Label-free peptide profiling of Orbitrap™ full mass spectra

Using clinical practice guidelines to manage dengue: a qualitative study in a Malaysian hospital

Background

Malaysia has rising dengue incidence. World Health Organization clinical practice guidelines for managing dengue have been adapted by the Ministry of Health in Malaysia, with evidence of good awareness by clinicians. However, dengue mortality has not reduced. This study aimed to explore the challenges of dengue management for Medical Officers, with a particular focus on use of clinical practice guidelines.

Methods

Qualitative study using six focus groups and 14 semi-structured interviews with doctors responsible for dengue management at a large tertiary hospital in Malaysia.

Results

Dengue was recognised as difficult to diagnose and manage. Wide awareness and use of both WHO and Ministry of Health guidelines was reported, but several limitations noted in their coverage of particular patient groups. However, the phrase ‘guidelines’ also referred to local algorithms for fluid management, which were less clinically evidence-based. Where Medical Officers were well trained in the appropriate use of evidence-based guidelines, barriers to use included: the potential for ‘following the algorithm’ to undermine junior clinicians’ claims to clinical expertise; inability to recognise the pattern of clinical progress; and lack of clinical experience. Other reported barriers to improved case management were resource constraints, poor referral practices, and insufficient awareness of the need for timely help seeking.

Conclusions

Awareness of clinical practice guidelines is a necessary, but not sufficient, condition for optimal dengue management. In high prevalence settings, all clinical staff would benefit from regular dengue management training which should include diagnosis, practice in monitoring disease progression and the use of clinical practice guidelines in a range of clinical contexts.

Electronic supplementary material

The online version of this article (10.1186/s12879-019-3680-5) contains supplementary material, which is available to authorized users.

SBP2 plays an important role in the virulence changes of different artificial mutants of Streptococcus suis

Comparative proteomics analysis using the proteomes of the two mutants with different virulence found a promising putative virulence factor, SBP2, which can bind fibronectin and laminin.

Custom 4-Plex DiLeu Isobaric Labels Enable Relative Quantification of Urinary Proteins in Men with Lower Urinary Tract Symptoms (LUTS)

The relative quantification of proteins using liquid chromatography mass spectrometry (LC-MS) has allowed researchers to compile lists of potential disease markers. These complex quantitative workflows often include isobaric labeling of enzymatically-produced peptides to analyze their relative abundances across multiple samples in a single LC-MS run. Recent efforts by our lab have provided scientists with cost-effective alternatives to expensive commercial labels. Although the quantitative performance of these dimethyl leucine (DiLeu) labels has been reported using known ratios of complex protein and peptide standards, their potential in large-scale proteomics studies using a clinically relevant system has never been investigated. Our work rectifies this oversight by implementing 4-plex DiLeu to quantify proteins in the urine of aging human males who suffer from lower urinary tract symptoms (LUTS). Protein abundances in 25 LUTS and 15 control patients were compared, revealing that of the 836 proteins quantified, 50 were found to be differentially expressed (>20% change) and statistically significant (p-value <0.05). Gene ontology (GO) analysis of the differentiated proteins showed that many were involved in inflammatory responses and implicated in fibrosis. While confirmation of individual protein abundance changes would be required to verify protein expression, this study represents the first report using the custom isobaric label, 4-plex DiLeu, to quantify protein abundances in a clinically relevant system.

Lipopolysaccharide challenge significantly influences lipid metabolism and proteome of white adipose tissue in growing pigs

Background

White adipose tissue is recognized as a highly active organ, which is closely related to a large number of physiological and metabolic processes besides storing triglycerides. However, little is known regarding the response of adipose tissue to acute inflammation. Therefore, in this study we employed growing pigs to investigate the changes of lipid metabolism and proteome in white adipose tissue after lipopolysaccharide (LPS) stimulation as a model for bacterial infection.

Methods

The expression of lipid metabolism and inflammation related genes was determined by quantitative real-time polymerase chain reaction. Label-free proteomics analysis was used to investigate changes of the protein profile in white adipose tissue and western blot was used to verify changes of selected adipokines.

Results

The results indicated that LPS significantly increased the expression of toll-like receptor (TLR) 2/4 pathway-related genes and pro-inflammatory factors. Lipid metabolism related genes, including acetyl-CoA carboxylase 1 (ACACA), fatty acid synthase (FASN), stearoyl-CoA desaturase (SCD), uncoupling protein 2 (UCP2), and 11 β-hydroxysteroid dehydrogenase type 1 (11β-HSD1), were down-regulated and the lipolytic enzyme activity was decreased after LPS injection. Proteome analysis revealed 47 distinct proteins with > 2-fold changes. The down-regulation of two proteins (cAMP-dependent protein kinase type II-alpha regulatory subunit and β-tubulin) has been verified by western blot analysis. In addition, the abundance of two adipokines (adiponectin and zinc-α2-glycoprotein) was significantly increased after LPS injection.

Conclusion

In conclusion, LPS challenge can cause acute inflammation in white adipose tissue. Concurrently, lipid metabolism was significantly suppressed and the abundance of several proteins changed in white adipose tissue. The results provide new clues to understand the adipose dysfunction during inflammation.

Electronic supplementary material

The online version of this article (doi:10.1186/s12944-015-0067-5) contains supplementary material, which is available to authorized users.

Candidate biomarker discovery for angiogenesis by automatic integration of Orbitrap MS1 spectral- and X!Tandem MS2 sequencing information

Candidate protein biomarker discovery by full automatic integration of Orbitrap full MS1 spectral peptide profiling and X!Tandem MS2 peptide sequencing is investigated by analyzing mass spectra from brain tumor samples using Peptrix. Potential protein candidate biomarkers found for angiogenesis are compared with those previously reported in the literature and obtained from previous Fourier transform ion cyclotron resonance (FT-ICR) peptide profiling. Lower mass accuracy of peptide masses measured by Orbitrap compared to those measured by FT-ICR is compensated by the larger number of detected masses separated by liquid chromatography (LC), which can be directly linked to protein identifications. The number of peptide sequences divided by the number of unique sequences is 9248/6911 ≈ 1.3. Peptide sequences appear 1.3 times redundant per up-regulated protein on average in the peptide profile matrix, and do not seem always up-regulated due to tailing in LC retention time (40%), modifications (40%) and mass determination errors (20%). Significantly up-regulated proteins found by integration of X!Tandem are described in the literature as tumor markers and some are linked to angiogenesis. New potential biomarkers are found, but need to be validated independently. Eventually more proteins could be found by actively involving MS2 sequence information in the creation of the MS1 peptide profile matrix.