Sum of peak intensities outperforms peak area integration in iTRAQ protein expression measurement by LC-MS/MS using a TripleTOF 5600+ platform

The study of acidic/basic nature of metallothioneins and other metal-binding biomolecules in the soluble hepatic fraction of the northern pike (Esox lucius)

Since fish metalloproteins are still not thoroughly characterized, the aim of this study was to investigate the acidic/basic nature of biomolecules involved in the sequestration of twelve selected metals in the soluble hepatic fraction of an important aquatic bioindicator organism, namely the fish species northern pike (Esox lucius). For this purpose, the hyphenated system HPLC-ICP-MS was applied, with chromatographic separation based on anion/cation-exchange principle at physiological pH (7.4). The results indicated predominant acidic nature of metal-binding peptides/proteins in the studied hepatic fraction. More than 90 % of Ag, Cd, Co, Cu, Fe, Mo, and Pb were eluted with negatively charged biomolecules, and >70 % of Bi, Mn, and Zn. Thallium was revealed to bind equally to negatively and positively charged biomolecules, and Cs predominantly to positively charged ones. The majority of acidic (negatively charged) metalloproteins/peptides were coeluted within the elution time range of applied standard proteins, having pIs clustered around 4-6. Furthermore, binding of several metals (Ag, Cd, Cu, Zn) to two MT-isoforms was assumed, with Cd and Zn preferentially bound to MT1 and Ag to MT2, and Cu evenly distributed between the two. The results presented here are the first of their kind for the important bioindicator species, the northern pike, as well as one of the rare comprehensive studies on the acidic/basic nature of metal-binding biomolecules in fish, which can contribute significantly to a better understanding of the behaviour and fate of metals in the fish organism, specifically in liver as main metabolic and detoxification organ.

Signal-noise metrics for RNA binding protein identification reveal broad spectrum protein-RNA interaction frequencies and dynamics

Recent efforts towards the comprehensive identification of RNA-bound proteomes have revealed a large, surprisingly diverse family of candidate RNA-binding proteins (RBPs). Quantitative metrics for characterization and validation of protein-RNA interactions and their dynamic interactions have, however, proven analytically challenging and prone to error. Here we report a method termed LEAP-RBP (Liquid-Emulsion-Assisted-Purification of RNA-Bound Protein) for the selective, quantitative recovery of UV-crosslinked RNA-protein complexes. By virtue of its high specificity and yield, LEAP-RBP distinguishes RNA-bound and RNA-free protein levels and reveals common sources of experimental noise in RNA-centric RBP enrichment methods. We introduce strategies for accurate RBP identification and signal-based metrics for quantifying protein-RNA complex enrichment, relative RNA occupancy, and method specificity. In this work, the utility of our approach is validated by comprehensive identification of RBPs whose association with mRNA is modulated in response to global mRNA translation state changes and through in-depth benchmark comparisons with current methodologies.

CIL-ExPMRM: An Ultrasensitive Chemical Isotope Labeling Assisted Pseudo-MRM Platform to Accelerate Exposomic Suspect Screening

Exposome is the future of next-generation environmental health to establish the association between environmental exposure and diseases. However, due to low concentrations of exposure chemicals, exposome has been hampered by lacking an effective analytical platform to characterize its composition. In this study, by combining the benefit of chemical isotope labeling and pseudo-multiple reaction monitoring (CIL-pseudo-MRM), we have developed one highly sensitive and high-throughput platform (CIL-ExPMRM) by isotope labeling urinary exposure biomarkers. Dansyl chloride (DnsCl), N-methylphenylethylamine (MPEA), and their isotope-labeled forms were used to derivatize polar hydroxyl and carboxyl compounds, respectively. We have programmed a series of scripts to optimize MRM transition parameters, curate the MRM database (>70,000 compounds), predict accurate retention time (RT), and automize dynamic MRMs. This was followed by an automated MRM peak assignment, peak alignment, and statistical analysis. A computational pipeline was eventually incorporated into a user-friendly website interface, named CIL-ExPMRM (http://www.exposomemrm.com/). The performance of this platform has been validated with a relatively low false positive rate (10.7%) across instrumental platforms. CIL-ExPMRM has systematically overcome key bottlenecks of exposome studies to some extent and outperforms previous methods due to its independence of MS/MS availability, accurate RT prediction, and collision energy optimization, as well as the ultrasensitivity and automated robust intensity-based quantification. Overall, CIL-ExPMRM has great potential to advance the exposomic studies based on urinary biomarkers.

Subcellular Proteomic Analysis Reveals Dysregulation in Organization of Human A549 Cells Infected with Influenza Virus H7N9

Background:

H7N9 influenza virus poses a high risk to human beings and proteomic evaluations of these infections may help to better understand its pathogenic mechanisms in human systems. Objective: To find membrane proteins related to H7N9 infection.

Methods:

Here, we infected primary human alveolar adenocarcinoma epithelial cells (A549) cells with H7N9 (including wild and mutant strains) and then produced enriched cellular membrane isolations which were evaluated by western blot. The proteins in these cell membrane fractions were analyzed using the isobaric Tags for Relative and Absolute Quantitation (iTRAQ) proteome technologies.

Results:

Differentially expressed proteins (n = 32) were identified following liquid chromatography-tandem mass spectrometry, including 20 down-regulated proteins such as CD44 antigen, and CD151 antigen, and 12 up-regulated proteins such as tight junction protein ZO-1, and prostaglandin reductase 1. Gene Ontology database searching revealed that 20 out of the 32 differentially expressed proteins were localized to the plasma membrane. These proteins were primarily associated with cellular component organization (n = 20), and enriched in the Reactome pathway of extracellular matrix organization (n = 4).

Conclusion:

These findings indicate that H7N9 may dysregulate cellular organization via specific alterations to the protein profile of the plasma membrane.

Serum Metabolic Profiling Analysis of Chronic Gastritis and Gastric Cancer by Untargeted Metabolomics

Purpose

Gastric cancer is a common tumor of the digestive system. Identification of potential molecules associated with gastric cancer progression and validation of potential biomarkers for gastric cancer diagnosis are very important. Thus, the aim of our study was to determine the serum metabolic characteristics of the serum of patients with chronic gastritis (CG) or gastric cancer (GC) and validate candidate biomarkers for disease diagnosis.

Experimental Design

A total of 123 human serum samples from patients with CG or GC were collected for untargeted metabolomic analysis via UHPLC-Q-TOF/MS to determine characteristics of the serum. Principal component analysis (PCA), partial least squares discriminant analysis (PLS-DA), and heat map were used for multivariate analysis. In addition, commercial databases were used to identify the pathways of metabolites. Differential metabolites were identified based on a heat map with a t-test threshold (p < 0.05), fold-change threshold (FC > 1.5 or FC < 2/3) and variable importance in the projection (VIP >1). Then, differential metabolites were analyzed by receiver operating characteristic (ROC) curve to determine candidate biomarkers. All samples were analyzed for fasting lipid profiles.

Results

Analysis of serum metabolomic profiles indicated that most of the altered metabolic pathways in the three groups were associated with lipid metabolism (p < 0.05) and lipids and lipid-like molecules were the predominating metabolites within the top 100 differential metabolites (p < 0.05, FC > 1.5 or FC < 2/3, and VIP >1). Moreover, differential metabolites, including hexadecasphinganine, linoleamide, and N-Hydroxy arachidonoyl amine had high diagnostic performance according to PLS-DA. In addition, fasting lipid profile analysis showed the serum levels of total cholesterol (TC), high-density lipoprotein cholesterol (HDL-C) and apolipoprotein A1 (Apo-A1) were decreased concomitant to the progression of the progression of the disease compared with those in the control group (p < 0.05).

Conclusions

Thus, this study demonstrated that lipid metabolism may influence the development of CG to GC. Hexadecasphinganine, linoleamide, and N-Hydroxy arachidonoyl amine were selected as candidate diagnostic markers for CG and GC.

Multi-Evaluating Strategy for Siji-kangbingdu Mixture: Chemical Profiling, Fingerprint Characterization, and Quantitative Analysis

Siji-kangbingdu mixture is an anti-inflammatory, anti-bacterial, and anti-viral herbal mixture which is frequently used by doctors to treat upper respiratory infections. It's important to establish an efficient and economical quality-control method to ensure the quality consistency and efficacy stability of Siji-kangbingdu mixture. In this study, an integrated multi-evaluation method was established, sequentially involving UPLC-TripleTOF-MS analysis, UPLC fingerprint analysis, and the quantitative analysis of multi-components using the single-marker (QAMS) method. With one chromatographic condition, a total of 71 compounds were identified by MS and MS/MS information, with a mass error of less than 5 ppm; 49 peaks detected in 254 nm were selected to establish the fingerprint similarity model, and 7 chemical compounds were simultaneously determined, namely, chlorogenic acid, liquiritin, rutin, isochlorogenic acid A, forsythin, forsythoside A, and glycyrrhizic acid, with forsythoside A as the reference standard. There was no significant difference in the content of the seven compounds between the QAMS method and the external standard method (ESM). The established multi-evaluation method will largely promote the quality control and standardization process of Siji-kangbingdu mixture. It also provides a reference workflow for the overall evaluation of TCM patent medicines, from chemical profiling to fingerprint and quantitative analysis.