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Article ; Online: Role of Multiomics Data to Understand Host-Pathogen Interactions in COVID-19 Pathogenesis.

Aggarwal, Shalini / Acharjee, Arup / Mukherjee, Amrita / Baker, Mark S / Srivastava, Sanjeeva

2021 Volume 20, Issue 2, Page(s) 1107–1132

Abstract: Human infectious diseases are contributed equally by the host immune system's efficiency and any pathogens' infectivity. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the coronavirus strain causing the respiratory pandemic coronavirus ... ...

Abstract	Human infectious diseases are contributed equally by the host immune system's efficiency and any pathogens' infectivity. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the coronavirus strain causing the respiratory pandemic coronavirus disease 2019 (COVID-19). To understand the pathobiology of SARS-CoV-2, one needs to unravel the intricacies of host immune response to the virus, the viral pathogen's mode of transmission, and alterations in specific biological pathways in the host allowing viral survival. This review critically analyzes recent research using high-throughput "omics" technologies (including proteomics and metabolomics) on various biospecimens that allow an increased understanding of the pathobiology of SARS-CoV-2 in humans. The altered biomolecule profile facilitates an understanding of altered biological pathways. Further, we have performed a meta-analysis of significantly altered biomolecular profiles in COVID-19 patients using bioinformatics tools. Our analysis deciphered alterations in the immune response, fatty acid, and amino acid metabolism and other pathways that cumulatively result in COVID-19 disease, including symptoms such as hyperglycemic and hypoxic sequelae.
MeSH term(s)	COVID-19/epidemiology ; COVID-19/prevention & control ; COVID-19/virology ; Host-Pathogen Interactions ; Humans ; Metabolomics/methods ; Pandemics ; Proteomics/methods ; SARS-CoV-2/metabolism ; SARS-CoV-2/physiology
Language	English
Publishing date	2021-01-11
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2078618-9
ISSN	1535-3907 ; 1535-3893
ISSN (online)	1535-3907
ISSN	1535-3893
DOI	10.1021/acs.jproteome.0c00771
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Article ; Online: Building the 'practical' human proteome project - the next big thing in basic and clinical proteomics.

Baker, Mark S

Current opinion in molecular therapeutics

2009 Volume 11, Issue 6, Page(s) 600–602

MeSH term(s)	Biomarkers/metabolism ; Congresses as Topic ; Databases, Protein ; Humans ; Proteome ; Proteomics ; Translational Medical Research
Chemical Substances	Biomarkers ; Proteome
Language	English
Publishing date	2009-12
Publishing country	England
Document type	Editorial
ZDB-ID	2022273-7
ISSN	2040-3445 ; 1464-8431
ISSN (online)	2040-3445
ISSN	1464-8431
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Article ; Online: In Silico Peptide Repertoire of Human Olfactory Receptor Proteomes on High-Stringency Mass Spectrometry.

Adhikari, Subash / Sharma, Samridhi / Ahn, Seong Beom / Baker, Mark S

Journal of proteome research

2019 Volume 18, Issue 12, Page(s) 4117–4123

Abstract: Human olfactory receptors (ORs) are seven-pass transmembrane G-protein coupled receptors (GPCR) involved in smell perception and many other signaling pathways. They are primarily expressed in the olfactory epithelium and ectopically expressed in several ... ...

Abstract	Human olfactory receptors (ORs) are seven-pass transmembrane G-protein coupled receptors (GPCR) involved in smell perception and many other signaling pathways. They are primarily expressed in the olfactory epithelium and ectopically expressed in several other organs and tissues. neXtProt contains 4 PE1 (protein existence 1, evidenced at the protein level) ORs, determined on the basis of either protein interaction data (i.e., OR1D4 and OR2AG1) or convincing genetic, haplotype, or biochemical data (i.e., OR1D2 and OR2J3). Not a single OR currently qualifies for neXtProt PE1 status based on mass spectrometry (MS) evidence. Many reasons for this absence of MS-based identification have been proposed, including (i) confined or spatiotemporal or developmental expression, (ii) low copy number, (iii) OR repertoire gene silencing, and (iv) limited tissue availability. OR transmembrane domains (TMDs) inherently limit MS identification because the hydrophobic nature restricts the access of trypsin to potential cleavage sites. Equally, the extremely low frequency or lack of accessible arginine and lysine residues in TMDs renders trypsin cleavage ineffective. Here, we demonstrate an analytical approach specifically focused on the hydrophilic (trypsin-accessible) domains of ORs [i.e., with all transmembrane segments and anchored peptides excluded). We predicted the ability of OR soluble (hydrophilic) domains to yield 2 or more >9 amino acids (aa) length unique mapping (unique to a protein only), non-nested (peptides with varying length at the N or C terminal but containing the same core sequence), leucine/isoleucine (I/L) switch examined (I and L have same mass and cannot be distinguished by MS) tryptic peptides. Our analysis showed that ∼58% of the human OR proteome could potentially generate tryptic peptides that satisfy current the Human Proteome Project data interpretation guidelines (version 2.1) when no missed cleavages are allowed and increases to ∼78% when one missed cleavage is allowed. The utilization of current biological data (adjuvant genomics, expression profile, transcriptomics, epigenome silencing data, etc.) and the adoption of a non-conventional proteomics approach (e.g., Confetti multiprotease digestion, CNBr cleavage of TMDs, and more-extreme chromatographic and MS methods) could aid in the detection of the remaining ORs.
MeSH term(s)	Computer Simulation ; Databases, Protein ; Humans ; Hydrophobic and Hydrophilic Interactions ; Mass Spectrometry/methods ; Peptides ; Protein Domains ; Proteome ; Proteomics/methods ; Receptors, Odorant/chemistry ; Receptors, Odorant/metabolism ; Trypsin/chemistry ; Trypsin/metabolism
Chemical Substances	Peptides ; Proteome ; Receptors, Odorant ; Trypsin (EC 3.4.21.4)
Language	English
Publishing date	2019-05-22
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2078618-9
ISSN	1535-3907 ; 1535-3893
ISSN (online)	1535-3907
ISSN	1535-3893
DOI	10.1021/acs.jproteome.8b00494
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Article ; Online: Mass spectrometry-based protein identification in proteomics-a review.

Noor, Zainab / Ahn, Seong Beom / Baker, Mark S / Ranganathan, Shoba / Mohamedali, Abidali

Briefings in bioinformatics

2020 Volume 22, Issue 2, Page(s) 1620–1638

Abstract: Statistically, accurate protein identification is a fundamental cornerstone of proteomics and underpins the understanding and application of this technology across all elements of medicine and biology. Proteomics, as a branch of biochemistry, has in ... ...

Abstract	Statistically, accurate protein identification is a fundamental cornerstone of proteomics and underpins the understanding and application of this technology across all elements of medicine and biology. Proteomics, as a branch of biochemistry, has in recent years played a pivotal role in extending and developing the science of accurately identifying the biology and interactions of groups of proteins or proteomes. Proteomics has primarily used mass spectrometry (MS)-based techniques for identifying proteins, although other techniques including affinity-based identifications still play significant roles. Here, we outline the basics of MS to understand how data are generated and parameters used to inform computational tools used in protein identification. We then outline a comprehensive analysis of the bioinformatics and computational methodologies used in protein identification in proteomics including discussing the most current communally acceptable metrics to validate any identification.
MeSH term(s)	Chromatography, Gas/methods ; Chromatography, Liquid/methods ; Computational Biology/methods ; Mass Spectrometry/methods ; Proteins/chemistry ; Proteomics/methods
Chemical Substances	Proteins
Language	English
Publishing date	2020-02-05
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	2068142-2
ISSN	1477-4054 ; 1467-5463
ISSN (online)	1477-4054
ISSN	1467-5463
DOI	10.1093/bib/bbz163
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Article ; Online: Neuroserpin gene therapy inhibits retinal ganglion cell apoptosis and promotes functional preservation in glaucoma.

Chitranshi, Nitin / Rajput, Rashi / Godinez, Angela / Pushpitha, Kanishka / Mirzaei, Mehdi / Basavarajappa, Devaraj / Gupta, Veer / Sharma, Samridhi / You, Yuyi / Galliciotti, Giovanna / Salekdeh, Ghasem H / Baker, Mark S / Graham, Stuart L / Gupta, Vivek K

Molecular therapy : the journal of the American Society of Gene Therapy

2023 Volume 31, Issue 7, Page(s) 2056–2076

Abstract: Our research has proven that the inhibitory activity of the serine protease inhibitor neuroserpin (NS) is impaired because of its oxidation deactivation in glaucoma. Using genetic NS knockout ( ... ...

Abstract	Our research has proven that the inhibitory activity of the serine protease inhibitor neuroserpin (NS) is impaired because of its oxidation deactivation in glaucoma. Using genetic NS knockout (NS
MeSH term(s)	Mice ; Animals ; Retinal Ganglion Cells/metabolism ; Beclin-1/metabolism ; Disease Models, Animal ; Glaucoma/genetics ; Glaucoma/therapy ; Glaucoma/metabolism ; Apoptosis/genetics ; Intraocular Pressure ; Neuroserpin
Chemical Substances	Beclin-1
Language	English
Publishing date	2023-03-11
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2010592-7
ISSN	1525-0024 ; 1525-0016
ISSN (online)	1525-0024
ISSN	1525-0016
DOI	10.1016/j.ymthe.2023.03.008
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Article ; Online: Oncoproteomics: Current status and future opportunities.

He, Yujia / Mohamedali, Abidali / Huang, Canhua / Baker, Mark S / Nice, Edouard C

Clinica chimica acta; international journal of clinical chemistry

2019 Volume 495, Page(s) 611–624

Abstract: Oncoproteomics is the systematic study of cancer samples using omics technologies to detect changes implicated in tumorigenesis. Recent progress in oncoproteomics is already opening new avenues for the identification of novel biomarkers for early ... ...

Abstract	Oncoproteomics is the systematic study of cancer samples using omics technologies to detect changes implicated in tumorigenesis. Recent progress in oncoproteomics is already opening new avenues for the identification of novel biomarkers for early clinical stage cancer detection, targeted molecular therapies, disease monitoring, and drug development. Such information will lead to new understandings of cancer biology and impact dramatically on the future care of cancer patients. In this review, we will summarize the advantages and limitations of the key technologies used in (onco)proteogenomics, (the Omics Pipeline), explain how they can assist us in understanding the biology behind the overarching "Hallmarks of Cancer", discuss how they can advance the development of precision/personalised medicine and the future directions in the field.
MeSH term(s)	Big Data ; Drug Discovery ; Humans ; Neoplasms/drug therapy ; Neoplasms/genetics ; Neoplasms/metabolism ; Precision Medicine ; Proteomics/instrumentation ; Proteomics/methods
Language	English
Publishing date	2019-06-06
Publishing country	Netherlands
Document type	Journal Article ; Review
ZDB-ID	80228-1
ISSN	1873-3492 ; 0009-8981
ISSN (online)	1873-3492
ISSN	0009-8981
DOI	10.1016/j.cca.2019.06.006
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Article ; Online: Recent findings from the Human Proteome Project: opening the mass spectrometry toolbox to advance cancer diagnosis, surveillance and treatment.

Cantor, David I / Nice, Edouard C / Baker, Mark S

Expert review of proteomics

2015 Volume 12, Issue 3, Page(s) 279–293

Abstract: The Human Proteome Project stands to eclipse the Human Genome Project in terms of scope, content and interpretation. Its outputs, in conjunction with recent developments across the proteomics community, provide new tools for cancer research with the ... ...

Abstract	The Human Proteome Project stands to eclipse the Human Genome Project in terms of scope, content and interpretation. Its outputs, in conjunction with recent developments across the proteomics community, provide new tools for cancer research with the potential of providing clinically relevant insights into the disease. These collectively may guide the development of future diagnosis, surveillance and treatment strategies. Having established a robust organizational framework within the international community, the Human Proteome Organization and the proteomics community at large have made significant advances in biomarker discovery, detection, molecular imaging and in exploring tumor heterogeneity. Here, the authors discuss some developments in cancer proteomics and how they can be implemented to reduce the global burden of the disease.
MeSH term(s)	Biomarkers, Tumor/metabolism ; Human Genome Project ; Humans ; Mass Spectrometry/methods ; Neoplasms/diagnosis ; Neoplasms/metabolism ; Neoplasms/therapy ; Prognosis ; Proteome/metabolism
Chemical Substances	Biomarkers, Tumor ; Proteome
Language	English
Publishing date	2015-06
Publishing country	England
Document type	Journal Article ; Review
ZDB-ID	2299100-1
ISSN	1744-8387 ; 1478-9450
ISSN (online)	1744-8387
ISSN	1478-9450
DOI	10.1586/14789450.2015.1040770
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Article ; Online: iSwathX: an interactive web-based application for extension of DIA peptide reference libraries

Noor, Zainab / Wu, Jemma X. / Pascovici, Dana / Mohamedali, Abidali / Molloy, Mark P. / Baker, Mark S. / Ranganathan, Shoba

Bioinformatics. 2019 Feb. 01, v. 35, no. 3, p. 538-539

2019 , Page(s) 538–539

Abstract: Large-scale peptide mass spectrometry (MS)/MS reference libraries are essential for the comprehensive analysis of data-independent acquisition (DIA) MS datasets, providing a comprehensive set of spectra for identification and quantification of proteins. ... ...

Abstract	Large-scale peptide mass spectrometry (MS)/MS reference libraries are essential for the comprehensive analysis of data-independent acquisition (DIA) MS datasets, providing a comprehensive set of spectra for identification and quantification of proteins. We have developed a novel web-based R-package (iSwathX) for combining reference libraries that is compatible with different DIA analysis software. This open-source web GUI automates the process of normalization and combination of spectral libraries and provides a user-friendly method for performing library format conversions, analysis and visualizations, with no need for programing familiarity. iSwathX is freely accessible at https://biolinfo.shinyapps.io/iSwathX with the R-package and Shiny source code available from GitHub (https://github.com/znoor/iSwathX). Supplementary data are available at Bioinformatics online.
Keywords	Internet ; bioinformatics ; computer software ; data collection ; mass spectrometry ; peptides
Language	English
Dates of publication	2019-0201
Size	p. 538-539
Publishing place	Oxford University Press
Document type	Article ; Online
ZDB-ID	1468345-3
ISSN	1367-4811 ; 1460-2059
ISSN	1367-4811 ; 1460-2059
DOI	10.1093/bioinformatics/bty660
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Article ; Online: Pathology, proteomics and the pathway to personalised medicine.

Jin, Ping / Lan, Jiang / Wang, Kui / Baker, Mark S / Huang, Canhua / Nice, Edouard C

Expert review of proteomics

2018 Volume 15, Issue 3, Page(s) 231–243

Abstract: Introduction: As we move from a discovery to a translational phase in proteomics, with a focus on developing validated clinical assays to assist personalized medicine, there is a growing need for strong bidirectional interactions with the clinical ... ...

Abstract	Introduction: As we move from a discovery to a translational phase in proteomics, with a focus on developing validated clinical assays to assist personalized medicine, there is a growing need for strong bidirectional interactions with the clinical pathology community. Thus, while on one hand the proteomics community will provide candidate biomarkers to assist in diagnosis, prognosis, surveillance, identification of individualized patient medication, and development and validation of new assays for diagnostic use, on the other the pathology community will assist with specific tissue identification and selection (e.g. laser capture microdissection, tissue sections for MS imaging), biobanking, validation of emerging automated histopathology techniques, preparation and classification of relevant patient medical reports, and assisting with the optimization of experimental design for clinical trials. Areas covered: Here we discuss these topics with a particular emphasis on recent publications and relevant initiatives and outline some of the hurdles that still remain for personalized medicine. Expert commentary: It is clear that effective crosstalk between the proteomics and pathology communities will greatly accelerate crossover of candidate biomarkers to personalized medicine, which will have significant benefits not only for patient wellbeing, but also the global healthcare budget. However, analysis of the big data generated may become rate-limiting.
MeSH term(s)	Big Data ; Biological Specimen Banks ; Cytodiagnosis/methods ; Humans ; Mass Spectrometry/methods ; Precision Medicine/methods ; Proteomics/methods
Language	English
Publishing date	2018-01-16
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	2299100-1
ISSN	1744-8387 ; 1478-9450
ISSN (online)	1744-8387
ISSN	1478-9450
DOI	10.1080/14789450.2018.1425618
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Article ; Online: Proteomics and the microbiome: pitfalls and potential.

Lin, Huafeng / He, Qing-Yu / Shi, Lei / Sleeman, Mark / Baker, Mark S / Nice, Edouard C

Expert review of proteomics

2018 Volume 16, Issue 6, Page(s) 501–511

Abstract: ... ...

Abstract	Introduction
MeSH term(s)	Animals ; Biomarkers/metabolism ; Feces/microbiology ; Gastrointestinal Microbiome/physiology ; Humans ; Microbiota/physiology ; Precision Medicine ; Proteomics/methods
Chemical Substances	Biomarkers
Language	English
Publishing date	2018-09-28
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	2299100-1
ISSN	1744-8387 ; 1478-9450
ISSN (online)	1744-8387
ISSN	1478-9450
DOI	10.1080/14789450.2018.1523724
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