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Simultaneous monitoring of eight human respiratory viruses including SARS-CoV-2 using liquid chromatography-tandem mass spectrometry. Sci Rep 2022; 12:13392. [PMID: 35927299 PMCID: PMC9352774 DOI: 10.1038/s41598-022-16250-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 07/07/2022] [Indexed: 11/17/2022] Open
Abstract
Diagnosis of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection has primarily been achieved using reverse transcriptase polymerase chain reaction (RT-PCR) for acute infection, and serology for prior infection. Assay with RT-PCR provides data on presence or absence of viral RNA, with no information on virus replication competence, infectivity, or virus characterisation. Liquid chromatography-tandem mass spectrometry (LC–MS/MS) is typically not used in clinical virology, despite its potential to provide supplemental data about the presence of viral proteins and thus the potential for replication-competent, transmissible virus. Using the SARS-CoV-2 as a model virus, we developed a fast ‘bottom-up’ proteomics workflow for discovery of target virus peptides using ‘serum-free’ culture conditions, providing high coverage of viral proteins without the need for protein or peptide fractionation techniques. This workflow was then applied to Coronaviruses OC43 and 229E, Influenza A/H1N1 and H3N2, Influenza B, and Respiratory Syncytial Viruses A and B. Finally, we created an LC–MS/MS method for targeted detection of the eight-virus panel in clinical specimens, successfully detecting peptides from the SARS-CoV-2 ORF9B and nucleoprotein in RT-PCR positive samples. The method provides specific detection of respiratory viruses from clinical samples containing moderate viral loads and is an important further step to the use of LC–MS/MS in diagnosis of viral infection.
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Ghodasara P, Satake N, Sadowski P, Kopp S, Mills PC. Investigation of cattle plasma proteome in response to pain and inflammation using next generation proteomics technique, SWATH-MS. Mol Omics 2021; 18:133-142. [PMID: 34860232 DOI: 10.1039/d1mo00354b] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Pain assessment in farm animals has primarily relied on a combination of behavioral and physiological responses, although these are relatively subjective and difficult to quantify. It is essential to develop more effective biomarkers of pain in production animals since they are frequently exposed to routine surgical husbandry procedures. More effective biomarkers of pain would improve welfare, limit the loss of productivity associated with pain and permit better assessment of analgesics. This study aimed to investigate the use of a modern mass spectrometry data independent acquisition strategy, termed Sequential Window Acquisition of All Theoretical Mass Spectra (SWATH-MS), to detect candidate protein biomarkers that are known to associate with nociceptive and inflammatory processes in cattle, which could then be used to assess the efficacy of potential analgesics. Calves were randomly divided into two groups that were either surgically dehorned or subjected to restraint stress, without provision of anaesthesia or analgesia in accordance with current industry standards. Samples were analysed before and after dehorning at multiple timepoints. Significant changes in protein concentrations were detected predominantly at 24 and 96 h following dehorning, including kininogens, proteins associated with the coagulation and complement cascades and serine protease inhibitors. Gene ontology analysis revealed that the identified candidate biomarkers were associated with stress, wound healing, immune response, blood coagulation and the inflammatory and acute phase responses, which could be expected following surgical damage to tissues, but can now be more objectively assessed. These results offer more definitive and quantitative monitoring of response to tissue injury induced pain and inflammation.
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Affiliation(s)
- Priya Ghodasara
- The University of Queensland, School of Veterinary Science, Gatton, Queensland, Australia.,VIDO-InterVac, University of Saskatchewan, Saskatoon, Canada
| | - Nana Satake
- The University of Queensland, School of Veterinary Science, Gatton, Queensland, Australia.,School of Agriculture and Food Sciences, The University of Queensland, Saint Lucia, Queensland, Australia
| | - Pawel Sadowski
- Central Analytical Research Facility, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Steven Kopp
- The University of Queensland, School of Veterinary Science, Gatton, Queensland, Australia
| | - Paul C Mills
- The University of Queensland, School of Veterinary Science, Gatton, Queensland, Australia
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Ren W, Wang T, Hu X, Li Y, Ji Z, Guo H, Cao H, Huang J. Development and application of sequential window acquisition of all theoretical mass spectra data acquisition modes on ultra-high-performance liquid chromatography triple-quadrupole/time-of-flight mass spectrometry for metabolic profiling of amino acids in human plasma. J Sep Sci 2021; 44:4209-4221. [PMID: 34592055 DOI: 10.1002/jssc.202100573] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 09/16/2021] [Accepted: 09/17/2021] [Indexed: 11/06/2022]
Abstract
Accumulating evidence suggests that amino acids are important indicators of nutritional and metabolic status. A high-resolution mass spectrometry method based on sequential window acquisition of all theoretical mass spectra acquisition was developed for the simultaneous determination of 16 amino acids in human plasma. Sample preparation by protein precipitation using a mixture of acetonitrile and formic acid was followed by a BEH Amide column. The superiority of this method was investigated by comparing it to time-of-flight scan and multiple reaction monitoring modes. The limit of detection in sequential window acquisition of all theoretical mass spectra mode for threonine, methionine, histidine, citrulline, and tryptophan is 0.1 ng on the column; for lysine and asparagine is 0.2 ng; for alanine, pyroglutamic acid, leucine, ornithine, and aspartate is 0.5 ng, for arginine is 1.0 ng; for glutamate and serine is 2.0 ng; for glutamine is 10.0 ng. This method was linear in the range 0.8-40 μg/mL for arginine, citrulline, glutamate, histidine, leucine, methionine, pyroglutamic acid, threonine, tryptophan; 2-100 μg/mL for asparagine, aspartate, lysine, ornithine, serine; and 4-200 μg/mL for alanine, glutamine with good accuracy and precision. Significantly different levels in 11 amino acids were observed between childhood and adulthood, representing the growth and development of individuals relating to the level of amino acids.
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Affiliation(s)
- Wenbo Ren
- Department of Laboratory Medicine, the First Hospital of Jilin University, Jilin University, Changchun, P. R. China
| | - Tingting Wang
- Department of Laboratory Medicine, the First Hospital of Jilin University, Jilin University, Changchun, P. R. China
| | - Xiuhong Hu
- Department of Laboratory Medicine, the First Hospital of Jilin University, Jilin University, Changchun, P. R. China
| | - Yanyan Li
- Department of Laboratory Medicine, the First Hospital of Jilin University, Jilin University, Changchun, P. R. China
| | - Zhengchao Ji
- Department of Laboratory Medicine, the First Hospital of Jilin University, Jilin University, Changchun, P. R. China
| | - Haiyang Guo
- Department of Laboratory Medicine, the First Hospital of Jilin University, Jilin University, Changchun, P. R. China
| | - Haiwei Cao
- Department of Laboratory Medicine, the First Hospital of Jilin University, Jilin University, Changchun, P. R. China
| | - Jing Huang
- Department of Laboratory Medicine, the First Hospital of Jilin University, Jilin University, Changchun, P. R. China
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Majuta SN, DeBastiani A, Li P, Valentine SJ. Combining Field-Enabled Capillary Vibrating Sharp-Edge Spray Ionization with Microflow Liquid Chromatography and Mass Spectrometry to Enhance 'Omics Analyses. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:473-485. [PMID: 33417454 PMCID: PMC8132193 DOI: 10.1021/jasms.0c00376] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
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 state-of-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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Affiliation(s)
- Sandra N. Majuta
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown WV 26501
| | - Anthony DeBastiani
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown WV 26501
| | - Peng Li
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown WV 26501
| | - Stephen J. Valentine
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown WV 26501
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Pouliquen DL, Boissard A, Coqueret O, Guette C. Biomarkers of tumor invasiveness in proteomics (Review). Int J Oncol 2020; 57:409-432. [PMID: 32468071 PMCID: PMC7307599 DOI: 10.3892/ijo.2020.5075] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 05/07/2020] [Indexed: 12/13/2022] Open
Abstract
Over the past two decades, quantitative proteomics has emerged as an important tool for deciphering the complex molecular events involved in cancers. The number of references involving studies on the cancer metastatic process has doubled since 2010, while the last 5 years have seen the development of novel technologies combining deep proteome coverage capabilities with quantitative consistency and accuracy. To highlight key findings within this huge amount of information, the present review identified a list of tumor invasive biomarkers based on both the literature and data collected on a biocollection of experimental cell lines, tumor models of increasing invasiveness and tumor samples from patients with colorectal or breast cancer. Crossing these different data sources led to 76 proteins of interest out of 1,245 mentioned in the literature. Information on these proteins can potentially be translated into clinical prospects, since they represent potential targets for the development and evaluation of innovative therapies, alone or in combination. Herein, a systematical review of the biology of each of these proteins, including their specific subcellular/extracellular or multiple localizations is presented. Finally, as an important advantage of quantitative proteomics is the ability to provide data on all these molecules simultaneously in cell pellets, body fluids or paraffin‑embedded sections of tumors/invaded tissues, the significance of some of their interconnections is discussed.
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Affiliation(s)
| | - Alice Boissard
- Paul Papin ICO Cancer Center, CRCINA, Inserm, Université d'Angers, F‑44000 Nantes, France
| | | | - Catherine Guette
- Paul Papin ICO Cancer Center, CRCINA, Inserm, Université d'Angers, F‑44000 Nantes, France
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Rice SJ, Liu X, Zhang J, Belani CP. Absolute Quantification of All Identified Plasma Proteins from SWATH Data for Biomarker Discovery. Proteomics 2019; 19:e1800135. [DOI: 10.1002/pmic.201800135] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Revised: 09/27/2018] [Indexed: 02/05/2023]
Affiliation(s)
- Shawn J. Rice
- Penn State Cancer InstitutePenn State College of Medicine Hershey PA 17033 USA
| | - Xin Liu
- Penn State Cancer InstitutePenn State College of Medicine Hershey PA 17033 USA
| | - Jianhong Zhang
- Penn State Cancer InstitutePenn State College of Medicine Hershey PA 17033 USA
| | - Chandra P. Belani
- Penn State Cancer InstitutePenn State College of Medicine Hershey PA 17033 USA
- Department of MedicinePenn State College of Medicine Hershey PA 17033 USA
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Xu Z, Lee A, Nouwens A, Henderson RD, McCombe PA. Mass spectrometry analysis of plasma from amyotrophic lateral sclerosis and control subjects. Amyotroph Lateral Scler Frontotemporal Degener 2018; 19:362-376. [PMID: 29384411 DOI: 10.1080/21678421.2018.1433689] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Mass spectrometry was used to study blood samples from patients with amyotrophic lateral sclerosis (ALS) and healthy controls. Addenbrooke's cognitive examination-III (ACE-III) was used to test for cognitive impairment (CI). Nano liquid chromatography and time of flight mass spectrometry (MS) were performed on samples from 42 ALS patients and 18 healthy controls. SWATH™ proteomic analysis was utilized to look for differences between groups. Western blot analysis was used to study levels of 4 proteins, selected as being of possible interest in ALS, in the MS discovery cohort and a second validation group of 10 ALS patients and 10 healthy controls. INGENUITY PATHWAY ANALYSIS (IPA) was applied to the final proteomic data. Between ALS patients and controls, there were significant differences in the expression of 30 proteins. Between controls and ALS patients without CI, there were significant differences in 15 proteins. Between controls and ALS patients with CI, there were significant differences in 32 proteins. Changes in levels of gelsolin, clusterin, and CD5L were validated by using western blot analysis in the discovery cohort. Changes in the expression of gelsolin, clusterin, and ficolin 3 were replicated in a validation group. In ALS, the LXR/RXR and coagulation pathways were downregulated whereas the complement pathway was upregulated. The proteomic data were used to produce two new networks, centered on IL1 and on NFkB, which showed altered levels in ALS. This study highlights the usefulness of MS of blood samples as a tool to study ALS.
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Affiliation(s)
- Zhouwei Xu
- a The University of Queensland, UQ Centre for Clinical Research , Brisbane , Queensland , Australia
| | - Aven Lee
- a The University of Queensland, UQ Centre for Clinical Research , Brisbane , Queensland , Australia
| | - Amanda Nouwens
- b School of Chemistry and Molecular Biosciences , University of Queensland , Brisbane , Australia , and
| | - Robert David Henderson
- c Department of Neurology , Royal Brisbane & Women's Hospital , Brisbane , Queensland , Australia
| | - Pamela Ann McCombe
- a The University of Queensland, UQ Centre for Clinical Research , Brisbane , Queensland , Australia
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