scholarly journals Surface proteomics and label-free quantification of Leptospira interrogans serovar Pomona

2021 ◽  
Vol 15 (11) ◽  
pp. e0009983
Author(s):  
Teerasit Techawiwattanaboon ◽  
Praparat Thaibankluay ◽  
Chahya Kreangkaiwal ◽  
Suwitra Sathean-Anan-Kun ◽  
Prasong Khaenam ◽  
...  
Keyword(s):  
Outer Membrane Proteins ◽  
Proteinase K ◽  
Leptospira Interrogans ◽  
Label Free ◽  
Bacterial Host ◽  
Host Interactions ◽  
Leptospira Interrogans Serovar Pomona ◽  
Liquid Chromatography Tandem Mass ◽  
Abundance Profile ◽  
Free Quantification

Leptospirosis is a re-emerging zoonosis with a global distribution. Surface-exposed outer membrane proteins (SE-OMPs) are crucial for bacterial–host interactions. SE-OMPs locate and expose their epitope on cell surface where is easily accessed by host molecules. This study aimed to screen for surface-exposed proteins and their abundance profile of pathogenic Leptospira interrogans serovar Pomona. Two complementary approaches, surface biotinylation and surface proteolytic shaving, followed by liquid chromatography tandem-mass spectrometry (LC-MS/MS) were employed to identify SE-OMPs of intact leptospires. For quantitative comparison, in-depth label-free analysis of SE-OMPs obtained from each method was performed using MaxQuant. The total number of proteins identified was 1,001 and 238 for surface biotinylation and proteinase K shaving, respectively. Among these, 39 were previously known SE-OMPs and 68 were predicted to be localized on the leptospiral surface. Based on MaxQuant analysis for relative quantification, six known SE-OMPs including EF- Tu, LipL21, LipL41, LipL46, Loa22, and OmpL36, and one predicted SE-OMPs, LipL71 were found in the 20 most abundant proteins, in which LipL41 was the highest abundant SE-OMP. Moreover, uncharacterized LIC14011 protein (LIP3228 ortholog in serovar Pomona) was identified as a novel predicted surface βb-OMP. High-abundance leptospiral SE-OMPs identified in this study may play roles in virulence and infection and are potential targets for development of vaccine or diagnostic tests for leptospirosis.

scholarly journals Metabolomic and Proteomic Stratification of Equine Osteoarthritis

2020 ◽  
Author(s):  
James R Anderson ◽  
Marie M Phelan ◽  
Eva Caamaño-Gutiérrez ◽  
Peter D Clegg ◽  
Luis M Rubio-Martinez ◽  
...  
Keyword(s):  
Principal Component ◽  
Apolipoprotein A1 ◽  
Label Free ◽  
Thoroughbred Horses ◽  
Mixed Breed ◽  
Liquid Chromatography Tandem Mass ◽  
Metatarsophalangeal Joints ◽  
Equine Osteoarthritis ◽  
Free Quantification ◽  
Diagnostic Investigations

AbstractOsteoarthritis (OA) is characterised by loss of articular cartilage, synovial membrane dysfunction and subchondral sclerosis. Few studies have used a global approach to stratify equine synovial fluid (SF) molecular profiles according to OA severity. SF was collected from 58 metacarpophalangeal (MCP) and metatarsophalangeal joints of racing Thoroughbred horses (Hong Kong Jockey Club; HKJC) and 83 MCP joints of mixed breed horses from an abattoir and equine hospital (biobank). Joints were histologically and macroscopically assessed for OA severity. For proteomic analysis, native SF and SF loaded onto ProteoMiner™ equalisation columns, to deplete high abundant proteins, were analysed using liquid chromatography-tandem mass spectrometry (LC-MS/MS) and label-free quantification. Validation of selected differentially expressed proteins was undertaken using clinical SF collected during diagnostic investigations. Native SF metabolites were analysed using 1D 1H Nuclear Magnetic Resonance (NMR). 1,834 proteins and 40 metabolites were identified in equine SF. Afamin levels decreased with synovitis severity and four uncharacterised proteins decreased with OA severity. Gelsolin and lipoprotein binding protein decreased with OA severity and apolipoprotein A1 levels increased for mild and moderate OA. Within the biobank, glutamate levels decreased with OA severity and for the HKJC cohort, 2-aminobutyrate, alanine and creatine increased with severity. Proteomic and metabolomic integration was undertaken using linear regression via Lasso penalisation modelling, incorporating 29 variables (R2=0.82) with principal component 2 able to discriminate advanced OA from earlier stages, predominantly driven by H9GZQ9, F6ZR63 and alanine. Combining biobank and HKJC datasets, discriminant analysis of principal components modelling prediction was good for mild OA (90%). This study has stratified equine OA using both metabolomic and proteomic SF profiles and identified a panel of markers of interest which may be applicable to grading OA severity. This is also the first study to undertake computational integration of NMR metabolomic and LC-MS/MS proteomic datasets of any biological system.

290 CSF chitinases as novel biomarkers for MND

2018 ◽  
Vol 89 (10) ◽  
pp. A45.1-A45
Author(s):  
Thompson Alexander G ◽  
Gray Elizabeth ◽  
Thézénas Marie-Laetitia ◽  
Charles Philip D ◽  
Evetts Samuel ◽  
...  
Keyword(s):  
Diagnostic Delay ◽  
Label Free ◽  
Cross Sectional ◽  
Diagnostic Biomarkers ◽  
Csf Proteins ◽  
Liquid Chromatography Tandem Mass ◽  
Individual Participant ◽  
Novel Biomarkers ◽  
Free Quantification ◽  
Lateral Sclerosis

The development of biomarkers for amyotrophic lateral sclerosis (ALS, the commonest phenotype of MND) is a priority to reduce diagnostic delay, allow earlier assessment of therapeutic activity, and provide pathogenic insight.Liquid chromatography tandem mass spectrometry with label-free quantification was used to quantify CSF proteins in individual participant samples. A longitudinal cohort comprised patients with ALS (n=43) and primary lateral sclerosis (PLS, n=6). A cross-sectional cohort comprised healthy (n=20) and disease control patient CSF samples (Parkinson’s disease n=20, MND mimic disorders n=12).Among 773 identified proteins, significantly elevated levels of three macrophage-derived chitinase proteins were detected in the ALS group, specifically chitotriosidase (CHIT1), chitinase-3-like protein 1 (CHI3L1) and chitinase-3-like protein 2 (CHI3L2). Levels correlated with rate of disease progression (CHIT1 r=0.56, p<0.001; CHI3L1 r=0.31, p=0.028; CHI3L2 r=0.29, p=0.044), and levels of the axonal degeneration marker phosphorylated neurofilament heavy chain (r=0.62, p<0.001; r=0.49, p<0.001; r=0.41, p<0.001). Levels of CHI3L1, but not CHIT1 or CHI3L2, increased over time in those with low initial values (gradient=0.005 log abundance units/month, p=0.001).Microglial activation has been implicated in the pathogenesis of MND and neuroinflammatory pathways are a major target of therapeutic interest. CSF chitinases may be potential pharmacodynamic as well as diagnostic biomarkers.

scholarly journals Plasma proteomic analysis of systemic lupus erythematosus patients using liquid chromatography/tandem mass spectrometry with label-free quantification

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e4730 ◽  
Author(s):  
Rashmi Madda ◽  
Shih-Chang Lin ◽  
Wei-Hsin Sun ◽  
Shir-Ly Huang
Keyword(s):  
Lupus Erythematosus ◽  
Inflammatory Responses ◽  
Tandem Mass ◽  
Healthy Controls ◽  
Label Free ◽  
Systemic Lupus ◽  
Label Free Quantification ◽  
Chromatography Tandem Mass Spectrometry ◽  
Liquid Chromatography Tandem Mass ◽  
Free Quantification

Context Systemic lupus erythematosus (SLE) is a chronic inflammatory autoimmune disease with unknown etiology. Objective Human plasma is comprised of over 10 orders of magnitude concentration of proteins and tissue leakages. The changes in the abundance of these proteins have played an important role in various human diseases. Therefore, the research objective of this study is to identify the significantly altered expression levels of plasma proteins from SLE patients compared with healthy controls using proteomic analysis. The plasma proteome profiles of both SLE patients and controls were compared. Methods A total of 19 active SLE patients and 12 healthy controls plasma samples were analyzed using high-resolution electrospray ionization liquid chromatography-tandem mass spectrometry (LC-ESI-MS/MS) followed by label-free quantification. Results A total of 19 proteins showed a significant level of expression in the comparative LC-ESI-MS/MS triplicate analysis; among these, 14 proteins had >1.5- to three-fold up-regulation and five had <0.2- to 0.6-fold down-regulation. Gene ontology and DAVID (Database Annotation Visualization, and Integrated Discovery) functional enrichment analysis revealed that these proteins are involved in several important biological processes including acute phase inflammatory responses, complement activation, hemostasis, and immune system regulation. Conclusion Our study identified a group of differentially expressed proteins in the plasma of SLE patients that are involved in the imbalance of the immune system and inflammatory responses. Therefore, these findings may have the potential to be used as prognostic/diagnostic markers for SLE disease assessment or disease monitoring.

scholarly journals Label-Free Mass Spectrometry-Based Quantification of Linker Histone H1 Variants in Clinical Samples

2020 ◽  
Vol 21 (19) ◽  
pp. 7330
Author(s):  
Roberta Noberini ◽  
Cristina Morales Torres ◽  
Evelyn Oliva Savoia ◽  
Stefania Brandini ◽  
Maria Giovanna Jodice ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Histone H1 ◽  
Histone Variants ◽  
Linker Histone ◽  
Clinical Samples ◽  
Label Free ◽  
Complex Samples ◽  
Linker Histone H1 ◽  
Ideal Tool ◽  
Free Quantification

Epigenetic aberrations have been recognized as important contributors to cancer onset and development, and increasing evidence suggests that linker histone H1 variants may serve as biomarkers useful for patient stratification, as well as play an important role as drivers in cancer. Although traditionally histone H1 levels have been studied using antibody-based methods and RNA expression, these approaches suffer from limitations. Mass spectrometry (MS)-based proteomics represents the ideal tool to accurately quantify relative changes in protein abundance within complex samples. In this study, we used a label-free quantification approach to simultaneously analyze all somatic histone H1 variants in clinical samples and verified its applicability to laser micro-dissected tissue areas containing as low as 1000 cells. We then applied it to breast cancer patient samples, identifying differences in linker histone variants patters in primary triple-negative breast tumors with and without relapse after chemotherapy. This study highlights how label-free quantitation by MS is a valuable option to accurately quantitate histone H1 levels in different types of clinical samples, including very low-abundance patient tissues.

scholarly journals Spectral Clustering Improves Label-Free Quantification of Low-Abundant Proteins

2019 ◽  
Vol 18 (4) ◽  
pp. 1477-1485 ◽  
Author(s):  
Johannes Griss ◽  
Florian Stanek ◽  
Otto Hudecz ◽  
Gerhard Dürnberger ◽  
Yasset Perez-Riverol ◽  
...  
Keyword(s):  
Spectral Clustering ◽  
Label Free ◽  
Label Free Quantification ◽  
Free Quantification
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