to maintenance or growth conditions of the organism (<293 K), and it must separate or neutralize the oxidized layer and be physically gentle. Here, we describe a device that addresses these requirements and is compatible with low atmospheric pressure while using no pumps. The device contains a heated conical probe with a central orifice, which is forced into surface ice and directs the meltwater upward into a reservoir. The force on the probe is proportional to the height of meltwater (pressure) obtained in the system and allows regulation of the melt rate and temperature of the sample. The device can collect 5-50 mL of meltwater from the surface of an ice block at 233-208 K with an environmental pressure of less than 10^-2 atm while maintaining a sample temperature between 273 and 293 K. These conditions maintain most biological samples in a pristine state and maintain the integrity of most organisms' structure and function. Key Words: Europa-Icy moon-Microbe-Eukaryote-Spacecraft. Astrobiology 17, 709-720.

Increasing the coverage of the N-terminome with LysN amino terminal enrichment (LATE)

The field of N-terminomics has been advancing with the development of novel methods that provide a comprehensive and unbiased view of the N-terminome. Negative selection N-terminomics enables the identification of free and naturally modified protein N-termini. Here, we present a streamlined protocol that combines two negative selection N-terminomics methods, LATE and HYTANE, to increase N-terminome coverage by 1.5-fold compared to using a single methodology. Our protocol includes sample preparation and data analysis of both methods and can be applied to studying the N-terminome of diverse samples. The suggested approach enables researchers to achieve a more detailed and accurate understanding of the N-terminome.

HPLC analysis for the clinical-biochemical diagnosis of inborn errors of metabolism of purines and pyrimidines

The determination of purines and pyrimidines in biofluids is useful for the clinical-biochemical characterization of acute and chronic pathological states that induce transient or permanent alterations of metabolism. In particular, the diagnosis of several inborn errors of metabolism (IEMs) is accomplished by the analysis of circulating and excreted purines and pyrimidines. It is certainly advantageous to simultaneously determine the full purine and pyrimidine profile, as well as to quantify other compounds of relevance (e.g., organic acids, amino acids, sugars) in various metabolic hereditary diseases, in order to screen for a large number of IEMs using a reliable and sensitive analytical method characterized by mild to moderate costs. Toward this end, we have developed an ion-pairing HPLC method with diode array detection for the synchronous separation of several purines and pyrimidines. This method also allows the quantification of additional compounds such as N-acetylated amino acids and dicarboxylic acids, the concentrations of which are profoundly altered in different IEMs. The application of the method in the analysis of biological samples from patients with suspected purine and pyrimidine disorders is presented to illustrate its applicability for the clinical-biochemical diagnosis of IEM.

High-performance lectin affinity chromatography

Lectin high-performance liquid chromatography techniques have contributed to the growing interest in glycoproteomics. Affinity chromatography is a very effective method to separate and purify trace amount of biological substances. In this chapter, we describe a basic procedure for separation of glycoproteins using commercially available lectin-HPLC columns. As an example, α-fetoprotein, known as a biomarker of liver cancer, can be separated at the level of their glyco-isomers by using a Lens culinaris agglutinin (LCA) column.

Spectral reproducibility and quantification of peptides in MALDI of samples prepared by micro-spotting

Previously, we reported that MALDI spectra of peptides became reproducible when temperature was kept constant. Linear calibration curves derived from such spectral data could be used for quantification. Homogeneity of samples was one of the requirements. Among the three popular matrices used in peptide MALDI [i.e., α-cyano-4-hydroxycinnamic acid (CHCA), 2,5-dihydroxybenzoic acid (DHB), and sinapinic acid (SA)], homogeneous samples could be prepared by conventional means only for CHCA. In this work, we showed that sample preparation by micro-spotting improved the homogeneity for all three cases.

Quantitation of Parathyroid Hormone in Serum or Plasma by Liquid Chromatography-Tandem Mass Spectrometry

Parathyroid hormone (PTH), an 84 amino acid peptide hormone, is an important regulator of calcium homeostasis. Quantitation of PTH in serum is useful for the diagnosis of primary hyperparathyroidism, hypoparathyroidism, and for monitoring osteodystrophy in patients with renal failure. The biological activity of PTH arises from binding of PTH (N terminus) to its target receptor (D'Amour et al., Kidney Int 68: 998-1007, 2005). Several C-terminal and N-terminal fragments circulate in normal subjects. Recent studies have demonstrated that accurate quantitation of PTH fragments may be of clinical value. In this chapter a mass spectrometry based method for quantitation of PTH(1-84) is described. This method involves immunoaffinity capture of PTH followed by trypsinization and quantitation of PTH-specific tryptic peptides by liquid chromatography-tandem mass spectrometry (LC-MS/MS). The N-terminal tryptic peptide, PTH(1-13) as surrogate of 1-84 PTH, is used for quantitation.

[Multi-residue determination of 15 phenylurea herbicides in vegetables using solid phase extraction and online post-column ultraviolet decomposition-fluorescent derivatiztion-high performance liquid chromatography]

A high performance liquid chromatographic (HPLC) method for multi-residue analysis of phenylurea herbicides in vegetables was developed. The sample was extracted with acetonitrile and cleaned up by solid phase extraction (SPE) using a Florisil cartridge. The target compounds were separated on a C18 column (250 mm x 4.6 mm, 5 microm) and detected by a fluorescence detector (FLD) after online post-column ultraviolet (UV) decomposition with a UV lamp with 254 nm wavelength and fluorescent derivatization. The elution gradient, sample pretreatment and conditions of decomposition and derivatization were also studied. The elution gradient was as follows: the mobile phase started with 70% A (water) and 30% B (acetonitrile), which was increased linearly to 50% B in 15 min, and increased 90% B in the next 15 min and held for 2 min, then returned to the initial conditions in 0.5 min. The column was equilibrated for 10 min at 25 degrees C. The flow rate was 0.75 mL/min for HPLC and 0.2 mL/min for derivatization reagent. In the linear ranges of concentrations, the correlation coefficients were between 0.998 6 and 1.0000. The 15 herbicides were measured in fortified onion, spinach and cucumber samples at three spiked levels, the average recoveries (n=3) were in the range of 75.3%-121.6% with relative standard deviations of 0.4%-11.6%. The limits of detection (LOD) were 0.005-0.05 mg/kg. The method is simple, sensitive, selective and qualified for phenylurea herbicide multi-residue analysis.