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Peters-Clarke TM, Coon JJ, Riley NM. Instrumentation at the Leading Edge of Proteomics. Anal Chem 2024; 96:7976-8010. [PMID: 38738990 DOI: 10.1021/acs.analchem.3c04497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/14/2024]
Affiliation(s)
- Trenton M Peters-Clarke
- Department of Chemistry, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
- Department of Biomolecular Chemistry, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
| | - Joshua J Coon
- Department of Chemistry, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
- Department of Biomolecular Chemistry, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
- Morgridge Institute for Research, Madison, Wisconsin 53715, United States
| | - Nicholas M Riley
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
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Tian X, Hopfgartner G. Improved quantification of carbonyl sub-metabolome by liquid chromatography mass spectrometry using a fragment controlled multiplexed isotopic tag. Anal Chim Acta 2024; 1287:342117. [PMID: 38182390 DOI: 10.1016/j.aca.2023.342117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 11/03/2023] [Accepted: 12/04/2023] [Indexed: 01/07/2024]
Abstract
BACKGROUND Carbonyl-containing metabolites are a class of key intermediate in metabolism, which has potentials to be biomarkers. Since their poor ionization, derivatization reagents, such as dansylhydrazine, are usually used to improve the sensitivity and/or to facilitate quantification. However, most current carbonyl derivatization reagents only have two channels, one is isotopically labeled and the other one is non-labeled. To quantify more samples in a run and using data-independent acquisition (DIA) mode to get comprehensive and unbiased mass fragmentation, we proposed a fragment-controlled isotopic tag, called DiMe-FP-NHNH2 (FP) which has five channels: Δ0, Δ3, Δ6, Δ9, and Δ12, thus up to 5 samples can be analyzed in a run. RESULTS The most important improvement is that the FP tag can produce multiple characteristic signals in tandem mass, diagnostic ions and neutral losses, which helps to selectively detect aldehydes/ketones for targeted and untargeted analysis. To exhibit all capabilities of the FP tag, we mimicked an untargeted metabolomics experiment, which comprises two steps. First, discovery step, using Data-Independent Analysis (SWATH-MS) and the labeling of two channels (Δ0 and Δ3), we picked out aldehyde/ketone from the pooled urine samples based on three characteristic signals, including isotope patterns, diagnostic ions, and neutral losses. Second, five-plex quantification, relative and absolute quantification were achieved in a single LC-MS analysis. Notably, because of different nominal masses, the FP tag can be used on any low or high resolution mass spectrometers. SIGNIFICANCE The benefits and performance of the FP tag are demonstrated by the analysis of urine samples collected from patients from a prostate cancer study, in which more than a thousand features were found based on MS1 fingerprint, but only around 120 aldehyde/ketone candidates were confirmed with characteristic signals and nine of which were quantified showing significant differences from healthy and reference urine samples.
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Affiliation(s)
- Xiaobo Tian
- Life Sciences Mass Spectrometry, Department of Inorganic and Analytical Chemistry, University of Geneva, 24 Quai Ernest Ansermet, CH-1211, Geneva 4, Switzerland
| | - Gérard Hopfgartner
- Life Sciences Mass Spectrometry, Department of Inorganic and Analytical Chemistry, University of Geneva, 24 Quai Ernest Ansermet, CH-1211, Geneva 4, Switzerland.
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Abstract
Accurate protein quantification is key to identifying protein markers, regulatory relationships between proteins, and pathophysiological mechanisms. Realizing this potential requires sensitive and deep protein analysis of a large number of samples. Toward this goal, proteomics throughput can be increased by parallelizing the analysis of both precursors and samples using multiplexed data independent acquisition (DIA) implemented by the plexDIA framework: https://plexDIA.slavovlab.net. Here we demonstrate the improved precisions of retention time estimates within plexDIA and how this enables more accurate protein quantification. plexDIA has demonstrated multiplicative gains in throughput, and these gains may be substantially amplified by improving the multiplexing reagents, data acquisition, and interpretation. We discuss future directions for advancing plexDIA, which include engineering optimized mass-tags for high-plexDIA, introducing isotopologous carriers, and developing algorithms that utilize the regular structures of plexDIA data to improve sensitivity, proteome coverage, and quantitative accuracy. These advances in plexDIA will increase the throughput of functional proteomic assays, including quantifying protein conformations, turnover dynamics, modifications states and activities. The sensitivity of these assays will extend to single-cell analysis, thus enabling functional single-cell protein analysis.
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Affiliation(s)
- Jason Derks
- Departments of Bioengineering, Biology, Chemistry and Chemical Biology, Single Cell Proteomics Center, and Barnett Institute, Northeastern University, Boston, Massachusetts 02115, United States
| | - Nikolai Slavov
- Departments of Bioengineering, Biology, Chemistry and Chemical Biology, Single Cell Proteomics Center, and Barnett Institute, Northeastern University, Boston, Massachusetts 02115, United States
- Parallel Squared Technology Institute, Watertown, Massachusetts 02472, United States
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Derks J, Leduc A, Wallmann G, Huffman RG, Willetts M, Khan S, Specht H, Ralser M, Demichev V, Slavov N. Increasing the throughput of sensitive proteomics by plexDIA. Nat Biotechnol 2023; 41:50-59. [PMID: 35835881 PMCID: PMC9839897 DOI: 10.1038/s41587-022-01389-w] [Citation(s) in RCA: 82] [Impact Index Per Article: 82.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Accepted: 06/13/2022] [Indexed: 01/22/2023]
Abstract
Current mass spectrometry methods enable high-throughput proteomics of large sample amounts, but proteomics of low sample amounts remains limited in depth and throughput. To increase the throughput of sensitive proteomics, we developed an experimental and computational framework, called plexDIA, for simultaneously multiplexing the analysis of peptides and samples. Multiplexed analysis with plexDIA increases throughput multiplicatively with the number of labels without reducing proteome coverage or quantitative accuracy. By using three-plex non-isobaric mass tags, plexDIA enables quantification of threefold more protein ratios among nanogram-level samples. Using 1-hour active gradients, plexDIA quantified ~8,000 proteins in each sample of labeled three-plex sets and increased data completeness, reducing missing data more than twofold across samples. Applied to single human cells, plexDIA quantified ~1,000 proteins per cell and achieved 98% data completeness within a plexDIA set while using ~5 minutes of active chromatography per cell. These results establish a general framework for increasing the throughput of sensitive and quantitative protein analysis.
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Affiliation(s)
- Jason Derks
- Departments of Bioengineering, Biology, Chemistry and Chemical Biology, Single Cell Proteomics Center, and Barnett Institute, Northeastern University, Boston, MA, USA.
| | - Andrew Leduc
- Departments of Bioengineering, Biology, Chemistry and Chemical Biology, Single Cell Proteomics Center, and Barnett Institute, Northeastern University, Boston, MA, USA
| | - Georg Wallmann
- Departments of Bioengineering, Biology, Chemistry and Chemical Biology, Single Cell Proteomics Center, and Barnett Institute, Northeastern University, Boston, MA, USA
| | - R Gray Huffman
- Departments of Bioengineering, Biology, Chemistry and Chemical Biology, Single Cell Proteomics Center, and Barnett Institute, Northeastern University, Boston, MA, USA
| | | | - Saad Khan
- Departments of Bioengineering, Biology, Chemistry and Chemical Biology, Single Cell Proteomics Center, and Barnett Institute, Northeastern University, Boston, MA, USA
| | - Harrison Specht
- Departments of Bioengineering, Biology, Chemistry and Chemical Biology, Single Cell Proteomics Center, and Barnett Institute, Northeastern University, Boston, MA, USA
| | - Markus Ralser
- Charité - Universitätsmedizin Berlin, Berlin, Germany
- Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, UK
| | | | - Nikolai Slavov
- Departments of Bioengineering, Biology, Chemistry and Chemical Biology, Single Cell Proteomics Center, and Barnett Institute, Northeastern University, Boston, MA, USA.
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Phlairaharn T, Grégoire S, Woltereck LR, Petrosius V, Furtwängler B, Searle BC, Schoof EM. High Sensitivity Limited Material Proteomics Empowered by Data-Independent Acquisition on Linear Ion Traps. J Proteome Res 2022; 21:2815-2826. [DOI: 10.1021/acs.jproteome.2c00376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Teeradon Phlairaharn
- The Novo Nordisk Foundation Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, Copenhagen 2200, Denmark
- Department of Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Martinsried 82152, Germany
- Department of Chemistry, Technical University of Munich, Munich 80333, Germany
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby 2800, Denmark
- Pelotonia Institute for Immuno-Oncology, The Ohio State University Comprehensive Cancer Center, Columbus, Ohio 43210, United States
| | - Samuel Grégoire
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby 2800, Denmark
- Computational Biology Unit, de Duve Institute, Université Catholique de Louvain, Brussels 1200, Belgium
| | - Lukas R. Woltereck
- Department of Chemistry, Technical University of Munich, Munich 80333, Germany
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby 2800, Denmark
| | - Valdemaras Petrosius
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby 2800, Denmark
| | - Benjamin Furtwängler
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby 2800, Denmark
- The Finsen Laboratory, Rigshospitalet, Faculty of Health Sciences, University of Copenhagen, Copenhagen 2200, Denmark
- Biotech Research and Innovation Center (BRIC), University of Copenhagen, Copenhagen 2200, Denmark
- Novo Nordisk Foundation Center for Stem Cell Biology, DanStem, Faculty of Health Sciences, University of Copenhagen, Copenhagen 2200, Denmark
| | - Brian C. Searle
- Pelotonia Institute for Immuno-Oncology, The Ohio State University Comprehensive Cancer Center, Columbus, Ohio 43210, United States
- Department of Biomedical Informatics, The Ohio State University, Columbus, Ohio 43210, United States
| | - Erwin M. Schoof
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby 2800, Denmark
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Petrosius V, Schoof EM. Recent advances in the field of single-cell proteomics. Transl Oncol 2022; 27:101556. [PMID: 36270102 PMCID: PMC9587008 DOI: 10.1016/j.tranon.2022.101556] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 09/16/2022] [Accepted: 09/21/2022] [Indexed: 11/06/2022] Open
Abstract
The field of single-cell omics is rapidly progressing. Although DNA and RNA sequencing-based methods have dominated the field to date, global proteome profiling has also entered the main stage. Single-cell proteomics was facilitated by advancements in different aspects of mass spectrometry (MS)-based proteomics, such as instrument design, sample preparation, chromatography and ion mobility. Single-cell proteomics by mass spectrometry (scp-MS) has moved beyond being a mere technical development, and is now able to deliver actual biological application and has been successfully applied to characterize different cell states. Here, we review some key developments of scp-MS, provide a background to the field, discuss the various available methods and foresee possible future directions.
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Armbruster M, Grady SF, Arnatt CK, Edwards JL. Isobaric 4-Plex Tagging for Absolute Quantitation of Biological Acids in Diabetic Urine Using Capillary LC-MS/MS. ACS MEASUREMENT SCIENCE AU 2022; 2:287-295. [PMID: 35726255 PMCID: PMC9204807 DOI: 10.1021/acsmeasuresciau.1c00061] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 02/21/2022] [Accepted: 02/22/2022] [Indexed: 06/15/2023]
Abstract
Isobaric labeling in mass spectrometry enables multiplexed absolute quantitation and high throughput, while minimizing full scan spectral complexity. Here, we use 4-plex isobaric labeling with a fixed positive charge tag to improve quantitation and throughput for polar carboxylic acid metabolites. The isobaric tag uses an isotope-encoded neutral loss to create mass-dependent reporters spaced 2 Da apart and was validated for both single- and double-tagged analytes. Tags were synthesized in-house using deuterated formaldehyde and methyl iodide in a total of four steps, producing cost-effective multiplexing. No chromatographic deuterium shifts were observed for single- or double-tagged analytes, producing consistent reporter ratios across each peak. Perfluoropentanoic acid was added to the sample to drastically increase retention of double-tagged analytes on a C18 column. Excess tag was scavenged and extracted using hexadecyl chloroformate after reaction completion. This allowed for removal of excess tag that typically causes ion suppression and column overloading. A total of 54 organic acids were investigated, producing an average linearity of 0.993, retention time relative standard deviation (RSD) of 0.58%, and intensity RSD of 12.1%. This method was used for absolute quantitation of acid metabolites comparing control and type 1 diabetic urine. Absolute quantitation of organic acids was achieved by using one isobaric lane for standards, thereby allowing for analysis of six urine samples in two injections. Quantified acids showed good agreement with previous work, and six significant changes were found. Overall, this method demonstrated 4-plex absolute quantitation of acids in a complex biological sample.
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