Mass Spectrometry for Proteomics and Recent Developments in ESI, MALDI and other Ionization Methodologies

Farooq, Qurat ul Ain; Haq, Noor ul; Aziz, Abdul; Aimen, Sara; Haq, Muhammad Inam Ul

doi:10.2174/1570164616666190204154653

Cited by 3 publications

(2 citation statements)

References 65 publications

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“…Mass spectrometry (MS)-based proteomics and metabolomics platforms have advanced significantly over the last 20 years. Much of the development work has focused on MS instrumentation and techniques. − Additionally, developments in liquid chromatography (LC) have enabled complex mixture analysis. − This has led to the wide-scale adoption of LC-MS techniques by the scientific community for the study of human disease. Indeed, LC-MS ‘omics methods have been broadly utilized to investigate conditions such as cardiovascular disease, − cancer, − diabetes, ,− and neurodegenerative disorders. − …”

Section: Introductionmentioning

confidence: 99%

Combining Field-Enabled Capillary Vibrating Sharp-Edge Spray Ionization with Microflow Liquid Chromatography and Mass Spectrometry to Enhance ‘Omics Analyses

Majuta

DeBastiani

et al. 2021

J. Am. Soc. Mass Spectrom.

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Field-enabled capillary vibrating sharp-edge spray ionization (cVSSI) has been combined with high-flow liquid chromatography (LC) and mass spectrometry (MS) to establish current ionization capabilities for metabolomics and proteomics investigations. Comparisons are made between experiments employing cVSSI and a heated electrospray ionization probe representing the state-of-the-art in microflow LC-MS methods for 'omics studies. For metabolomics standards, cVSSI is shown to provide an ionization enhancement by factors of 4 ± 2 for both negative and positive ion mode analyses. For chymotryptic peptides, cVSSI is shown to provide an ionization enhancement by factors of 5 ± 2 and 2 ± 1 for negative and positive ion mode analyses, respectively. Slightly broader high-performance liquid chromatography peaks are observed in the cVSSI datasets, and several studies suggest that this results from a slightly decreased post-split flow rate. This may result from partial obstruction of the pulled-tip emitter over time. Such a challenge can be remedied with the use of LC pumps that operate in the 10 to 100 μL•min −1 flow regime. At this early stage, the proof-of-principle studies already show ion signal advantages over stateof-the-art electrospray ionization (ESI) for a wide variety of analytes in both positive and negative ion mode. Overall, this represents a ∼20−50-fold improvement over the first demonstration of LC-MS analyses by voltage-free cVSSI. Separate comparisons of the ion abundances of compounds eluting under identical solvent conditions reveal ionization efficiency differences between cVSSI and ESI and may suggest varied contributions to ionization from different physicochemical properties of the compounds. Future investigations of parameters that could further increase ionization gains in negative and positive ion mode analyses with the use of cVSSI are briefly presented.

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Section: Introductionmentioning

confidence: 99%

Combining Field-Enabled Capillary Vibrating Sharp-Edge Spray Ionization with Microflow Liquid Chromatography and Mass Spectrometry to Enhance ‘Omics Analyses

Majuta

DeBastiani

et al. 2021

J. Am. Soc. Mass Spectrom.

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“…MS is a powerful in vitro tool for the detection of macromolecular interactions. The principle of MS was explained extensively in one of our previous reviews[ 19 ]. MS allows us to identify polypeptide sequences by ionizing them and then detecting analyte ions based on their mass-to-charge ratios[ 20 , 21 ].…”

Section: Experimental Methods To Detect Ppismentioning

confidence: 99%

Protein-protein interactions: Methods, databases, and applications in virus-host study

Farooq¹,

Shaukat²,

Aiman³

et al. 2021

WJV

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Almost all the cellular processes in a living system are controlled by proteins: They regulate gene expression, catalyze chemical reactions, transport small molecules across membranes, and transmit signal across membranes. Even, a viral infection is often initiated through virus-host protein interactions. Protein-protein interactions (PPIs) are the physical contacts between two or more proteins and they represent complex biological functions. Nowadays, PPIs have been used to construct PPI networks to study complex pathways for revealing the functions of unknown proteins. Scientists have used PPIs to find the molecular basis of certain diseases and also some potential drug targets. In this review, we will discuss how PPI networks are essential to understand the molecular basis of virus-host relationships and several databases which are dedicated to virus-host interaction studies. Here, we present a short but comprehensive review on PPIs, including the experimental and computational methods of finding PPIs, the databases dedicated to virus-host PPIs, and the associated various applications in protein interaction networks of some lethal viruses with their hosts.

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Proteomic Analysis of the Vitreous Body in Proliferative and Non-Proliferative Diabetic Retinopathy

Duong

Ahn

Han

et al. 2021

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Background: Diabetic Retinopathy (DR), one of the major microvascular complications commonly occurring in diabetic patients, can be classified into Proliferative Diabetic Retinopathy (PDR) and Non-Proliferative Diabetic Retinopathy (NPDR). Currently available therapies are only targeted for later stages of the disease in which some pathologic changes may be irreversible. Thus, there is a need to develop new treatment options for earlier stages of DR through revealing pathological mechanisms of PDR and NPDR. Objective: The purpose of this study was to characterize proteomes of diabetic through quantitative analysis of PDR and NPDR. Methods: Vitreous body was collected from three groups: control (non-diabetes mellitus), NPDR, and PDR. Vitreous proteins were digested to peptide mixtures and analyzed using LC-MS/MS. MaxQuant was used to search against the database and statistical analyses were performed using Perseus. Gene ontology analysis, related-disease identification, and protein-protein interaction were performed using the differential expressed proteins. Results: Twenty proteins were identified as critical in PDR and NPDR. The NPDR group showed different expressions of kininogen-1, serotransferrin, ribonuclease pancreatic, osteopontin, keratin type II cytoskeletal 2 epidermal, and transthyretin. Also, prothrombin, signal transducer and activator of transcription 4, hemoglobin subunit alpha, beta, and delta were particularly up-regulated proteins for PDR group. The up-regulated proteins related to complement and coagulation cascades. Statherin was down-regulated in PDR and NPDR compared with the control group. Transthyretin was the unique protein that increased its abundance in NPDR compared with the PDR and control group. Conclusion: This study confirmed the different expressions of some proteins in PDR and NPDR. Additionally, we revealed uniquely expressed proteins of PDR and NPDR, which would be differential biomarkers: prothrombin, alpha-2-HS-glycoprotein, hemoglobin subunit alpha, beta, and transthyretin.

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Mass Spectrometry for Proteomics and Recent Developments in ESI, MALDI and other Ionization Methodologies

Cited by 3 publications

References 65 publications

Combining Field-Enabled Capillary Vibrating Sharp-Edge Spray Ionization with Microflow Liquid Chromatography and Mass Spectrometry to Enhance ‘Omics Analyses

Combining Field-Enabled Capillary Vibrating Sharp-Edge Spray Ionization with Microflow Liquid Chromatography and Mass Spectrometry to Enhance ‘Omics Analyses

Protein-protein interactions: Methods, databases, and applications in virus-host study

Proteomic Analysis of the Vitreous Body in Proliferative and Non-Proliferative Diabetic Retinopathy

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