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Challen B, Cramer R. Advances in ionisation techniques for mass spectrometry-based omics research. Proteomics 2022; 22:e2100394. [PMID: 35709387 DOI: 10.1002/pmic.202100394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 06/09/2022] [Accepted: 06/10/2022] [Indexed: 11/10/2022]
Abstract
Omics analysis by mass spectrometry (MS) is a vast field, with proteomics, metabolomics and lipidomics dominating recent research by exploiting biological MS ionisation techniques. Traditional MS ionisation techniques such as electrospray ionisation have limitations in analyte-specific sensitivity, modes of sampling and throughput, leading to many researchers investigating new ionisation methods for omics research. In this review, we examine the current landscape of these new ionisation techniques, divided into the three groups of (electro)spray-based, laser-based and other miscellaneous ionisation techniques. Due to the wide range of new developments, this review can only provide a starting point for further reading on each ionisation technique, as each have unique benefits, often for specialised applications, which promise beneficial results for different areas in the omics world.
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Affiliation(s)
- Bob Challen
- Department of Chemistry, University of Reading, Whiteknights, Reading, UK
| | - Rainer Cramer
- Department of Chemistry, University of Reading, Whiteknights, Reading, UK
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Glasius M, Thomsen D, Wang K, Iversen LS, Duan J, Huang RJ. Chemical characteristics and sources of organosulfates, organosulfonates, and carboxylic acids in aerosols in urban Xi'an, Northwest China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 810:151187. [PMID: 34756911 DOI: 10.1016/j.scitotenv.2021.151187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 09/30/2021] [Accepted: 10/20/2021] [Indexed: 06/13/2023]
Abstract
We investigated speciation and levels of organosulfates, organosulfonates as well as carboxylic acids in aerosol samples collected during summer (2014) and winter (2014/15) in Xi'an, Northwest China, to improve understanding of composition and sources of organic aerosols in this region heavily affected by air pollution. Organosulfates are formed from reactive gas-phase organic compounds and acidic sulfate aerosols, contributing to secondary organic aerosols, SOA. The aerosol samples show a large diversity in organosulfur species in line with other regions of China, reflecting the high levels and complexity of SOA precursors. In summer samples, organosulfates from isoprene are prevalent due to transport of air masses from southern regions with isoprene-emitting mountain forests. During winter, air masses are local or from areas north of the city with low population density and very low temperatures. The estimated levels of organosulfates and organosulfonates in summer (768 ± 346 ng m-3) and winter samples (938 ± 374 ng m-3) are more similar than expected given the high levels of sulfate and organic carbon in winter, indicating the complexity of organosulfur formation processes. We observed an organosulfonate with molecular weight 214 (C6H14O6S) at high estimated levels (254 ± 232 ng m-3) in winter, but much lower concentrations (12 ± 13 ng m-3) in summer. High levels of organosulfur compounds were mainly observed at aerosol pH below about 2.5. Concentrations of carboxylic acids from oxidation of monoterpenes were low (5.2 ± 2.7 ng m-3 in summer). Phthalic acid was as high as 90 ± 29 ng m-3 during winter and correlated highly with organic carbon, chloride and potassium, indicating a common origin, most likely burning of biomass and plastic-containing waste. Further research is needed to elucidate formation and sources of organosulfates and organosulfonates, as well as the impact on aerosol properties affecting e.g. health effects.
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Affiliation(s)
- Marianne Glasius
- Department of Chemistry, Aarhus University, 8000 Aarhus C, Denmark.
| | - Ditte Thomsen
- Department of Chemistry, Aarhus University, 8000 Aarhus C, Denmark
| | - Kai Wang
- Department of Chemistry, Aarhus University, 8000 Aarhus C, Denmark; Key Laboratory of Plant-Soil Interactions of MOE, College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, China Agricultural University, Beijing 100193, PR China
| | | | - Jing Duan
- State Key Laboratory of Loess and Quaternary Geology (SKLLQG), Center for Excellence in Quaternary Science and Global Change, and Key Laboratory of Aerosol Chemistry and Physics, Institute of Earth Environment, Chinese Academy of Sciences, Xi'an 710061, China
| | - Ru-Jin Huang
- State Key Laboratory of Loess and Quaternary Geology (SKLLQG), Center for Excellence in Quaternary Science and Global Change, and Key Laboratory of Aerosol Chemistry and Physics, Institute of Earth Environment, Chinese Academy of Sciences, Xi'an 710061, China.
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A Procedure for Analyzing the Proteomic Proteomics Profile of Schistosoma mansoni Cercariae. Methods Mol Biol 2021. [PMID: 32451997 DOI: 10.1007/978-1-0716-0635-3_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Schistosomiasis is one of the most important helminthic parasitic infections in the world, with over 700 million people at risk of infection. Species of Schistosoma have a complex life cycle involving the infection of freshwater snails before infecting their mammalian definitive host. Taking about 130,000 lives per annum, S. mansoni is the major cause of intestinal schistosomiasis worldwide. Within Biomphalaria glabrata snails, asexual replication of the parasite gives rise to cercariae larvae. Cercariae actively penetrate the host's skin to complete their life cycle and eventually transform into adult worms. If left untreated, intestinal schistosomiasis can lead to peripheral destruction of the portal vein system, gastric hemorrhage from esophageal varices, as well as hepatic failure. Mass spectrometry (MS) is the method of choice for proteomics analysis. The bottom-up proteomics approach-also known as "shotgun proteomics"-typically includes a protein extraction and solubilization step followed by proteolytic digestion and tandem MS (MS/MS) analysis. Proteins are later identified by peptide de novo sequencing upon MS and MS/MS spectra of digest peptides. In this chapter, we introduce an analytical workflow for proteome profiling of S. mansoni cercariae using bottom-up proteomics. The cercariae were isolated and lysed. Proteins were then extracted, enzymatically digested, and subjected to liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis. Proteins were identified using MaxQuant software. Cercariae are the first life stage of the parasite S. mansoni which humans encounter, and conducting proteomic analysis on this life cycle stage can shed light on possible drug or vaccine candidates to help disable the parasite's ability to infect or arm the immune system for parasite clearance.
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Detection and Identification of Low-Abundant Proteins Using HPE Gels, Fluorescent Stains, and MALDI-ToF-ToF-MS. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2019; 1841:79-93. [PMID: 30259481 DOI: 10.1007/978-1-4939-8695-8_7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Two-dimensional electrophoresis as a complementary approach to gel-free proteomic methods possesses the ability to separate physiologically important isoforms of proteins in an unbiased manner. Frequently, those isoforms are low-abundant regulators, and therefore, detection and identification of low-abundant proteins is highly necessary to exploit this advantage. We describe an experimental sequence of classical operations to process gels but optimized them, in order to identify each detectable protein spot on gel.
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Identification of Pathogenic Bacteria from Public Libraries via Proteomics Analysis. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2019; 16:ijerph16060912. [PMID: 30875719 PMCID: PMC6466425 DOI: 10.3390/ijerph16060912] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 02/25/2019] [Accepted: 03/12/2019] [Indexed: 12/14/2022]
Abstract
Hazardous organisms may thrive on surfaces that are often exposed to human contact, including children’s library books. In this study, swab samples were taken from 42 children’s books collected from four public libraries in Texas and California. Samples were then cultivated in brain–heart infusion (BHI) medium and then in Luria broth (LB) medium containing either ampicillin or kanamycin. All 42 samples (100%) were positive for bacterial growth in normal BHI medium. Furthermore, 35 samples (83.3%) and 20 samples (47.6%) in total were positive in LB medium containing ampicillin or kanamycin, respectively. Bacterial populations were then identified in samples using an Orbitrap Fusion™ Tribrid ™ mass spectrometer, a state-of-the-art proteomic analysis tool. Identified bacterial species grown in ampicillin included Bacillus, Acinetobacter, Pseudomonas, Staphylococcus, Enterobacter, Klebsiella, Serratia, Streptococcus, Escherichia, Salmonella, and Enterococcus. In contrast, identified bacteria grown in kanamycin included Staphylococcus, Streptococcus, Enterococcus, and Bacillus. The presences of pathogenic bacteria species were also confirmed. The results of this study warrant follow up studies to assess the potential health risks of identified pathogens. This study demonstrates the utility of proteomics in identifying environmental pathogenic bacteria for specific public health risk evaluations.
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Maus A, Mignon R, Basile F. Enhanced protein identification using graphite-modified MALDI plates for offline LC-MALDI-MS/MS bottom-up proteomics. Anal Biochem 2018; 545:31-37. [PMID: 29326070 DOI: 10.1016/j.ab.2018.01.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Revised: 12/22/2017] [Accepted: 01/02/2018] [Indexed: 10/18/2022]
Abstract
The use of offline liquid chromatography-matrix assisted laser desorption/ionization (LC-MALDI) tandem mass spectrometry (MS/MS) for bottom-up proteomics offers advantages in terms of cost, ease of use, and the time-decoupled nature of the separation step and the mass analysis. A method was developed to improve the capabilities of LC-MALDI-MS/MS in terms of protein identification in a bottom-up proteomic workflow. Enhanced protein identification is achieved by an increase in the MALDI signal intensity of the precursor peptides brought about by coating the MALDI plate with a thin film of graphite powder. Using the Escherichia coli proteome, it is demonstrated that the graphite-modified MALDI plates used in an offline LC-MALDI-MS/MS bottom-up protocol led to a 50-135% increase in the number of peptide identifications, and a concomitant 21%-105% increase in the number of proteins inferred. We identify factors that lead to improvements in peptide sequence identifications and in the number of unique proteins identified when compared to using an unmodified MALDI plate. These improvements are achieved using a low cost approach that it is easy to implement, requires no hardware/protocol modification, it is compatible with LC and adds no additional analysis time.
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Affiliation(s)
- Anthony Maus
- Department of Chemistry, University of Wyoming, 1000 E. University Ave., Laramie, WY 82072, United States
| | - Rudolph Mignon
- Department of Chemistry, University of Wyoming, 1000 E. University Ave., Laramie, WY 82072, United States
| | - Franco Basile
- Department of Chemistry, University of Wyoming, 1000 E. University Ave., Laramie, WY 82072, United States.
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Nadler WM, Waidelich D, Kerner A, Hanke S, Berg R, Trumpp A, Rösli C. MALDI versus ESI: The Impact of the Ion Source on Peptide Identification. J Proteome Res 2017; 16:1207-1215. [PMID: 28176526 DOI: 10.1021/acs.jproteome.6b00805] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
For mass spectrometry-based proteomic analyses, electrospray ionization (ESI) and matrix-assisted laser desorption/ionization (MALDI) are the commonly used ionization techniques. To investigate the influence of the ion source on peptide detection in large-scale proteomics, an optimized GeLC/MS workflow was developed and applied either with ESI/MS or with MALDI/MS for the proteomic analysis of different human cell lines of pancreatic origin. Statistical analysis of the resulting data set with more than 72 000 peptides emphasized the complementary character of the two methods, as the percentage of peptides identified with both approaches was as low as 39%. Significant differences between the resulting peptide sets were observed with respect to amino acid composition, charge-related parameters, hydrophobicity, and modifications of the detected peptides and could be linked to factors governing the respective ion yields in ESI and MALDI.
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Affiliation(s)
- Wiebke Maria Nadler
- German Cancer Research Center and HI-STEM gGmbH , Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | | | - Alexander Kerner
- German Cancer Research Center and HI-STEM gGmbH , Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Sabrina Hanke
- German Cancer Research Center and HI-STEM gGmbH , Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Regina Berg
- Department of Chemistry, University of Zurich , Winterthurerstr. 190, 8057 Zurich, Switzerland
| | - Andreas Trumpp
- German Cancer Research Center and HI-STEM gGmbH , Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Christoph Rösli
- German Cancer Research Center and HI-STEM gGmbH , Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
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Ruprecht B, Roesli C, Lemeer S, Kuster B. MALDI-TOF and nESI Orbitrap MS/MS identify orthogonal parts of the phosphoproteome. Proteomics 2016; 16:1447-56. [PMID: 26990019 DOI: 10.1002/pmic.201500523] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2015] [Revised: 03/02/2016] [Accepted: 03/11/2016] [Indexed: 01/01/2023]
Abstract
Phosphorylation is a reversible posttranslational protein modification which plays a pivotal role in intracellular signaling. Despite extensive efforts, phosphorylation site mapping of proteomes is still incomplete motivating the exploration of alternative methods that complement existing workflows. In this study, we compared tandem mass spectrometry (MS/MS) on matrix assisted laser desorption/ionization time-of-flight (MALDI-TOF) and nano-electrospray ionization (nESI) Orbitrap instruments with respect to their ability to identify phosphopeptides from complex proteome digests. Phosphopeptides were enriched from tryptic digests of cell lines using Fe-IMAC column chromatography and subjected to LC-MS/MS analysis. We found that the two analytical workflows exhibited considerable orthogonality. For instance, MALDI-TOF MS/MS favored the identification of phosphopeptides encompassing clear motif signatures for acidic residue directed kinases. The extent of orthogonality of the two LC-MS/MS systems was comparable to that of using alternative proteases such as Asp-N, Arg-C, chymotrypsin, Glu-C and Lys-C on just one LC-MS/MS instrument. Notably, MALDI-TOF MS/MS identified an unexpectedly high number and percentage of phosphotyrosine sites (∼20% of all sites), possibly as a direct consequence of more efficient ionization. The data clearly show that LC-MALDI MS/MS can be a useful complement to LC-nESI MS/MS for phosphoproteome mapping and particularly so for acidic and phosphotyrosine containing peptides.
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Affiliation(s)
- Benjamin Ruprecht
- Chair of Proteomics and Bioanalytics, Technische Universität München, Freising, Germany.,Center for Protein Science Munich (CIPSM), Freising, Germany
| | - Christoph Roesli
- HI-STEM - Heidelberg, Institute for Stem Cell Technology and Experimental Medicine gemeinnützige GmbH, Heidelberg, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Simone Lemeer
- Chair of Proteomics and Bioanalytics, Technische Universität München, Freising, Germany.,Center for Protein Science Munich (CIPSM), Freising, Germany
| | - Bernhard Kuster
- Chair of Proteomics and Bioanalytics, Technische Universität München, Freising, Germany.,Center for Protein Science Munich (CIPSM), Freising, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany.,Bavarian Biomolecular Mass Spectrometry Center, Technische Universität München, Freising, Germany
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Depke M, Michalik S, Rabe A, Surmann K, Brinkmann L, Jehmlich N, Bernhardt J, Hecker M, Wollscheid B, Sun Z, Moritz RL, Völker U, Schmidt F. A peptide resource for the analysis of Staphylococcus aureus in host-pathogen interaction studies. Proteomics 2015. [PMID: 26224020 DOI: 10.1002/pmic.201500091] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Staphylococcus aureus is an opportunistic human pathogen, which can cause life-threatening disease. Proteome analyses of the bacterium can provide new insights into its pathophysiology and important facets of metabolic adaptation and, thus, aid the recognition of targets for intervention. However, the value of such proteome studies increases with their comprehensiveness. We present an MS-driven, proteome-wide characterization of the strain S. aureus HG001. Combining 144 high precision proteomic data sets, we identified 19 109 peptides from 2088 distinct S. aureus HG001 proteins, which account for 72% of the predicted ORFs. Peptides were further characterized concerning pI, GRAVY, and detectability scores in order to understand the low peptide coverage of 8.7% (19 109 out of 220 245 theoretical peptides). The high quality peptide-centric spectra have been organized into a comprehensive peptide fragmentation library (SpectraST) and used for identification of S. aureus-typic peptides in highly complex host-pathogen interaction experiments, which significantly improved the number of identified S. aureus proteins compared to a MASCOT search. This effort now allows the elucidation of crucial pathophysiological questions in S. aureus-specific host-pathogen interaction studies through comprehensive proteome analysis. The S. aureus-specific spectra resource developed here also represents an important spectral repository for SRM or for data-independent acquisition MS approaches. All MS data have been deposited in the ProteomeXchange with identifier PXD000702 (http://proteomecentral.proteomexchange.org/dataset/PXD000702).
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Affiliation(s)
- Maren Depke
- ZIK-FunGene Junior Research Group "Applied Proteomics", Interfaculty Institute for Genetics and Functional Genomics, Department of Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Stephan Michalik
- ZIK-FunGene Junior Research Group "Applied Proteomics", Interfaculty Institute for Genetics and Functional Genomics, Department of Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Alexander Rabe
- ZIK-FunGene Junior Research Group "Applied Proteomics", Interfaculty Institute for Genetics and Functional Genomics, Department of Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Kristin Surmann
- Interfaculty Institute for Genetics and Functional Genomics, Department of Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Lars Brinkmann
- Interfaculty Institute for Genetics and Functional Genomics, Department of Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Nico Jehmlich
- Interfaculty Institute for Genetics and Functional Genomics, Department of Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Jörg Bernhardt
- Institute for Microbiology, Ernst-Moritz-Arndt-University Greifswald, Greifswald, Germany
| | - Michael Hecker
- Institute for Microbiology, Ernst-Moritz-Arndt-University Greifswald, Greifswald, Germany
| | - Bernd Wollscheid
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Zhi Sun
- Institute for Systems Biology (ISB), Seattle, WA, USA
| | | | - Uwe Völker
- Interfaculty Institute for Genetics and Functional Genomics, Department of Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Frank Schmidt
- ZIK-FunGene Junior Research Group "Applied Proteomics", Interfaculty Institute for Genetics and Functional Genomics, Department of Functional Genomics, University Medicine Greifswald, Greifswald, Germany
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