Bayesian identification of protein differential expression in multi-group isobaric labelled mass spectrometry data

AbstractIn this paper we develop a Bayesian statistical inference approach to the unified analysis of isobaric labelled MS/MS proteomic data across multiple experiments. An explicit probabilistic model of the log-intensity of the isobaric labels’ reporter ions across multiple pre-defined groups and experiments is developed. This is then used to develop a full Bayesian statistical methodology for the identification of differentially expressed proteins, with respect to a control group, across multiple groups and experiments. This methodology is implemented and then evaluated on simulated data and on two model experimental datasets (for which the differentially expressed proteins are known) that use a TMT labelling protocol.

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MetaMSD: meta analysis for mass spectrometry data

PeerJ ◽

10.7717/peerj.6699 ◽

2019 ◽

Vol 7 ◽

pp. e6699

Author(s):

So Young Ryu ◽

George A. Wendt

Keyword(s):

Mass Spectrometry ◽

Biomarker Discovery ◽

Meta Analysis ◽

Simulated Data ◽

Mass Spectrometry Data ◽

Transplant Patients ◽

Proteomic Data ◽

Differential Proteins ◽

Command Line Tool ◽

Kidney Transplant Patients

Mass spectrometry-based proteomics facilitate disease understanding by providing protein abundance information about disease progression. For the same type of disease studies, multiple mass spectrometry datasets may be generated. Integrating multiple mass spectrometry datasets can provide valuable information that a single dataset analysis cannot provide. In this article, we introduce a meta-analysis software, MetaMSD (Meta Analysis for Mass Spectrometry Data) that is specifically designed for mass spectrometry data. Using Stouffer’s or Pearson’s test, MetaMSD detects significantly more differential proteins than the analysis based on the single best experiment. We demonstrate the performance of MetaMSD using simulated data, urinary proteomic data of kidney transplant patients, and breast cancer proteomic data. Noting the common practice of performing a pilot study prior to a main study, this software will help proteomics researchers fully utilize the benefit of multiple studies (or datasets), thus optimizing biomarker discovery. MetaMSD is a command line tool that automatically outputs various graphs and differential proteins with confidence scores. It is implemented in R and is freely available for public use at https://github.com/soyoungryu/MetaMSD. The user manual and data are available at the site. The user manual is written in such a way that scientists who are not familiar with R software can use MetaMSD.

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Identification of differentially expressed proteins in retinoblastoma tumors using mass spectrometry-based comparative proteomic approach

Journal of Proteomics ◽

10.1016/j.jprot.2017.02.006 ◽

2017 ◽

Vol 159 ◽

pp. 77-91 ◽

Cited By ~ 7

Author(s):

Jasmine Naru ◽

Ritu Aggarwal ◽

Ashok Kumar Mohanty ◽

Usha Singh ◽

Deepak Bansal ◽

...

Keyword(s):

Mass Spectrometry ◽

Differentially Expressed ◽

Differentially Expressed Proteins ◽

Proteomic Approach

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2-DE-MS based proteomic investigation of dairy cows with footrot

Journal of Veterinary Research ◽

10.1515/jvetres-2016-0010 ◽

2016 ◽

Vol 60 (1) ◽

pp. 63-69

Author(s):

Jiasan Zheng ◽

Shi Shu ◽

Cheng Xia ◽

Chuang Xu ◽

Hongyou Zhang ◽

...

Keyword(s):

Plasma Proteins ◽

Differentially Expressed ◽

Control Group ◽

Differentially Expressed Proteins ◽

Defence Mechanisms ◽

Flight Mass Spectrometry ◽

Mass Spectrum Analysis ◽

Proteomic Investigation ◽

Dimensional Electrophoresis ◽

Control Group Group

Abstract Introduction: The differentially expressed proteins between healthy cows and those with footrot were identified to explore changes in protein profiles associated with the disease. Material and Methods: Out of 36 cows selected for the experiment, 18 footrot-affected cows were included in the treatment group (group T) and 18 unaffected cows were included in the control group (group C). Plasma samples from groups T and C were subjected to two-dimensional electrophoresis analysis and differentially expressed proteins were identified by matrix-assisted laser desorption/ionisation tandem time-of-flight mass spectrometry. Bioinformatics, including gene ontology analysis and pathway analysis, was used for analysing all proteins. Results: Out of 63 spots identified by 2DE, 33 were selected for mass spectrum analysis, which identified 11 differentially expressed proteins in 26 spots. Footrot led to changes in profiles in plasma proteins that were classified to the pathway of inflammatory response, complement, and blood coagulation, among others. Conclusion: This study provides evidence of the defence mechanisms of cows with footrot to explore strategies for treatment.

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Serum Proteomic Analysis of Cannabis Use Disorder in Male Patients

Molecules ◽

10.3390/molecules26175311 ◽

2021 ◽

Vol 26 (17) ◽

pp. 5311

Author(s):

Fawaz Alasmari ◽

Sary Alsanea ◽

Assim A. Alfadda ◽

Ibrahim O. Alanazi ◽

Mohthash Musambil ◽

...

Keyword(s):

Signaling Pathways ◽

Proteomic Analysis ◽

Cannabis Use ◽

Farnesoid X Receptor ◽

Differentially Expressed ◽

Interleukin 12 ◽

Control Group ◽

Cannabis Use Disorder ◽

Differentially Expressed Proteins ◽

Healthy Control

Cannabis use has been growing recently and it is legally consumed in many countries. Cannabis has a variety of phytochemicals including cannabinoids, which might impair the peripheral systems responses affecting inflammatory and immunological pathways. However, the exact signaling pathways that induce these effects need further understanding. The objective of this study is to investigate the serum proteomic profiling in patients diagnosed with cannabis use disorder (CUD) as compared with healthy control subjects. The novelty of our study is to highlight the differentially changes proteins in the serum of CUD patients. Certain proteins can be targeted in the future to attenuate the toxicological effects of cannabis. Blood samples were collected from 20 male individuals: 10 healthy controls and 10 CUD patients. An untargeted proteomic technique employing two-dimensional difference in gel electrophoresis coupled with mass spectrometry was employed in this study to assess the differentially expressed proteins. The proteomic analysis identified a total of 121 proteins that showed significant changes in protein expression between CUD patients (experimental group) and healthy individuals (control group). For instance, the serum expression of inactive tyrosine protein kinase PEAK1 and tumor necrosis factor alpha-induced protein 3 were increased in CUD group. In contrast, the serum expression of transthyretin and serotransferrin were reduced in CUD group. Among these proteins, 55 proteins were significantly upregulated and 66 proteins significantly downregulated in CUD patients as compared with healthy control group. Ingenuity pathway analysis (IPA) found that these differentially expressed proteins are linked to p38MAPK, interleukin 12 complex, nuclear factor-κB, and other signaling pathways. Our work indicates that the differentially expressed serum proteins between CUD and control groups are correlated to liver X receptor/retinoid X receptor (RXR), farnesoid X receptor/RXR activation, and acute phase response signaling.

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Proteomic analysis of tears and serum for dry eye disease using ovariectomized cynomolgus monkey

10.21203/rs.2.21889/v1 ◽

2020 ◽

Author(s):

xiaolong yang ◽

Yue Xu ◽

Yun Wang ◽

Chang Li ◽

Xiaofeng Zhang

Keyword(s):

Gene Ontology ◽

Growth Factor ◽

Dry Eye ◽

Cynomolgus Monkey ◽

Enrichment Analysis ◽

Differentially Expressed ◽

Control Group ◽

Differentially Expressed Proteins ◽

Dry Eyes ◽

Experimental Group

Abstract Background Ovariectomized cynomolgus monkey 30 months after surgery was selected as the research object to identify protein changes in tears and serum to provide a reference for the diagnosis and pathogenesis of dry eye in menopausal women. Methods Six cynomolgus monkey were randomly divided into an experimental group and a control group (3 in each group). The experimental group underwent bilateral ovariectomy, while the control group underwent sham surgery with their ovaries reserved. Proteomic analysis was performed by LC-MS/MS on tears and serum collected from two groups. Differentially expressed proteins were identified and were performed cluster analysis, which included gene ontology, the Kyoto Encyclopedia of Genes and Genomes pathway and protein-protein interaction. Results 33 differentially expressed proteins have been identified in tears and17 differentially expressed proteins have been identified in serum. Kyoto Encyclopedia of Genes and Genomes enrichment analysis in tears has discovered Glucagon signaling pathway and neurotrophin signaling pathway may play an important role in the pathogenesis of dry eye. Gene ontology enrichment analysis in serum has discovered insulin-like growth factor binding and growth factor binding in molecular function probably make effort in pathogenesis of dry eye. KEGG analysis in serum has discovered salivary secretion may be the key pathway in pathogenesis of dry eye. Conclusions Protein G7PCH4, Q2PG17 and G7PT55 in tears may be the key protein in pathogenesis of dry eyes. Protein G7P1T1, G7PUN9 and G8F302 in serum may play an important role in pathogenesis of dry eyes.

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iTRAQ-Based Proteomics of Chronic Renal Failure Rats after FuShengong Decoction Treatment Reveals Haptoglobin and Alpha-1-Antitrypsin as Potential Biomarkers

Evidence-based Complementary and Alternative Medicine ◽

10.1155/2017/1480514 ◽

2017 ◽

Vol 2017 ◽

pp. 1-9 ◽

Cited By ~ 1

Author(s):

Yu Yang ◽

Junmeng Wei ◽

Xuekuan Huang ◽

Mingjun Wu ◽

Zhenbing Lv ◽

...

Keyword(s):

Renal Failure ◽

Chronic Renal Failure ◽

Differentially Expressed ◽

Coagulation Cascade ◽

Control Group ◽

Differentially Expressed Proteins ◽

Sprague Dawley ◽

Sprague Dawley Rats ◽

Alpha 1 Antitrypsin ◽

Global Health Problem

Background. Chronic renal failure (CRF) has become a global health problem and bears a huge economic burden. FuShengong Decoction (FSGD) as traditional Chinese medicine has multiple pharmacological effects. Objectives. To understand the underlying molecular mechanism and signaling pathway involved in the FSGD treatment of CRF and screen differentially expressed proteins in rats with CRF treated with FSGD. Methods. Thirty-three male Sprague-Dawley rats were randomly divided into control group, CRF group, and FSGD group. Differentially expressed proteins were screened by iTRAQ coupled with nanoLC-MS/MS, and these identified proteins were later analyzed by GO, KEGG, and STRING. Additionally, haptoglobin (HP) and alpha-1-antitrypsin (AAT) were finally verified by ELISA, Western blot, and real time PCR. Results. A total of 417 proteins were identified. Nineteen differentially expressed proteins were identified in the FSGD group compared with the model group, of which 3 proteins were upregulated and 16 proteins were downregulated. Cluster analysis indicated that inflammatory response was associated with these proteins and complement and coagulation cascade pathways were predominantly involved. The validation methods further confirmed that the levels of HP and AAT were significantly increased. Conclusions. HP and AAT may be the important biomarkers in the pathogenesis of CRF and FSGD therapy.

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