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Britt HM, Cragnolini T, Khatun S, Hatimy A, James J, Page N, Williams JP, Hughes C, Denny R, Thalassinos K, Vissers JPC. Evaluation of acquisition modes for semi-quantitative analysis by targeted and untargeted mass spectrometry. Rapid Commun Mass Spectrom 2022; 36:e9308. [PMID: 35353398 PMCID: PMC9287043 DOI: 10.1002/rcm.9308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 03/26/2022] [Accepted: 03/27/2022] [Indexed: 06/14/2023]
Abstract
RATIONALE Analyte quantitation by mass spectrometry underpins a diverse range of scientific endeavors. The fast-growing field of mass spectrometer development has resulted in several targeted and untargeted acquisition modes suitable for these applications. By characterizing the acquisition methods available on an ion mobility (IM)-enabled orthogonal acceleration time-of-flight (oa-ToF) instrument, the optimum modes for analyte semi-quantitation can be deduced. METHODS Serial dilutions of commercial metabolite, peptide, or cross-linked peptide analytes were prepared in matrices of human urine or Escherichia coli digest. Each analyte dilution was introduced into an IM separation-enabled oa-ToF mass spectrometer by reversed-phase liquid chromatography and electrospray ionization. Data were acquired for each sample in duplicate using nine different acquisition modes, including four IM-enabled acquisitions modes, available on the mass spectrometer. RESULTS Five (metabolite) or seven (peptide/cross-linked peptide) point calibration curves were prepared for analytes across each of the acquisition modes. A nonlinear response was observed at high concentrations for some modes, attributed to saturation effects. Two correction methods, one MS1 isotope-correction and one MS2 ion intensity-correction, were applied to address this observation, resulting in an up to twofold increase in dynamic range. By averaging the semi-quantitative results across analyte classes, two parameters, linear dynamic range (LDR) and lower limit of quantification (LLOQ), were determined to evaluate each mode. CONCLUSION A comparison of the acquisition modes revealed that data-independent acquisition and parallel reaction monitoring methods are most robust for semi-quantitation when considering achievable LDR and LLOQ. IM-enabled modes exhibited sensitivity increases, but a simultaneous reduction in dynamic range required correction methods to recover. These findings will assist users in identifying the optimum acquisition mode for their analyte quantitation needs, supporting a diverse range of applications and providing guidance for future acquisition mode developments.
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Affiliation(s)
- Hannah M. Britt
- Institute of Structural and Molecular Biology, Division of BiosciencesUniversity College LondonLondonUK
| | - Tristan Cragnolini
- Institute of Structural and Molecular Biology, Division of BiosciencesUniversity College LondonLondonUK
- Institute of Structural and Molecular Biology, Birkbeck CollegeUniversity of LondonLondonUK
| | - Suniya Khatun
- Institute of Structural and Molecular Biology, Division of BiosciencesUniversity College LondonLondonUK
| | - Abubakar Hatimy
- Institute of Structural and Molecular Biology, Division of BiosciencesUniversity College LondonLondonUK
| | - Juliette James
- Institute of Structural and Molecular Biology, Division of BiosciencesUniversity College LondonLondonUK
| | - Nathanael Page
- Institute of Structural and Molecular Biology, Division of BiosciencesUniversity College LondonLondonUK
- LGC GroupTeddingtonUK
| | | | | | | | - Konstantinos Thalassinos
- Institute of Structural and Molecular Biology, Division of BiosciencesUniversity College LondonLondonUK
- Institute of Structural and Molecular Biology, Birkbeck CollegeUniversity of LondonLondonUK
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Vissers JPC, McCullagh M. An Analytical Perspective on Protein Analysis and Discovery Proteomics by Ion Mobility-Mass Spectrometry. Methods Mol Biol 2020; 2084:161-178. [PMID: 31729660 DOI: 10.1007/978-1-0716-0030-6_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Ion mobility combined with mass spectrometry (IM-MS) is a powerful technique for the analysis of biomolecules and complex mixtures. This chapter reviews the current state-of-the-art in ion mobility technology and its application to biology, protein analysis, and quantitative discovery proteomics in particular, from an analytical perspective. IM-MS can be used as a technique to separate mixtures, to determine structural information (rotationally averaged cross-sectional area) and to enhance MS duty cycle and sensitivity. Moreover, IM-MS is ideally suited for hyphenating with liquid chromatography, or other front-end separation techniques such as, GC, microcolumn LC, capillary electrophoresis, and direct analysis, including MALDI and DESI, providing an semiorthogonal layer of separation, which affords the more unambiguous and confident detection of a wide range of analytes. To illustrate these enhancements, as well as recent developments, the principle of in-line IM separation and hyphenation to orthogonal acceleration time-of-flight mass spectrometers are discussed, in addition to the enhancement of biophysical MS-based analysis using typical proteomics and related application examples.
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Gethings LA, Connolly JB. Simplifying the Proteome: Analytical Strategies for Improving Peak Capacity. Adv Exp Med Biol 2019; 1140:501-13. [PMID: 31347067 DOI: 10.1007/978-3-030-15950-4_29] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
The diversity of biological samples and dynamic range of analytes being analyzed can prove to be an analytical challenge and is particularly prevalent to proteomic studies. Maximizing the peak capacity of the workflow employed can extend the dynamic range and increase identification rates. The focus of this chapter is to present means of achieving this for various analytical techniques such as liquid chromatography, mass spectrometry and ion mobility. A combination of these methods can be used as part of a data independent acquisition strategy, thereby limiting issues such as chimericy when analyzing regions of extreme analyte density.
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Jacobsen MD, Beynon RJ, Gethings LA, Claydon AJ, Langridge JI, Vissers JPC, Brown AJP, Hammond DE. Specificity of the osmotic stress response in Candida albicans highlighted by quantitative proteomics. Sci Rep 2018; 8:14492. [PMID: 30262823 PMCID: PMC6160413 DOI: 10.1038/s41598-018-32792-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Accepted: 09/13/2018] [Indexed: 11/18/2022] Open
Abstract
Stress adaptation is critical for the survival of microbes in dynamic environments, and in particular, for fungal pathogens to survive in and colonise host niches. Proteomic analyses have the potential to significantly enhance our understanding of these adaptive responses by providing insight into post-transcriptional regulatory mechanisms that contribute to the outputs, as well as testing presumptions about the regulation of protein levels based on transcript profiling. Here, we used label-free, quantitative mass spectrometry to re-examine the response of the major fungal pathogen of humans, Candida albicans, to osmotic stress. Of the 1,262 proteins that were identified, 84 were down-regulated in response to 1M NaCl, reflecting the decrease in ribosome biogenesis and translation that often accompanies stress. The 64 up-regulated proteins included central metabolic enzymes required for glycerol synthesis, a key osmolyte for this yeast, as well as proteins with functions during stress. These data reinforce the view that adaptation to salt stress involves a transient reduction in ribosome biogenesis and translation together with the accumulation of the osmolyte, glycerol. The specificity of the response to salt stress is highlighted by the small proportion of quantified C. albicans proteins (5%) whose relative elevated abundances were statistically significant.
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Affiliation(s)
- Mette D Jacobsen
- Medical Research Council Centre for Medical Mycology at the University of Aberdeen, Aberdeen Fungal Group, Institute of Medical Sciences, Foresterhill, Aberdeen, AB25 2ZD, United Kingdom
| | - Robert J Beynon
- Centre for Proteome Research, Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool, L697ZB, United Kingdom
| | - Lee A Gethings
- Waters Corporation, Stamford Avenue, Altrincham Road, Wilmslow, SK9 4AX, United Kingdom
| | - Amy J Claydon
- Centre for Proteome Research, Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool, L697ZB, United Kingdom
| | - James I Langridge
- Waters Corporation, Stamford Avenue, Altrincham Road, Wilmslow, SK9 4AX, United Kingdom
| | - Johannes P C Vissers
- Waters Corporation, Stamford Avenue, Altrincham Road, Wilmslow, SK9 4AX, United Kingdom
| | - Alistair J P Brown
- Medical Research Council Centre for Medical Mycology at the University of Aberdeen, Aberdeen Fungal Group, Institute of Medical Sciences, Foresterhill, Aberdeen, AB25 2ZD, United Kingdom.
| | - Dean E Hammond
- Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool, Liverpool, L69 3BX, United Kingdom.
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Moseley MA, Hughes CJ, Juvvadi PR, Soderblom EJ, Lennon S, Perkins SR, Thompson JW, Steinbach WJ, Geromanos SJ, Wildgoose J, Langridge JI, Richardson K, Vissers JPC. Scanning Quadrupole Data-Independent Acquisition, Part A: Qualitative and Quantitative Characterization. J Proteome Res 2017; 17:770-779. [PMID: 28901143 DOI: 10.1021/acs.jproteome.7b00464] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A novel data-independent acquisition (DIA) method incorporating a scanning quadrupole in front of a collision cell and orthogonal acceleration time-of-flight mass analyzer is described. The method has been characterized for the qualitative and quantitative label-free proteomic analysis of complex biological samples. The principle of the scanning quadrupole DIA method is discussed, and analytical instrument characteristics, such as the quadrupole transmission width, scan/integration time, and chromatographic separation, have been optimized in relation to sample complexity for a number of different model proteomes of varying complexity and dynamic range including human plasma, cell lines, and bacteria. In addition, the technological merits over existing DIA approaches are described and contrasted. The qualitative and semiquantitative performance of the method is illustrated for the analysis of relatively simple protein digest mixtures and a well-characterized human cell line sample using untargeted and targeted search strategies. Finally, the results from a human cell line were compared against publicly available data that used similar chromatographic conditions but were acquired with DDA technology and alternative mass analyzer systems. Qualitative comparison showed excellent concordance of results with >90% overlap of the detected proteins.
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Affiliation(s)
- M Arthur Moseley
- Proteomics and Metabolomics Shared Resource Center for Genomic and Computational Biology, Duke University Medical Center , Durham, North Carolina 27710, United States
| | | | - Praveen R Juvvadi
- Division of Pediatric Infectious Diseases, Department of Pediatrics, Duke University Medical Center , Durham, North Carolina 27710, United States
| | - Erik J Soderblom
- Proteomics and Metabolomics Shared Resource Center for Genomic and Computational Biology, Duke University Medical Center , Durham, North Carolina 27710, United States
| | - Sarah Lennon
- Waters Corporation , Wilmslow SK9 4AX, United Kingdom
| | - Simon R Perkins
- Institute of Integrative Biology, University of Liverpool , Liverpool L69 3BX, United Kingdom
| | - J Will Thompson
- Proteomics and Metabolomics Shared Resource Center for Genomic and Computational Biology, Duke University Medical Center , Durham, North Carolina 27710, United States
| | - William J Steinbach
- Division of Pediatric Infectious Diseases, Department of Pediatrics, Duke University Medical Center , Durham, North Carolina 27710, United States.,Department of Molecular Genetics and Microbiology, Duke University Medical Center , Durham, North Carolina 27710, United States
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Hernandez JL, Davda D, Majmudar JD, Won SJ, Prakash A, Choi AI, Martin BR. Correlated S-palmitoylation profiling of Snail-induced epithelial to mesenchymal transition. Mol Biosyst 2017; 12:1799-808. [PMID: 27030425 DOI: 10.1039/c6mb00019c] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Epithelial cells form spatially-organized adhesion complexes that establish polarity gradients, regulate cell proliferation, and direct wound healing. As cells accumulate oncogenic mutations, these key tumor suppression mechanisms are disrupted, eliminating many adhesion complexes and bypassing contact inhibition. The transcription factor Snail is often expressed in malignant cancers, where it promotes transcriptional reprogramming to drive epithelial-mesenchymal transition (EMT) and establishes a more invasive state. S-Palmitoylation describes the fatty-acyl post-translational modification of cysteine residues in proteins, and is required for membrane anchoring, trafficking, localization and function of hundreds of proteins involved in cell growth, polarity, and signaling. Since Snail-expression disrupts apico-basolateral cell polarity, we asked if Snail-dependent transformation induces proteome-wide changes in S-palmitoylation. MCF10A breast cancer cells were retrovirally transduced with Snail and correlated proteome-wide changes in protein abundance and S-palmitoylation were profiled by using stable isotope labeling in cell culture with amino acid (SILAC) mass spectrometry. This analysis identified increased levels of proteins involved in migration, glycolysis, and cell junction remodeling, and decreased levels of proteins involved in cell adhesion. Overall, protein S-palmitoylation is highly correlated with protein abundance, yet for a subset of proteins, this correlation is uncoupled. These findings suggest that Snail-overexpression affects the S-palmitoylation cycle of some proteins, which may participate in cell polarity and tumor suppression.
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Affiliation(s)
- Jeannie L Hernandez
- Department of Chemistry, University of Michigan, 930 N. University Ave., Ann Arbor, MI 48109, USA.
| | - Dahvid Davda
- Department of Chemistry, University of Michigan, 930 N. University Ave., Ann Arbor, MI 48109, USA. and Program in Chemical Biology, University of Michigan, 930 N. University Ave., Ann Arbor, MI 48109, USA
| | - Jaimeen D Majmudar
- Department of Chemistry, University of Michigan, 930 N. University Ave., Ann Arbor, MI 48109, USA.
| | - Sang Joon Won
- Program in Chemical Biology, University of Michigan, 930 N. University Ave., Ann Arbor, MI 48109, USA
| | - Ashesh Prakash
- Department of Chemistry, University of Michigan, 930 N. University Ave., Ann Arbor, MI 48109, USA.
| | - Alexandria I Choi
- Department of Chemistry, University of Michigan, 930 N. University Ave., Ann Arbor, MI 48109, USA.
| | - Brent R Martin
- Department of Chemistry, University of Michigan, 930 N. University Ave., Ann Arbor, MI 48109, USA. and Program in Chemical Biology, University of Michigan, 930 N. University Ave., Ann Arbor, MI 48109, USA
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Abstract
Proteomic tools can only be implemented in clinical settings if high-throughput, automated, sensitive, and accurate methods are developed. This has driven researchers to the edge of mass spectrometry (MS)-based proteomics capacity. Here we provide an overview of recent achievements in mass spectrometric technologies and instruments. This includes development of high and ultra definition-MSE (HDMSE and UDMSE) through implementation of ion mobility (IM) MS towards sensitive and accurate label-free proteomics using ultra performance liquid chromatography (UPLC). Label free UPLC-HDMSE is less expensive than labeled-based quantitative proteomics and has no limits regarding the number of samples that can be analyzed and compared, which is an important requirement for supporting clinical applications.
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Affiliation(s)
- Gustavo Henrique Martins Ferreira Souza
- Mass Spectrometry Applications & Development Laboratory, Waters Corporation, 125, Alphaville Industrial, Barueri, 06455-020, Campinas, São Paulo, SP, Brazil.
| | - Paul C Guest
- Laboratory of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, SP, Brazil
| | - Daniel Martins-de-Souza
- Laboratory of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, SP, Brazil
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Abstract
Proteomics has emerged as a promising field in the post-genomic era. Notwithstanding the great advances provided by gene expression analysis in cancer, the lack of a correlation between gene expression and protein levels has highlighted the need for a proteomic focus on cancer. Although the increasing knowledge regarding cancer biology, a reliable marker to improve diagnosis, prognosis and treatment for cancer patients is not a reality at present. In this review, we address the main considerations regarding proteomics-based studies and their clinical applications on cancer research, highlighting some considerations related to strengths and limitations of proteomics-based studies and its application to clinical practice.
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Affiliation(s)
- Carolina Panis
- Laboratório de Células Tronco, Instituto Nacional de Câncer, INCA, Rio de Janeiro, Brazil; Laboratório de Mediadores Inflamatórios, Universidade Estadual do Oeste do Paraná, UNIOESTE, Campus Francisco Beltrão, Paraná, Brazil.
| | - Luciana Pizzatti
- Laboratório de Biologia Molecular e Proteômica do Sangue - LABMOPS, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | | | - Eliana Abdelhay
- Laboratório de Células Tronco, Instituto Nacional de Câncer, INCA, Rio de Janeiro, Brazil
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Chapman JD, Goodlett DR, Masselon CD. Multiplexed and data-independent tandem mass spectrometry for global proteome profiling. Mass Spectrom Rev 2014; 33:452-70. [PMID: 24281846 DOI: 10.1002/mas.21400] [Citation(s) in RCA: 180] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2012] [Revised: 05/13/2013] [Accepted: 05/15/2013] [Indexed: 05/20/2023]
Abstract
One of the most important early developments in the field of proteomics was the advent of automated data acquisition routines that allowed high-throughput unattended data acquisition during HPLC introduction of peptide mixtures to a tandem mass spectrometer. Prior to this, data acquisition was orders of magnitude less efficient being based entirely on lists of predetermined ions generated in a prior HPLC-MS experiment. This process, known generically as data-dependent analysis, empowered the development of shotgun proteomics where hundreds to thousands of peptide sequences are matched per experiment. In their most popular implementation, the most abundant ionized species from every precursor ion scan at each moment in chromatographic time are successively selected for isolation, activation and tandem mass analysis. While extremely powerful, this strategy has one primary limitation in that detectable dynamic range is restricted (in a top-down manner) to the peptides that ionize the best. To circumvent the serial nature of the data-dependent process and increase detectable dynamic range, the concepts of multiplexed and data-independent acquisition (DIA) have emerged. Multiplexed-data acquisition is based on more efficient co-selection and co-dissociation of multiple precursor ions in parallel, the data from which is subsequently de-convoluted to provide polypeptide sequences for each individual precursor ion. DIA has similar goals, but there is no real-time ion selection based on prior precursor ion scans. Instead, predefined m/z ranges are interrogated either by fragmenting all ions entering the mass spectrometer at every single point in chromatographic time; or by dividing the m/z range into smaller m/z ranges for isolation and fragmentation. These approaches aim to fully utilize the capabilities of mass spectrometers to maximize tandem MS acquisition time and to address the need to expand the detectable dynamic range, lower the limit of detection, and improve the overall confidence of peptide identifications and relative protein quantification measurements. This review covers all aspects of multiplexed- and data-independent tandem mass spectrometry in proteomics, from experimental implementations to advances in software for data interpretation.
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Affiliation(s)
- John D Chapman
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington, 98195-1700
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Gethings LA, Connolly JB. Simplifying the Proteome: Analytical Strategies for Improving Peak Capacity. Advances in Experimental Medicine and Biology 2014; 806:59-77. [DOI: 10.1007/978-3-319-06068-2_3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
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Wickramasekara SI, Zandkarimi F, Morré J, Kirkwood J, Legette L, Jiang Y, Gombart AF, Stevens JF, Maier CS. Electrospray Quadrupole Travelling Wave Ion Mobility Time-of-Flight Mass Spectrometry for the Detection of Plasma Metabolome Changes Caused by Xanthohumol in Obese Zucker (fa/fa) Rats. Metabolites 2013; 3:701-17. [PMID: 24958146 PMCID: PMC3901285 DOI: 10.3390/metabo3030701] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2013] [Revised: 08/01/2013] [Accepted: 08/07/2013] [Indexed: 12/12/2022] Open
Abstract
This study reports on the use of traveling wave ion mobility quadrupole time-of-flight (ToF) mass spectrometry for plasma metabolomics. Plasma metabolite profiles of obese Zucker fa/fa rats were obtained after the administration of different oral doses of Xanthohumol; a hop-derived dietary supplement. Liquid chromatography coupled data independent tandem mass spectrometry (LC-MSE) and LC-ion mobility spectrometry (IMS)-MSE acquisitions were conducted in both positive and negative modes using a Synapt G2 High Definition Mass Spectrometry (HDMS) instrument. This method provides identification of metabolite classes in rat plasma using parallel alternating low energy and high energy collision spectral acquisition modes. Data sets were analyzed using pattern recognition methods. Statistically significant (p < 0.05 and fold change (FC) threshold > 1.5) features were selected to identify the up-/down-regulated metabolite classes. Ion mobility data visualized using drift scope software provided a graphical read-out of differences in metabolite classes.
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Affiliation(s)
| | | | - Jeff Morré
- Department of Chemistry, Oregon State University, Corvallis, OR 97331, USA.
| | - Jay Kirkwood
- Department of Pharmaceutical Sciences, Oregon State University, Corvallis, OR 97331, USA.
| | - LeeCole Legette
- Department of Pharmaceutical Sciences, Oregon State University, Corvallis, OR 97331, USA.
| | - Yuan Jiang
- Department of Statistics, Oregon State University, Corvallis, OR 97331, USA.
| | - Adrian F Gombart
- Linus Pauling Institute, Oregon State University, Corvallis, OR 97331, USA.
| | - Jan F Stevens
- Department of Pharmaceutical Sciences, Oregon State University, Corvallis, OR 97331, USA.
| | - Claudia S Maier
- Department of Chemistry, Oregon State University, Corvallis, OR 97331, USA.
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