Determination of 2'-Fucosyllactose and Lacto-N-neotetraose in Infant Formula.

Human milk oligosaccharides (HMO) are the third most abundant solid component of human milk. It is likely that they are responsible for at least some of the benefits experienced by breast-fed infants. Until recently HMO were absent from infant formula, but 2'-fucosyllactose (2'-FL) and lacto-N-neoteraose (LNnT) have recently become available as ingredients. The development of formula containing these HMO and the quality control of such formula require suitable methods for the accurate determination of the HMO. We developed two different approaches for analysis of 2'-FL and LNnT in formula; high performance anion exchange chromatography with pulsed amperometric detection (HPAEC-PAD) and hydrophilic interaction liquid chromatography with fluorescence detection (HILIC-FLD). In lab trials using blank formula spiked with the two oligosaccharides, both approaches worked well with recoveries of 94⁻111% (HPAEC-PAD) and 94⁻104% (HILIC-FLD) and RSD (iR) of 2.1⁻7.9% (HPAEC-PAD) and 2.0⁻7.4% (HILIC-FLD). However, when applied to products produced in a pilot plant, the HPAEC-PAD approach sometimes delivered results below those expected from the addition rate of the ingredients. We hypothesize that the oligosaccharides interact with the formula matrix during the production process and, during sample preparation for HPAEC-PAD those interactions have not been broken. The conditions required for labeling the HMO for detection by the FLD apparently disrupt those interactions, and result in improved recoveries. It is likely that both analytical approaches are appropriate if a suitable extraction process is used to recover the HMO.

Protein networks in induced sputum from smokers and COPD patients.

RATIONALE: Subtypes of cigarette smoke-induced disease affect different lung structures and may have distinct pathophysiological mechanisms. OBJECTIVE: To determine if proteomic classification of the cellular and vascular origins of sputum proteins can characterize these mechanisms and phenotypes. SUBJECTS AND METHODS: Individual sputum specimens from lifelong nonsmokers (n=7) and smokers with normal lung function (n=13), mucous hypersecretion with normal lung function (n=11), obstructed airflow without emphysema (n=15), and obstruction plus emphysema (n=10) were assessed with mass spectrometry. Data reduction, logarithmic transformation of spectral counts, and Cytoscape network-interaction analysis were performed. The original 203 proteins were reduced to the most informative 50. Sources were secretory dimeric IgA, submucosal gland serous and mucous cells, goblet and other epithelial cells, and vascular permeability. RESULTS: Epithelial proteins discriminated nonsmokers from smokers. Mucin 5AC was elevated in healthy smokers and chronic bronchitis, suggesting a continuum with the severity of hypersecretion determined by mechanisms of goblet-cell hyperplasia. Obstructed airflow was correlated with glandular proteins and lower levels of Ig joining chain compared to other groups. Emphysema subjects' sputum was unique, with high plasma proteins and components of neutrophil extracellular traps, such as histones and defensins. In contrast, defensins were correlated with epithelial proteins in all other groups. Protein-network interactions were unique to each group. CONCLUSION: The proteomes were interpreted as complex "biosignatures" that suggest distinct pathophysiological mechanisms for mucin 5AC hypersecretion, airflow obstruction, and inflammatory emphysema phenotypes. Proteomic phenotyping may improve genotyping studies by selecting more homogeneous study groups. Each phenotype may require its own mechanistically based diagnostic, risk-assessment, drug- and other treatment algorithms.

Advances in proteomic techniques for biomarker discovery in COPD.

Chronic obstructive pulmonary disease (COPD) is a disorder characterized by chronic inflammation of the lung with airflow obstruction and progressive deterioration of pulmonary function. The need to discover and validate biomarkers as prognostic tools of development and progression of the disease has received further support with the advent of proteomic techniques. Liquid chromatography-mass spectrometry (LC/MS) and gel electrophoresis-mass spectrometry (2-DE/MS) have been applied to investigate the proteome of a number of lung-origin samples, including sputum, bronchoalveolar lavage fluid, exhaled-breath condensate, cells and biopsies from COPD patients. In particular, 2-DE and MS are the main proteomic approaches with 2-DE presenting the major approach for quantitative proteomics. The molecules identified as potential biomarkers of COPD may represent a preliminary step for better comprehension of the mechanisms involved in the onset/progression of the disease.

Qualitative and quantitative profiling of the bovine milk fat globule membrane proteome.

Milk is a biological fluid of unique quality and complexity. It has co-evolved with mammals and mankind to nourish offspring and contains macro- and micronutrients for growth and development of the newborn. The milk fat globule membrane (MFGM) represents an important milk fraction, which is rich in bioactive proteins. In order to better understand functionality of milk fractions and, thereby, enhance the benefits of milk products, detailed qualitative and quantitative protein knowledge of fractions such as MFGM is required. We report the qualitative and quantitative profiling of two MFGM-enriched milk fractions, a whey protein concentrate (WPC) and a buttermilk protein concentrate (BMP), as derived from three different analytical workflows. First, an LC-MS/MS-based shotgun approach revealed 244 protein identities in WPC and 133 in BMP, respectively, and provided an extensive characterisation of the protein content in those two fractions. Second, label-free profiling resulted in rapid and efficient semi-quantitative comparison and yielded valuable protein fingerprints. Third, absolute quantification of selected MFGM proteins was achieved by stable isotope dilution (SID)-MS, in combination with multiple reaction monitoring (MRM) detection. In summary, we provide new information on composition, quantity and possible health benefits of two MFGM-enriched milk fractions highly valuable for future nutritional applications.

Deciphering the proteomic profile of rice (Oryza sativa) bran: a pilot study.

The exact knowledge of the qualitative and quantitative protein components of rice bran is an essential aspect to be considered for a better understanding of the functional properties of this resource. Aim of the present investigation was to extract the largest number of rice bran proteins and to obtain their qualitative characterization. For this purpose, three different extraction protocols have been applied either on full-fat or on defatted rice bran. Likewise, to identify the highest number of proteins, MS data collected from 1-DE, 2-DE and gel-free procedures have been combined. These approaches allowed to unambiguously identify 43 proteins that were classified as signalling/regulation proteins (30%), proteins with enzymatic activity (30%), storage proteins (30%), transfer (5%) and structural (5%) proteins. The fact that all extraction and identification procedures have been performed in triplicate with an excellent reproducibility provides a rationale for considering the platform of proteins shown in this study as the potential proteome profile of rice bran. It also represents a source of information to evaluate better the qualities of rice bran as food resource.

OMICS-rooted studies of milk proteins, oligosaccharides and lipids.

Milk has co-evolved with mammals and mankind to nourish their offspring and is a biological fluid of unique complexity and richness. It contains all necessary nutrients for the growth and development of the newborn. Structure and function of biomolecules in milk such as the macronutrients (glyco-) proteins, lipids, and oligosaccharides are central topics in nutritional research. Omics disciplines such as proteomics, glycomics, glycoproteomics, and lipidomics enable comprehensive analysis of these biomolecule components in food science and industry. Mass spectrometry has largely expanded our knowledge on these milk bioactives as it enables identification, quantification and characterization of milk proteins, carbohydrates, and lipids. In this article, we describe the biological importance of milk macronutrients and review the application of proteomics, glycomics, glycoproteomics, and lipidomics to the analysis of milk. Proteomics is a central platform among the Omics tools that have more recently been adapted and applied to nutrition and health research in order to deliver biomarkers for health and comfort as well as to discover beneficial food bioactives.

Proteomics-based diagnosis of chronic obstructive pulmonary disease: the hunt for new markers.

Chronic obstructive pulmonary disease (COPD) is an inflammatory disease characterized by the progressive deterioration of pulmonary function and irreversible airway obstruction. Investigations of the molecular pathogenesis of COPD have not yet provided complete answers to the mechanisms that determine the onset and progression of this illness. Therefore, therapeutic choices are limited and new strategies are needed to prevent, manage and treat this disorder. In particular, the application of complementary approaches, including gel- and liquid chromatography mass spectrometry-based proteomic techniques on sputum and/or bronchoalveolar lavage may provide a better understanding of the proteome differentially expressed by COPD patients in the course of the disease. The identification of appropriate and reliable biomarkers is, thus, an essential step for the diagnostics and treatment of these patients.

Preparation of nasal secretions for proteome analysis.

The determination of protein patterns in nasal secretions of healthy subjects can help in the early diagnosis of diseases such as acute sinusitis. The comparison of nasal lavage fluid collected from subjects with acute sinusitis before and after pharmacological treatment gives information about the drug effects on glandular secretions. Nasal secretions were stimulated with 1x NS (0.9% Normal Saline) and 24x NS in healthy subjects and in sinusitis subjects before and after pharmacological treatment. The nasal lavage fluid (NLF) proteins are precipitated with a solution of "acid-ethanol." Using this solution, the high molecular weight proteins precipitate and separate from the low molecular weight proteins. The proteins are digested and the peptides are separated using a capillary liquid chromatographic system. Eluted peptides are analyzed on ESI-Q-TOF mass spectrometry instrument.

Protein expression in sputum of smokers and chronic obstructive pulmonary disease patients: a pilot study by CapLC-ESI-Q-TOF.

The current report describes the use of CapLC-ESI-Q/TOF-MS for investigating the proteome profiles of hypertonic saline-induced sputum samples from 56 smokers. The severity of their lung disease ranged from normal (healthy smokers) to chronic bronchitis, chronic obstructive pulmonary disease (COPD), and COPD with emphysema. This pilot study examined the hypothesis that there were distinct differences in protein expression profiles that were related to the phenotype and cigarette smoking illness severity. A total of 203 unique proteins were identified. These may represent the most highly expressed proteins in induced sputum. Our results provide evidence that different proteins are expressed, as the disease progresses from health to more advanced stages, and support our contention that a proteomic approach would be beneficial in discovering selective molecules linked to specific COPD stages.

Progress in the methodological strategies for the detection in real samples of desmosine and isodesmosine, two biological markers of elastin degradation.

Desmosines are crosslinking amino acids unique to mature elastin in humans. Owing to this unicity, they have been discussed as potentially attractive indicators of connective tissue disorders whose clinical manifestations are mostly the result of elastin degradation. This review covers advances in immunochemical, chromatographic, and electrophoretic procedures applied in the last 25 years to detect and quantitate these crosslinksin a variety of biological samples. Recent applications of CE with LIF detection (CE-LIF) for investigating the content of desmosines in different fluids will also be discussed.

The role of emerging techniques in the investigation of prolidase deficiency: from diagnosis to the development of a possible therapeutical approach.

The aim of the present article is to review the efforts performed in the past two decades by numerous research groups for the development of methods that allow a correct diagnosis of prolidase deficiency (PD), a rare autosomal recessive disorder and for the rationalization of a possible therapeutic intervention on these patients. In particular, the interest of the reader is focused on the application of capillary electrophoresis (i) for the detection of biological markers that reflect the pathological feature of the disease and (ii) for the determination of the efficiency of a carrier system in delivering prolidase inside cells in a possible therapy based on enzyme replacement.

A Chronic Fatigue Syndrome - related proteome in human cerebrospinal fluid.

BACKGROUND: Chronic Fatigue Syndrome (CFS), Persian Gulf War Illness (PGI), and fibromyalgia are overlapping symptom complexes without objective markers or known pathophysiology. Neurological dysfunction is common. We assessed cerebrospinal fluid to find proteins that were differentially expressed in this CFS-spectrum of illnesses compared to control subjects. METHODS: Cerebrospinal fluid specimens from 10 CFS, 10 PGI, and 10 control subjects (50 mul/subject) were pooled into one sample per group (cohort 1). Cohort 2 of 12 control and 9 CFS subjects had their fluids (200 mul/subject) assessed individually. After trypsin digestion, peptides were analyzed by capillary chromatography, quadrupole-time-of-flight mass spectrometry, peptide sequencing, bioinformatic protein identification, and statistical analysis. RESULTS: Pooled CFS and PGI samples shared 20 proteins that were not detectable in the pooled control sample (cohort 1 CFS-related proteome). Multilogistic regression analysis (GLM) of cohort 2 detected 10 proteins that were shared by CFS individuals and the cohort 1 CFS-related proteome, but were not detected in control samples. Detection of >or=1 of a select set of 5 CFS-related proteins predicted CFS status with 80% concordance (logistic model). The proteins were alpha-1-macroglobulin, amyloid precursor-like protein 1, keratin 16, orosomucoid 2 and pigment epithelium-derived factor. Overall, 62 of 115 proteins were newly described. CONCLUSION: This pilot study detected an identical set of central nervous system, innate immune and amyloidogenic proteins in cerebrospinal fluids from two independent cohorts of subjects with overlapping CFS, PGI and fibromyalgia. Although syndrome names and definitions were different, the proteome and presumed pathological mechanism(s) may be shared.

Identification of human nasal mucous proteins using proteomics.

The determination of possible biomarkers in nasal secretion of healthy subjects can have a role in early diagnosis of diseases such as rhinosinusitis. For this purpose, nasal lavage fluids (NLFs) from ten volunteers, collected before and after they had been submitted to nasal provocations, were investigated. Separation and analysis of proteins present in this complex matrix was performed using a capillary liquid chromatography-electrospray-quadrupole-time of flight mass spectrometry equipment. From among a total of 111 proteins found (89 known and two unknown proteins), 42 of which had never been previously described in this fluid, such as Deleted in Malignant Brain Tumors 1 isoform a precursors, and cytoskeletal proteins were identified with high statistical score. Three proteins of palate lung nasal epithelial clone (PLUNC) family: SPLUNC1, LPLUNC1, and LPLUNC2 were identified. Proteins involved in innate (27%) and acquired immunity (21%) systems were major components of NLF. Cellular (52% of all proteins identified) such as cytoskeletal (33%), functional (15%), and regulatory (4%) proteins, normally present in the nasal cavity, have also been identified. The proteomic approach presented here allowed us to identify the proteins involved in acquired and innate immune response in the nose against microbial infections and unclean inhaled air.

Human neuroglobin protein in cerebrospinal fluid.

BACKGROUND: Neuroglobin is a hexacoordinated member of the globin family of proteins. It is predominantly localized to various brain regions and retina where it may play a role in protection against ischemia and nitric oxide-induced neural injury. Cerebrospinal fluid was collected from 12 chronic regional or systemic pain and 5 control subjects. Proteins were precipitated by addition of 50% 0.2 N acetic acid, 50% ethanol, 0.02% sodium bisulfite. The pellet was extensively digested with trypsin. Peptides were separated by capillary liquid chromatography using a gradient from 95% water to 95% acetonitrile in 0.2% formic acid, and eluted through a nanoelectrospray ionization interface into a quadrapole - time-of-flight dual mass spectrometer (QToF2, Waters, Milford, MA). Peptides were sequenced (PepSeq, MassLynx v3.5) and proteins identified using MASCOT (R). RESULTS: Six different neuroglobin peptides were identified in various combinations in 3 of 9 female pain subjects, but none in male pain, or female or male control subjects. CONCLUSION: This is the first description of neuroglobin in cerebrospinal fluid. The mechanism(s) leading to its release in chronic pain states remain to be defined.

Micellar electrokinetic chromatographic and capillary zone electrophoretic methods for screening urinary biomarkers of human disorders: a critical review of the state-of-the-art.

Human urine plays a central role in clinical diagnostic being one of the most-frequently used body fluid for detection of biological markers. Samples from patients with different diseases display patterns of biomarkers that differ significantly from those obtained from healthy subjects. The availability of fast, reproducible, and easy-to-apply analytical techniques that would allow identification of a large number of these analytes is thus highly desiderable since they may provide detailed information about the progression of a pathological process. From among the variety of methods so far applied for the determination of urinary metabolites, capillary electrophoresis, both in the capillary zone electrophoresis (CZE) and micellar electrokinetic chromatography (MEKC) modes, represents a robust and reliable analytical tool widely used in this area. The aim of the present article is to focus the interest of the reader on recent applications of MEKC and CZE in the field of urinary biomarkers and to discuss advantages and/or limitations of each mode.

Urinary electrophoretic profiles from chronic fatigue syndrome and chronic fatigue syndrome/fibromyalgia patients: a pilot study for achieving their normalization.

Aim of our study was to determine if there were distinct, disease-related patterns of urinary analytes in chronic fatigue syndrome (CFS) and chronic fatigue syndrome/fibromyalgia (CFS/FM) compared to normal controls (NC). Urine was collected from these subjects for two consecutive 24 h periods and aliquots were submitted to micellar electrokinetic chromatography (MEKC). To compensate for the differences in peak migration times, these were normalized from the 35 min duration of run to a 100-point scale, and each peak was assigned its normalized time measure. Peak heights were also normalized by dividing the mAU by that of the internal standard (creatinine) and multiplying by 100. MEKC with normalization for peak height and migration time generated comparable results within each of the patient groups. CFS/FM and CFS had significant differences in peaks compared to NC that may be of significance as biomarkers of illnesses.

Proteomics: a primer for otologists.

OBJECTIVE: On July 9, 2003, the National Institutes of Health (NIH) released a new program announcement entitled "Proteomics in Auditory and Developmental Disease Processes." This initiative makes it clear that proteomic analysis in otology is a multi-year research priority for the NIH. The goal of this article is to describe the mechanics of modern proteomic techniques and review their applications in otology to date. DATA SOURCES: General articles from the proteomic literature were used to construct a review of modern proteomic techniques. For literature on proteomics in otology, MEDLINE and CRISP databases were searched by various topics in otology and cross-referenced with principle proteomic technologies. STUDY SELECTION: The criterion for selection was any study in otology that employs proteomic technology. CONCLUSIONS: Incredible progress has been made in proteomic technology. However, modern proteomic techniques are currently underutilized in otologic research. The NIH proteomics initiative referenced above, in combination with an understanding of the basic tools of modern proteomic science, should help motivate otologists to discover innovative ways to apply modern proteomic techniques to specific problems in otology.

Analysis of the sinusitis nasal lavage fluid proteome using capillary liquid chromatography interfaced to electrospray ionization-quadrupole time of flight- tandem mass spectrometry.

The nasal lavage fluids (NLFs) from four subjects with acute sinusitis were analyzed to investigate the amount of proteins expressed in this pathology at the beginning of the event (day 1) and after 6 days of treatment with antibiotics and a nasal steroid spray. The protein identification was performed with capillary liquid chromatography-electrospray-quadrupole time of flight-(LC-ESI-Q-TOF)-mass spectrometry. The samples collected on the first day contained high-abundant plasma proteins, such as albumin and immunoglobulins, glandular serous cell proteins (lysozyme, lactoferrin, and polymeric immunoglobulin receptor), epithelial keratins, and inflammatory cell proteins (myeloperoxidase, IL-16, and IL-17E). After six days of therapy, the complexity of the proteome was reduced to plasma proteins and lysozyme with no inflammatory markers. The presence of hemoglobin, however, suggested that significant squamous metaplasia with breaches in the epithelial barrier, or nasal steroid-related bleeding, had occurred. The proteomic approach presented here allowed us to identify, in the high complexity of acute sinusitis nasal secretions, the proteins that respond to a pharmacological treatment and that could be suitable as markers of this pathology.