"Zoom-ln"--A targeted database search for identification of glycation modifications analyzed by untargeted tandem mass spectrometry

Characterisation of hyper tolerant Bacillus firmus L-148 for arsenic oxidation

Groundwater arsenic pollution causes millions of deaths worldwide. Long term natural and anthropogenic activities have increased arsenic levels in groundwater causing higher threats of arsenic exposure. Arsenic hyper-tolerant Firmicute Bacillus firmus L-148 was isolated from arsenic limiting Lonar lake soil, which tolerated more than 3 M arsenic and could oxidize 75 mM arsenite [As(III)] in 14 days. It oxidized As(III) in presence of heavy metals and had unusual pH optima at 9.2. B. firmus L-148 was studied at the biochemical, protein, genomic and transcript level for understanding its arsenic oxidizing machinery. The proteomic and transcript analysis exhibited the presence of ars and aio operon and supported the inducible nature of ars operon. Robust, hyper-tolerant, fast As(III) oxidizing, least nutrient requiring and multi-metal resistance qualities of the strain were used in microcosm studies for bioremediation. Artificial groundwater mimicking microcosm with 75 mM As(III) was developed. Modulation of carbon source, iron and multi metals affected growth and As(III) oxidation rate. The As(III) oxidation was recorded to be 77% in 15 days in presence of sodium acetate and Fe ions. This microcosm study can be explored for bioremediation of arsenic contaminated water and followed by precipitation using other methods.

Characterization of residue-specific glutathionylation of CSF proteins in multiple sclerosis - A MS-based approach

Reduction of a disulfide linkage between cysteine residues in proteins, a standard step in the preanalytical preparation of samples in conventional proteomics approach, presents a challenge to characterize S-glutathionylation of proteins. S-glutathionylation of proteins has been reported in medical conditions associated with high oxidative stress. In the present study, we attempted to characterize glutathionylation of CSF proteins in patients with multiple sclerosis which is associated with high oxidative stress. Using the nano-LC/ESI-MS platform, we adopted a modified proteomics approach and a targeted database search to investigate glutathionylation at the residue level of CSF proteins. Compared to patients with Intracranial hypertension, the following CSF proteins: Extracellular Superoxide dismutase (ECSOD) at Cys195, α1-antitrypsin (A1AT) at Cys232, Phospholipid transfer protein (PLTP) at Cys318, Alpha-2-HS-glycoprotein at Cys340, Ectonucleotide pyrophosphate (ENPP-2) at Cys773, Gelsolin at Cys304, Interleukin-18 (IL-18) at Cys38 and Ig heavy chain V III region POM at Cys22 were found to be glutathionylated in patients with multiple sclerosis during a relapse. ECSOD, A1AT, and PLTP were observed to be glutathionylated at the functionally important cysteine residues. In conclusion, in the present study using a modified proteomics approach we have identified and characterized glutathionylation of CSF proteins in patients with multiple sclerosis.

Targeted Quantification of the Glycated Peptides of Human Serum Albumin

Glycated human serum albumin (HSA) serves as an important marker for monitoring the glycemic status. Developing methods for unambiguous identification and quantification of glycated peptides of HSA using high-throughput technologies such as mass spectrometry has a great clinical significance. The following protocol describes the construction of reference spectral libraries for Amadori-modified lysine (AML), N(ε)-(carboxymethyl) lysine (CML)-, and N(ε)-(carboxyethyl)lysine (CEL)-modified peptides of synthetically modified HSA using high-resolution mass spectrometers. The protocol also describes work flows, for unambiguous identification and quantification of glycated modified peptides of HSA in clinical plasma using standard spectral libraries by various mass spectrometry approaches such as parallel reaction monitoring (PRM), sequential window acquisition of all theoretical fragment ion spectra (SWATH), and MS^E.

Identification and characterization of glycation adducts on osteocalcin

Osteocalcin is an important extracellular matrix bone protein that contributes to the structural properties of bone through its interactions with hydroxyapatite mineral and with collagen I. This role may be affected by glycation, a labile modification the levels of which has been shown to correlate with bone fragility. Glycation starts with the spontaneous addition of a sugar onto a free amine group on a protein, forming an Amadori product, and then proceeds through several environment-dependent stages resulting in the formation of an advanced glycation end product. Here, we induce the first step of this modification on synthetic osteocalcin, and then use multiple mass spectrometry fragmentation techniques to determine the location of this modification. Collision-induced dissociation resulted in spectra dominated by neutral loss, and was unable to identify Amadori products. Electron-transfer dissociation showed that the Amadori product formed solely on osteocalcin's N-terminus. This suggests that the glycation of osteocalcin is unlikely to interfere with osteocalcin's interaction with hydroxyapatite. Instead, glycation may interfere with its interaction with collagen I or another bone protein, osteopontin. Potentially, the levels of glycated osteocalcin fragments released from bone during bone resorption could be used to assess bone quality, should the N-terminal fragments be targeted.

Proteomics in India: the clinical aspect

Proteomics has emerged as a highly promising bioanalytical technique in various aspects of applied biological research. In Indian academia, proteomics research has grown remarkably over the last decade. It is being extensively used for both basic as well as translation research in the areas of infectious and immune disorders, reproductive disorders, cardiovascular diseases, diabetes, eye disorders, human cancers and hematological disorders. Recently, some seminal works on clinical proteomics have been reported from several laboratories across India. This review aims to shed light on the increasing use of proteomics in India in a variety of biological conditions. It also highlights that India has the expertise and infrastructure needed for pursuing proteomics research in the country and to participate in global initiatives. Research in clinical proteomics is gradually picking up pace in India and its future seems very bright.

Proteomic Insight Reveals Elevated Levels of Albumin in Circulating Immune Complexes in Diabetic Plasma

A Hyperglycemic condition in diabetes promotes formation of advanced glycation end products, which are known to elicit immune response and form complexes with immunoglobulins called circulating immune complexes. To investigate the involvement of advanced glycation end product (AGE)-modified proteins in the elicitation of an immune response, circulating immune complexes were isolated and proteins associated were identified and characterized. Label-free-based mass spectrometric analysis of circulating immune complexes in clinical plasma of prediabetic, newly diagnosed diabetes, and diabetic microalbuminurea revealed elevated levels of serum albumin in the circulating immune complexes, which were also observed to be AGE modified. Further, to examine the role of glycation, circulating immune complexeswere analyzed in the streptozotocin-induced diabetic mice treated with or without aminoguanidine, a prototype glycation inhibitor. Mass spectrometric analysis of circulating immune complexes showed elevated levels of serum albumin in plasma from diabetic mice over that of control animals. Aminoguanidine-treated diabetic mice displayed decreased AGE modification of plasma albumin, accompanied by a reduced level of albumin in the circulating immune complexes. In addition, elevated levels of proinflammatory cytokines such as IL-1b, IL-2, and TNF-alpha were observed in diabetes, which were reduced with aminoguanidine treatment, suggesting the involvement of glycation in the immune response.

Targeted quantification of N-1-(carboxymethyl) valine and N-1-(carboxyethyl) valine peptides of β-hemoglobin for better diagnostics in diabetes

Background

N-1-(Deoxyfructosyl) valine (DFV) β-hemoglobin (β-Hb), commonly referred as HbA1c, is widely used diagnostic marker in diabetes, believed to provide glycemic status of preceding 90–120 days. However, the turnover of hemoglobin is about 120 days, the DFV-β-Hb, an early and reversible glycation product eventually may undergo irreversible advanced glycation modifications such as carboxymethylation or carboxyethylation. Hence quantification of N-1-(carboxymethyl) valine (CMV) and N-1-(carboxyethyl) valine (CEV) peptides of β-Hb would be useful in assessing actual glycemic status.

Results

Fragment ion library for synthetically glycated peptides of hemoglobin was generated by using high resolution–accurate mass spectrometry (HR/AM). Using parallel reaction monitoring, deoxyfructosylated, carboxymethylated and carboxyethylated peptides of hemoglobin were quantified in clinical samples from healthy control, pre-diabetes, diabetes and poorly controlled diabetes. For the first time, we report N-1-β-valine undergoes carboxyethylation and mass spectrometric quantification of CMV and CEV peptides of β-hemoglobin. Carboxymethylation was found to be the most abundant modification of N-1-β-valine. Both CMV-β-Hb and CEV-β-Hb peptides showed better correlation with severity of diabetes in terms of fasting glucose, postprandial glucose and microalbuminuria.

Conclusions

This study reports carboxymethylation as a predominant modification of N-1-β-valine of Hb, and quantification of CMV-β-Hb and CEV-β-Hb could be useful parameter for assessing the severity of diabetes.

Electronic supplementary material

The online version of this article (doi:10.1186/s12014-016-9108-y) contains supplementary material, which is available to authorized users.

Potential Dual Role of Eugenol in Inhibiting Advanced Glycation End Products in Diabetes: Proteomic and Mechanistic Insights

Medicinally important genus Ocimum harbors a vast pool of chemically diverse metabolites. Current study aims at identifying anti-diabetic candidate compounds from Ocimum species. Major metabolites in O. kilimandscharicum, O. tenuiflorum, O. gratissimum were purified, characterized and evaluated for anti-glycation activity. In vitro inhibition of advanced glycation end products (AGEs) by eugenol was found to be highest. Preliminary biophysical analysis and blind docking studies to understand eugenol-albumin interaction indicated eugenol to possess strong binding affinity for surface exposed lysines. However, binding of eugenol to bovine serum albumin (BSA) did not result in significant change in secondary structure of protein. In vivo diabetic mice model studies with eugenol showed reduction in blood glucose levels by 38% likely due to inhibition of α-glucosidase while insulin and glycated hemoglobin levels remain unchanged. Western blotting using anti-AGE antibody and mass spectrometry detected notably fewer AGE modified peptides upon eugenol treatment both in vivo and in vitro. Histopathological examination revealed comparatively lesser lesions in eugenol-treated mice. Thus, we propose eugenol has dual mode of action in combating diabetes; it lowers blood glucose by inhibiting α-glucosidase and prevents AGE formation by binding to ε-amine group on lysine, protecting it from glycation, offering potential use in diabetic management.

Molecules with O-acetyl group protect protein glycation by acetylating lysine residues

In-vitro and in-vivo chemical proteomic studies of acetyl group molecules revealed that, O-acetyl molecules competitively inhibits the protein glycation by acetylating the lysine residues.

Development of Diagnostic Fragment Ion Library for Glycated Peptides of Human Serum Albumin: Targeted Quantification in Prediabetic, Diabetic, and Microalbuminuria Plasma by Parallel Reaction Monitoring, SWATH, and MSE

Human serum albumin is one of the most abundant plasma proteins that readily undergoes glycation, thus glycated albumin has been suggested as an additional marker for monitoring glycemic status. Hitherto, only Amadori-modified peptides of albumin were quantified. In this study, we report the construction of fragment ion library for Amadori-modified lysine (AML), N(ε)-(carboxymethyl)lysine (CML)-, and N(ε)-(carboxyethyl)lysine (CEL)-modified peptides of the corresponding synthetically modified albumin using high resolution accurate mass spectrometry (HR/AM). The glycated peptides were manually inspected and validated for their modification. Further, the fragment ion library was used for quantification of glycated peptides of albumin in the context of diabetes. Targeted Sequential Window Acquisition of all THeoretical Mass Spectra (SWATH) analysis in pooled plasma samples of control, prediabetes, diabetes, and microalbuminuria, has led to identification and quantification of 13 glycated peptides comprised of four AML, seven CML, and two CEL modifications, representing nine lysine sites of albumin. Five lysine sites namely K549, K438, K490, K88, and K375, were observed to be highly sensitive for glycation modification as their respective m/z showed maximum fold change and had both AML and CML modifications. Thus, peptides involving these lysine sites could be potential novel markers to assess the degree of glycation in diabetes.

Investigation of antiglycation activity of isoprenaline

Isoprenaline reduces the advanced glycation end products and may be suitable candidate for the treatment of glycation associated diseases.

N-(3-Aminoalkyl)proline derivatives with potent antigycation activity

The synthesis and anti-glycation properties of non-naturalN-aminoalkylproline derivatives are reported. They also exhibit good anti-oxidant properties and may be useful in the treatment of complications that arise as a result of increased glycation.