1
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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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2
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Shuken SR, Yu Q, Gygi SP. Inserting Pre-analytical Chromatographic Priming Runs Significantly Improves Targeted Pathway Proteomics with Sample Multiplexing. J Proteome Res 2024; 23:1834-1843. [PMID: 38594897 PMCID: PMC11068481 DOI: 10.1021/acs.jproteome.4c00096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/11/2024]
Abstract
GoDig, a platform for targeted pathway proteomics without the need for manual assay scheduling or synthetic standards, is a powerful, flexible, and easy-to-use method that uses tandem mass tags to increase sample throughput up to 18-fold relative to label-free methods. Though the protein-level success rates of GoDig are high, the peptide-level success rates are more limited, hampering assays of harder-to-quantify proteins and site-specific phenomena. To guide the optimization of GoDig assays as well as improvements to the GoDig platform, we created GoDigViewer, a new stand-alone software that provides detailed visualizations of GoDig runs. GoDigViewer guided the implementation of "priming runs," an acquisition mode with significantly higher success rates. In this mode, two or more chromatographic priming runs are automatically performed to improve the accuracy and precision of target elution orders, followed by analytical runs which quantify targets. Using priming runs, success rates exceeded 97% for a list of 400 peptide targets and 95% for a list of 200 targets that are usually not quantified using untargeted mass spectrometry. We used priming runs to establish a quantitative assay of 125 macroautophagy proteins that had a >95% success rate and revealed differences in macroautophagy expression profiles across four human cell lines.
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Affiliation(s)
- Steven R Shuken
- Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, Massachusetts 02115, United States
| | - Qing Yu
- Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, Massachusetts 02115, United States
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, Massachusetts 02115, United States
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3
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Gomez SM, Axtman AD, Willson TM, Major MB, Townsend RR, Sorger PK, Johnson GL. Illuminating function of the understudied druggable kinome. Drug Discov Today 2024; 29:103881. [PMID: 38218213 DOI: 10.1016/j.drudis.2024.103881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Revised: 12/21/2023] [Accepted: 01/09/2024] [Indexed: 01/15/2024]
Abstract
The human kinome, with more than 500 proteins, is crucial for cell signaling and disease. Yet, about one-third of kinases lack in-depth study. The Data and Resource Generating Center for Understudied Kinases has developed multiple resources to address this challenge including creation of a heavy amino acid peptide library for parallel reaction monitoring and quantitation of protein kinase expression, use of understudied kinases tagged with a miniTurbo-biotin ligase to determine interaction networks by proximity-dependent protein biotinylation, NanoBRET probe development for screening chemical tool target specificity in live cells, characterization of small molecule chemical tools inhibiting understudied kinases, and computational tools for defining kinome architecture. These resources are available through the Dark Kinase Knowledgebase, supporting further research into these understudied protein kinases.
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Affiliation(s)
- Shawn M Gomez
- University of North Carolina School of Medicine, Chapel Hill, NC, USA.
| | - Alison D Axtman
- University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Timothy M Willson
- University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Michael B Major
- Washington University School of Medicine in St. Louis, MO, USA
| | - Reid R Townsend
- Washington University School of Medicine in St. Louis, MO, USA
| | | | - Gary L Johnson
- University of North Carolina School of Medicine, Chapel Hill, NC, USA.
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4
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Shuken SR, Yu Q, Gygi SP. Inserting Pre-Analytical Chromatographic Priming Runs Significantly Improves Targeted Pathway Proteomics With Sample Multiplexing. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.08.579551. [PMID: 38370708 PMCID: PMC10871336 DOI: 10.1101/2024.02.08.579551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
GoDig, a recent platform for targeted pathway proteomics without the need for manual assay scheduling or synthetic standard peptides, is a relatively flexible and easy-to-use method that uses tandem mass tags (TMT) to increase sample throughput up to 18-fold relative to label-free targeted proteomics. Though the protein quantification success rate of GoDig is generally high, the peptide-level success rate is more limited, hampering the extension of GoDig to assays of harder-to-quantify proteins and site-specific phenomena. In order to guide the optimization of GoDig assays as well as improvements to the GoDig platform, we created GoDigViewer, a new stand-alone software that provides detailed visualizations of GoDig runs. GoDigViewer guided the implementation of "priming runs," an acquisition mode with significantly higher success rates due to improved elution order calibration. In this mode, one or more chromatographic priming runs are automatically performed to determine accurate and precise target elution orders, followed by analytical runs which quantify targets. Using priming runs, peptide-level quantification success rates exceeded 97% for a list of 400 peptide targets and 95% for a list of 200 targets that are usually not quantified using untargeted mass spectrometry. We used priming runs to establish a quantitative assay of 125 macroautophagy proteins that had a >95% success rate and revealed differences in macroautophagy protein expression profiles across four human cell lines.
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Affiliation(s)
- Steven R. Shuken
- Department of Cell Biology, Harvard Medical School, 240 Longwood Ave, Boston, MA 02115, USA
| | - Qing Yu
- Department of Cell Biology, Harvard Medical School, 240 Longwood Ave, Boston, MA 02115, USA
| | - Steven P. Gygi
- Department of Cell Biology, Harvard Medical School, 240 Longwood Ave, Boston, MA 02115, USA
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5
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Liu X, Fu B, Chen J, Sun Z, Zheng D, Li Z, Gu B, Zhang Y, Lu H. High-throughput intact Glycopeptide quantification strategy with targeted-MS (HTiGQs-target) reveals site-specific IgG N-glycopeptides as biomarkers for hepatic disorder diagnosis and staging. Carbohydr Polym 2024; 325:121499. [PMID: 38008487 DOI: 10.1016/j.carbpol.2023.121499] [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: 08/10/2023] [Revised: 10/12/2023] [Accepted: 10/13/2023] [Indexed: 11/28/2023]
Abstract
Liver disease is one of the leading causes of global mortality, and identifying biomarkers for diagnosing the progression of liver diseases is crucial for improving its outcomes. Targeted mass spectrometry technology is a powerful tool with unique advantages for verifying biomarker candidates and clinical applications. It is particularly useful in validating protein biomarkers with post-translational modifications, eliminating the need for site-specific antibodies. Especially, targeted mass spectrometry technique is particularly critical for translation of glycoproteins into clinical applications as there are no site-specific antibodies for N-glycosylation. Nevertheless, its limitation in analyzing only one sample per run has become apparent when dealing with a large number of clinical samples. Herein, we developed a high-throughput intact N-glycopeptides quantification strategy with targeted-MS (HTiGQs-Target), which allows the validation of 20 samples per run with an average analysis time of only 3 min per sample. We applied HTiGQs-Target in a cohort of 461 serum samples (including 120 healthy controls (HC), 127 chronic hepatitis B (CHB) cases, 106 liver cirrhosis (LC) cases, and 108 hepatocellular carcinomas (HCC) cases) and found that a panel of 10 IgG N-glycopeptides have strong clinical utility in evaluating the severity of the liver disease.
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Affiliation(s)
- Xuejiao Liu
- Liver Cancer Institute of Zhongshan Hospital and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China; Department of Chemistry and NHC Key Laboratory of Glycoconjugates Research, Fudan University, Shanghai 200032, China
| | - Bin Fu
- Department of Chemistry and NHC Key Laboratory of Glycoconjugates Research, Fudan University, Shanghai 200032, China
| | - Jierong Chen
- Laboratory Medicine of Guangdong Provincial People's Hospital and Guangdong, Academy of Medical Sciences, Guangzhou, Guangdong 510000, China
| | - Zhenyu Sun
- Liver Cancer Institute of Zhongshan Hospital and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Dongdong Zheng
- Department of Ultrasound, Fudan University Shanghai Cancer Center, Shanghai, 200032, China
| | - Zhonghua Li
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Bing Gu
- Laboratory Medicine of Guangdong Provincial People's Hospital and Guangdong, Academy of Medical Sciences, Guangzhou, Guangdong 510000, China.
| | - Ying Zhang
- Liver Cancer Institute of Zhongshan Hospital and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China; Department of Chemistry and NHC Key Laboratory of Glycoconjugates Research, Fudan University, Shanghai 200032, China.
| | - Haojie Lu
- Liver Cancer Institute of Zhongshan Hospital and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China; Department of Chemistry and NHC Key Laboratory of Glycoconjugates Research, Fudan University, Shanghai 200032, China.
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6
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Chen YT, Liao WR, Wang HT, Chen HW, Chen SF. Targeted protein quantitation in human body fluids by mass spectrometry. MASS SPECTROMETRY REVIEWS 2023; 42:2379-2403. [PMID: 35702881 DOI: 10.1002/mas.21788] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 01/11/2022] [Accepted: 04/08/2022] [Indexed: 06/15/2023]
Abstract
Human body fluids (biofluids) contain various proteins, some of which reflect individuals' physiological conditions or predict diseases. Therefore, the analysis of biofluids can provide substantial information on novel biomarkers for clinical diagnosis and prognosis. In the past decades, mass spectrometry (MS)-based technologies have been developed as proteomic strategies not only for the identification of protein biomarkers but also for biomarker verification/validation in body fluids for clinical applications. The main advantage of targeted MS-based methodologies is the accurate and specific simultaneous quantitation of multiple biomarkers with high sensitivity. Here, we review MS-based methodologies that are currently used for the targeted quantitation of protein components in human body fluids, especially in plasma, urine, cerebrospinal fluid, and saliva. In addition, the currently used MS-based methodologies are summarized with a specific focus on applicable clinical sample types, MS configurations, and acquisition modes.
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Affiliation(s)
- Yi-Ting Chen
- Department of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- Department of Nephrology, Kidney Research Center, Linkou Medical Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan
- Molecular and Medicine Research Center, Chang Gung University, Taoyuan, Taiwan
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Wan-Rou Liao
- Department of Chemistry, National Taiwan Normal University, Taipei, Taiwan
| | - Hsueh-Ting Wang
- Instrumentation Center, National Taiwan Normal University, Taipei, Taiwan
| | - Hsiao-Wei Chen
- Molecular and Medicine Research Center, Chang Gung University, Taoyuan, Taiwan
| | - Sung-Fang Chen
- Department of Chemistry, National Taiwan Normal University, Taipei, Taiwan
- Instrumentation Center, National Taiwan Normal University, Taipei, Taiwan
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7
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Huffman RG, Leduc A, Wichmann C, Di Gioia M, Borriello F, Specht H, Derks J, Khan S, Khoury L, Emmott E, Petelski AA, Perlman DH, Cox J, Zanoni I, Slavov N. Prioritized mass spectrometry increases the depth, sensitivity and data completeness of single-cell proteomics. Nat Methods 2023; 20:714-722. [PMID: 37012480 PMCID: PMC10172113 DOI: 10.1038/s41592-023-01830-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 02/27/2023] [Indexed: 04/05/2023]
Abstract
Major aims of single-cell proteomics include increasing the consistency, sensitivity and depth of protein quantification, especially for proteins and modifications of biological interest. Here, to simultaneously advance all these aims, we developed prioritized Single-Cell ProtEomics (pSCoPE). pSCoPE consistently analyzes thousands of prioritized peptides across all single cells (thus increasing data completeness) while maximizing instrument time spent analyzing identifiable peptides, thus increasing proteome depth. These strategies increased the sensitivity, data completeness and proteome coverage over twofold. The gains enabled quantifying protein variation in untreated and lipopolysaccharide-treated primary macrophages. Within each condition, proteins covaried within functional sets, including phagosome maturation and proton transport, similarly across both treatment conditions. This covariation is coupled to phenotypic variability in endocytic activity. pSCoPE also enabled quantifying proteolytic products, suggesting a gradient of cathepsin activities within a treatment condition. pSCoPE is freely available and widely applicable, especially for analyzing proteins of interest without sacrificing proteome coverage. Support for pSCoPE is available at http://scp.slavovlab.net/pSCoPE .
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Affiliation(s)
- R Gray Huffman
- Departments of Bioengineering, Biology, Chemistry and Chemical Biology, Single Cell Center and Barnett Institute, Northeastern University, Boston, MA, USA
| | - Andrew Leduc
- Departments of Bioengineering, Biology, Chemistry and Chemical Biology, Single Cell Center and Barnett Institute, Northeastern University, Boston, MA, USA
| | - Christoph Wichmann
- Computational Systems Biochemistry Research Group, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Marco Di Gioia
- Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
| | | | - Harrison Specht
- Departments of Bioengineering, Biology, Chemistry and Chemical Biology, Single Cell Center and Barnett Institute, Northeastern University, Boston, MA, USA
| | - Jason Derks
- Departments of Bioengineering, Biology, Chemistry and Chemical Biology, Single Cell Center and Barnett Institute, Northeastern University, Boston, MA, USA
| | - Saad Khan
- Departments of Bioengineering, Biology, Chemistry and Chemical Biology, Single Cell Center and Barnett Institute, Northeastern University, Boston, MA, USA
| | - Luke Khoury
- Departments of Bioengineering, Biology, Chemistry and Chemical Biology, Single Cell Center and Barnett Institute, Northeastern University, Boston, MA, USA
| | - Edward Emmott
- Departments of Bioengineering, Biology, Chemistry and Chemical Biology, Single Cell Center and Barnett Institute, Northeastern University, Boston, MA, USA
- Centre for Proteome Research, Department of Biochemistry and Systems Biology, University of Liverpool, Liverpool, UK
| | - Aleksandra A Petelski
- Departments of Bioengineering, Biology, Chemistry and Chemical Biology, Single Cell Center and Barnett Institute, Northeastern University, Boston, MA, USA
- Parallel Squared Technology Institute, Watertown, MA, USA
| | - David H Perlman
- Merck Exploratory Sciences Center, Merck Sharp and Dohme Corp., Cambridge, MA, USA
| | - Jürgen Cox
- Computational Systems Biochemistry Research Group, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Ivan Zanoni
- Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
| | - Nikolai Slavov
- Departments of Bioengineering, Biology, Chemistry and Chemical Biology, Single Cell Center and Barnett Institute, Northeastern University, Boston, MA, USA.
- Parallel Squared Technology Institute, Watertown, MA, USA.
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8
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Hu A, Zhang J, Shen H. Progress in Targeted Mass Spectrometry (Parallel Accumulation-Serial Fragmentation) and Its Application in Plasma/Serum Proteomics. Methods Mol Biol 2023; 2628:339-352. [PMID: 36781796 DOI: 10.1007/978-1-0716-2978-9_22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023]
Abstract
Targeted mass spectrometry using multiple reaction monitoring (MRM) or parallel reaction monitoring (PRM) has been commonly used for protein biomarker validation in plasma, serum, or other clinically relevant specimens due to its high specificity, selectivity, and multiplexing capability compared with immunoassays. As the emerging mode termed parallel accumulation-serial fragmentation (prmPASEF) significantly improved analyte throughput (100-1000), sensitivity (attomole level), and acquisition speed, it promises to broaden the application of targeted mass spectrometry to simultaneous biomarker discovery and validation with high accuracy. Here, we summarize the general approach of the MRM and PRM techniques used for serum/plasma proteomics and describe a detailed step-by-step procedure for the development of MRM/PRM assays for secreted proteins.
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Affiliation(s)
- Anqi Hu
- Institutes of Biomedical Sciences and Minhang Hospital, Fudan University, Shanghai, China
| | - Jiayi Zhang
- Institutes of Biomedical Sciences and Minhang Hospital, Fudan University, Shanghai, China
| | - Huali Shen
- Institutes of Biomedical Sciences and Minhang Hospital, Fudan University, Shanghai, China.
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9
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Mun DG, Budhraja R, Bhat FA, Zenka RM, Johnson KL, Moghekar A, Pandey A. Four-dimensional proteomics analysis of human cerebrospinal fluid with trapped ion mobility spectrometry using PASEF. Proteomics 2023; 23:e2200507. [PMID: 36752121 DOI: 10.1002/pmic.202200507] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 02/02/2023] [Accepted: 02/03/2023] [Indexed: 02/09/2023]
Abstract
A quadrupole time-of-flight mass spectrometer coupled with a trapped ion mobility spectrometry (timsTOF) operated in parallel accumulation-serial fragmentation (PASEF) mode has recently emerged as a platform capable of providing four-dimensional (4D) features comprising of elution time, collision cross section (CCS), mass-to-charge ratio, and intensity of peptides. The PASEF mode provides ∼100% ion sampling efficiency both in data-dependent acquisition (DDA) and data-independent acquisition (DIA) modes without sacrificing sensitivity. In addition, targeted measurements using PASEF integrated parallel reaction monitoring (PRM) mode have also been described. However, only limited number of studies have used timsTOF for analysis of clinical samples. Although Orbitrap mass spectrometers have been used for biomarker discovery from cerebrospinal fluid (CSF) in a variety of neurological diseases, these Orbitrap-derived datasets cannot readily be applied for driving experiments on timsTOF mass spectrometers. We generated a catalog of peptides and proteins in human CSF in DDA mode on a timsTOF mass spectrometer and used these data to build a spectral library. This strategy allowed us to use elution times and ion mobility values from the spectral library to design PRM experiments for quantifying previously discovered biomarkers from CSF samples in Alzheimer's disease. When the same samples were analyzed using a DIA approach combined with a spectral library search, a higher number of proteins were identified than in a library-free approach. Overall, we have established a spectral library of CSF as a resource and demonstrated its utility for PRM and DIA studies, which should facilitate studies of neurological disorders.
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Affiliation(s)
- Dong-Gi Mun
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Rohit Budhraja
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Firdous A Bhat
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Roman M Zenka
- Proteomics Core, Mayo Clinic, Rochester, Minnesota, USA
| | | | - Abhay Moghekar
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Akhilesh Pandey
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA.,Manipal Academy of Higher Education, Manipal, Karnataka, India.,Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, USA
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10
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Chan WC, Liu X, Magin RS, Girardi NM, Ficarro SB, Hu W, Tarazona Guzman MI, Starnbach CA, Felix A, Adelmant G, Varca AC, Hu B, Bratt AS, DaSilva E, Schauer NJ, Jaen Maisonet I, Dolen EK, Ayala AX, Marto JA, Buhrlage SJ. Accelerating inhibitor discovery for deubiquitinating enzymes. Nat Commun 2023; 14:686. [PMID: 36754960 PMCID: PMC9908924 DOI: 10.1038/s41467-023-36246-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 01/20/2023] [Indexed: 02/10/2023] Open
Abstract
Deubiquitinating enzymes (DUBs) are an emerging drug target class of ~100 proteases that cleave ubiquitin from protein substrates to regulate many cellular processes. A lack of selective chemical probes impedes pharmacologic interrogation of this important gene family. DUBs engage their cognate ligands through a myriad of interactions. We embrace this structural complexity to tailor a chemical diversification strategy for a DUB-focused covalent library. Pairing our library with activity-based protein profiling as a high-density primary screen, we identify selective hits against 23 endogenous DUBs spanning four subfamilies. Optimization of an azetidine hit yields a probe for the understudied DUB VCPIP1 with nanomolar potency and in-family selectivity. Our success in identifying good chemical starting points as well as structure-activity relationships across the gene family from a modest but purpose-build library challenges current paradigms that emphasize ultrahigh throughput in vitro or virtual screens against an ever-increasing scope of chemical space.
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Affiliation(s)
- Wai Cheung Chan
- Department of Cancer Biology and the Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Xiaoxi Liu
- Department of Cancer Biology and the Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Robert S Magin
- Department of Cancer Biology and the Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Nicholas M Girardi
- Department of Cancer Biology and the Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Scott B Ficarro
- Department of Cancer Biology and the Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Blais Proteomics Center, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Emergent Drug Targets, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Wanyi Hu
- Department of Cancer Biology and the Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Maria I Tarazona Guzman
- Department of Cancer Biology and the Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Cara A Starnbach
- Department of Cancer Biology and the Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Alejandra Felix
- Department of Cancer Biology and the Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Guillaume Adelmant
- Department of Cancer Biology and the Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Blais Proteomics Center, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Anthony C Varca
- Department of Cancer Biology and the Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Bin Hu
- Department of Cancer Biology and the Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Ariana S Bratt
- Department of Cancer Biology and the Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Ethan DaSilva
- Department of Cancer Biology and the Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Nathan J Schauer
- Department of Cancer Biology and the Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Isabella Jaen Maisonet
- Department of Cancer Biology and the Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Emma K Dolen
- Department of Cancer Biology and the Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Anthony X Ayala
- Department of Cancer Biology and the Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Jarrod A Marto
- Department of Cancer Biology and the Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Blais Proteomics Center, Dana-Farber Cancer Institute, Boston, MA, USA.
- Center for Emergent Drug Targets, Dana-Farber Cancer Institute, Boston, MA, USA.
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
| | - Sara J Buhrlage
- Department of Cancer Biology and the Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA.
- Center for Emergent Drug Targets, Dana-Farber Cancer Institute, Boston, MA, USA.
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
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11
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Yu Q, Liu X, Keller MP, Navarrete-Perea J, Zhang T, Fu S, Vaites LP, Shuken SR, Schmid E, Keele GR, Li J, Huttlin EL, Rashan EH, Simcox J, Churchill GA, Schweppe DK, Attie AD, Paulo JA, Gygi SP. Sample multiplexing-based targeted pathway proteomics with real-time analytics reveals the impact of genetic variation on protein expression. Nat Commun 2023; 14:555. [PMID: 36732331 PMCID: PMC9894840 DOI: 10.1038/s41467-023-36269-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 01/20/2023] [Indexed: 02/04/2023] Open
Abstract
Targeted proteomics enables hypothesis-driven research by measuring the cellular expression of protein cohorts related by function, disease, or class after perturbation. Here, we present a pathway-centric approach and an assay builder resource for targeting entire pathways of up to 200 proteins selected from >10,000 expressed proteins to directly measure their abundances, exploiting sample multiplexing to increase throughput by 16-fold. The strategy, termed GoDig, requires only a single-shot LC-MS analysis, ~1 µg combined peptide material, a list of up to 200 proteins, and real-time analytics to trigger simultaneous quantification of up to 16 samples for hundreds of analytes. We apply GoDig to quantify the impact of genetic variation on protein expression in mice fed a high-fat diet. We create several GoDig assays to quantify the expression of multiple protein families (kinases, lipid metabolism- and lipid droplet-associated proteins) across 480 fully-genotyped Diversity Outbred mice, revealing protein quantitative trait loci and establishing potential linkages between specific proteins and lipid homeostasis.
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Affiliation(s)
- Qing Yu
- Department of Cell Biology, Harvard Medical School, Boston, MA, 02115, USA
| | - Xinyue Liu
- Department of Cell Biology, Harvard Medical School, Boston, MA, 02115, USA
| | - Mark P Keller
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | | | - Tian Zhang
- Department of Cell Biology, Harvard Medical School, Boston, MA, 02115, USA
| | - Sipei Fu
- Department of Cell Biology, Harvard Medical School, Boston, MA, 02115, USA
| | - Laura P Vaites
- Department of Cell Biology, Harvard Medical School, Boston, MA, 02115, USA
| | - Steven R Shuken
- Department of Cell Biology, Harvard Medical School, Boston, MA, 02115, USA
| | - Ernst Schmid
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
| | | | - Jiaming Li
- Department of Cell Biology, Harvard Medical School, Boston, MA, 02115, USA
| | - Edward L Huttlin
- Department of Cell Biology, Harvard Medical School, Boston, MA, 02115, USA
| | - Edrees H Rashan
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Judith Simcox
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | | | - Devin K Schweppe
- Department of Genome Sciences, University of Washington, Seattle, WA, 98105, USA
| | - Alan D Attie
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Joao A Paulo
- Department of Cell Biology, Harvard Medical School, Boston, MA, 02115, USA
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, Boston, MA, 02115, USA.
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12
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Liu L, Wang Z, Zhang Q, Mei Y, Li L, Liu H, Wang Z, Yang L. Ion Mobility Mass Spectrometry for the Separation and Characterization of Small Molecules. Anal Chem 2023; 95:134-151. [PMID: 36625109 DOI: 10.1021/acs.analchem.2c02866] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Longchan Liu
- The MOE Key Laboratory of Standardization of Chinese Medicines, The SATCM Key Laboratory of New Resources and Quality Evaluation of Chinese Medicines, The Shanghai Key Laboratory for Compound Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai201203, China
| | - Ziying Wang
- The MOE Key Laboratory of Standardization of Chinese Medicines, The SATCM Key Laboratory of New Resources and Quality Evaluation of Chinese Medicines, The Shanghai Key Laboratory for Compound Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai201203, China
| | - Qian Zhang
- The MOE Key Laboratory of Standardization of Chinese Medicines, The SATCM Key Laboratory of New Resources and Quality Evaluation of Chinese Medicines, The Shanghai Key Laboratory for Compound Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai201203, China
| | - Yuqi Mei
- The MOE Key Laboratory of Standardization of Chinese Medicines, The SATCM Key Laboratory of New Resources and Quality Evaluation of Chinese Medicines, The Shanghai Key Laboratory for Compound Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai201203, China
| | - Linnan Li
- The MOE Key Laboratory of Standardization of Chinese Medicines, The SATCM Key Laboratory of New Resources and Quality Evaluation of Chinese Medicines, The Shanghai Key Laboratory for Compound Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai201203, China
| | - Huwei Liu
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing100871, China
| | - Zhengtao Wang
- The MOE Key Laboratory of Standardization of Chinese Medicines, The SATCM Key Laboratory of New Resources and Quality Evaluation of Chinese Medicines, The Shanghai Key Laboratory for Compound Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai201203, China
| | - Li Yang
- The MOE Key Laboratory of Standardization of Chinese Medicines, The SATCM Key Laboratory of New Resources and Quality Evaluation of Chinese Medicines, The Shanghai Key Laboratory for Compound Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai201203, China.,Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai201203, China
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13
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High-end ion mobility mass spectrometry: A current review of analytical capacity in omics applications and structural investigations. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116761] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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14
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Cifani P, Kentsis A. Quantitative Cell Proteomic Atlas: Pathway-Scale Targeted Mass Spectrometry for High-Resolution Functional Profiling of Cell Signaling. J Proteome Res 2022; 21:2535-2544. [PMID: 36154077 PMCID: PMC10494574 DOI: 10.1021/acs.jproteome.2c00223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
In spite of extensive studies of cellular signaling, many fundamental processes such as pathway integration, cross-talk, and feedback remain poorly understood. To enable integrated and quantitative measurements of cellular biochemical activities, we have developed the Quantitative Cell Proteomics Atlas (QCPA). QCPA consists of panels of targeted mass spectrometry assays to determine the abundance and stoichiometry of regulatory post-translational modifications of sentinel proteins from most known physiologic and pathogenic signaling pathways in human cells. QCPA currently profiles 1 913 peptides from 469 effectors of cell surface signaling, apoptosis, stress response, gene expression, quiescence, and proliferation. For each protein, QCPA includes triplets of isotopically labeled peptides covering known post-translational regulatory sites to determine their stoichiometries and unmodified protein regions to measure total protein abundance. The QCPA framework incorporates analytes to control for technical variability of sample preparation and mass spectrometric analysis, including TrypQuant, a synthetic substrate for accurate quantification of proteolysis efficiency for proteins containing chemically modified residues. The ability to precisely and accurately quantify most known signaling pathways should enable improved chemoproteomic approaches for the comprehensive analysis of cell signaling and clinical proteomics of diagnostic specimens. QCPA is openly available at https://qcpa.mskcc.org.
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Affiliation(s)
- Paolo Cifani
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, 10065 USA
| | - Alex Kentsis
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, 10065 USA
- Tow Center for Developmental Oncology, Department of Pediatrics, Memorial Sloan Kettering Cancer Center, NY, 10065 USA
- Departments of Pediatrics, Pharmacology, and Physiology & Biophysics, Weill Medical College of Cornell University, NY, 10065 USA
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15
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Zhu H, Mellors JS, Chan WC, Thompson JW, Ficarro SB, Tavares I, Bratt AS, Decker J, Krause M, Kruppa G, Buhrlage SJ, Marto JA. On-Chip Preconcentration Microchip Capillary Electrophoresis Based CE-PRM-LIVE for High-Throughput Selectivity Profiling of Deubiquitinase Inhibitors. Anal Chem 2022; 94:9508-9513. [PMID: 35729701 PMCID: PMC10654755 DOI: 10.1021/acs.analchem.2c01337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The family of deubiquitinases (DUBs) comprises ∼100 enzymes that cleave ubiquitin from substrate proteins and thereby regulate key aspects of human physiology. DUBs have recently emerged as disease-relevant and chemically tractable, although currently there are no approved DUB-targeting drugs and most preclinical small molecules are low-potency and/or multitargeted. We paired a novel capillary electrophoresis microchip containing an integrated, "on-chip" C18 bed (SPE-ZipChip) with a TMT version of our recently described PRM-LIVE acquisition scheme on a timsTOF Pro mass spectrometer to facilitate rapid activity-based protein profiling of DUB inhibitors. We demonstrate the ability of the SPE-ZipChip to improve proteome coverage of complex samples as well as the quantitation integrity of CE-PRM-LIVE for TMT labeled samples. These technologies provide a platform to accurately quantify competitive binding of covalent and reversible inhibitors in a multiplexed assay that spans 49 endogenous DUBs in less than 15 min.
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Affiliation(s)
- He Zhu
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
| | - J Scott Mellors
- 908 Devices Inc., Boston, Massachusetts 02210, United States
| | - Wai Cheung Chan
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
| | - J Will Thompson
- 908 Devices Inc., Boston, Massachusetts 02210, United States
| | - Scott B Ficarro
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
| | - Isidoro Tavares
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
| | - Ariana S Bratt
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
| | - Jens Decker
- Bruker Daltonics GmbH & Co. KG, Bremen 28359, Germany
| | | | - Gary Kruppa
- Bruker S.R.O., District Brno-City 61900 Czech Republic
| | - Sara J Buhrlage
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
| | - Jarrod A Marto
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
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16
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Mendes ML, Dittmar G. Targeted proteomics on its way to discovery. Proteomics 2022; 22:e2100330. [PMID: 35816345 DOI: 10.1002/pmic.202100330] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 06/20/2022] [Accepted: 06/27/2022] [Indexed: 11/06/2022]
Abstract
For a long time, targeted and discovery proteomics covered different corners of the detection spectrum, with targeted proteomics focused on small target sets. This changed with the recent advances in highly multiplexed analysis. While discovery proteomics still pushes higher numbers of identified and quantified proteins, the advances in targeted proteomics rose to cover large parts of less complex proteomes or proteomes with low protein detection counts due to dynamic range restrictions, like the blood proteome. These new developments will impact, especially on the field of biomarker discovery and the possibility of using targeted proteomics for diagnostic purposes. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Marta L Mendes
- Proteomics of cellular signalling, Department of Infection and Immunity, Luxembourg Institute of Health, L-1445, Strassen, Luxembourg
| | - Gunnar Dittmar
- Proteomics of cellular signalling, Department of Infection and Immunity, Luxembourg Institute of Health, L-1445, Strassen, Luxembourg.,Department of Life Sciences and Medicine, University of Luxembourg, L-4367, Belvaux, Luxembourg
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17
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Plank MJ. Modern Data Acquisition Approaches in Proteomics Based on Dynamic Instrument Control. J Proteome Res 2022; 21:1209-1217. [PMID: 35362319 DOI: 10.1021/acs.jproteome.2c00096] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Traditionally, data acquisition in mass spectrometry-based proteomics is directed by user-defined parameters and relatively simple decision making, such as selection of the highest MS1 peaks for fragmentation. In recent years, access to two-way-communication with instrument codebases has led to a surge in algorithms instructing more complex decision processes on-the-fly. A closer matching between the time windows for monitoring peptides in targeted proteomics and their actual chromatographic elution peaks has been addressed through dynamic retention time scheduling and through triggered acquisition. Strategies based on real-time database searching and spectral matching have, among others, been used to adjust acquisition parameters for selected peptides for improved quantitative accuracy. While initial studies were mainly performed on a proof-of-concept level, dynamic acquisition approaches recently became more broadly available through software and increasing integration into standard instrument control and are likely to transform the field of proteomics in the coming years.
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Affiliation(s)
- Michael J Plank
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona 85721, United States.,Bio5 Institute, University of Arizona, Tucson, Arizona 85721, United States
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