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Cai J, Yun Q, Zhang CY, Wang Z, Hinshaw SM, Zhou H, Suhandynata RT. Concatemer Assisted Stoichiometry Analysis (CASA): targeted mass spectrometry for protein quantification. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.26.605382. [PMID: 39091769 PMCID: PMC11291133 DOI: 10.1101/2024.07.26.605382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/04/2024]
Abstract
Large multi-protein machines are central to multiple biological processes. However, stoichiometric determination of protein complex subunits in their native states presents a significant challenge. This study addresses the limitations of current tools in accuracy and precision by introducing concatemer-assisted stoichiometry analysis (CASA). CASA leverages stable isotope-labeled concatemers and liquid chromatography parallel reaction monitoring mass spectrometry (LC-PRM-MS) to achieve robust quantification of proteins with sub-femtomole sensitivity. As a proof-of-concept, CASA was applied to study budding yeast kinetochores. Stoichiometries were determined for ex vivo reconstituted kinetochore components, including the canonical H3 nucleosomes, centromeric (Cse4CENP-A) nucleosomes, centromere proximal factors (Cbf1 and CBF3 complex), inner kinetochore proteins (Mif2CENP-C, Ctf19CCAN complex), and outer kinetochore proteins (KMN network). Absolute quantification by CASA revealed Cse4CENP-A as a cell-cycle controlled limiting factor for kinetochore assembly. These findings demonstrate that CASA is applicable for stoichiometry analysis of multi-protein assemblies.
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Affiliation(s)
- Jiaxi Cai
- Department of Cellular and Molecular Medicine, University of California, San Diego, California
- Department of Bioengineering, University of California, San Diego, California
| | - Quan Yun
- Department of Cellular and Molecular Medicine, University of California, San Diego, California
| | - Cindy Yuxuan Zhang
- Department of Cellular and Molecular Medicine, University of California, San Diego, California
| | - Ziyi Wang
- Department of Cellular and Molecular Medicine, University of California, San Diego, California
| | - Stephen M. Hinshaw
- Department of Chemical and Systems Biology, Stanford University, Palo Alto, California
| | - Huilin Zhou
- Department of Cellular and Molecular Medicine, University of California, San Diego, California
- Department of Bioengineering, University of California, San Diego, California
- Moores Cancer Center, University of California, San Diego, California
| | - Raymond T. Suhandynata
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, California
- Department of Pathology, University of California, San Diego, California
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Stachniuk A, Trzpil A, Czeczko R, Nowicki Ł, Ziomkowska M, Fornal E. Absolute quantification of targeted rabbit liver- and meat tissue-specific peptide markers in highly processed food products. Food Chem 2024; 438:138069. [PMID: 38007955 DOI: 10.1016/j.foodchem.2023.138069] [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: 09/07/2023] [Revised: 11/05/2023] [Accepted: 11/20/2023] [Indexed: 11/28/2023]
Abstract
A highly sensitive and selective method for the simultaneous absolute quantification of peptides unique to rabbit meat- and liver-specific tissue was developed using liquid chromatography - triple quadrupole mass spectrometry. Two rabbit skeletal muscle-specific peptides (SSVFVADPK and PHSHPALTPEQK), three rabbit liver tissue-specific peptides (FNLEALVTHTLPFEK, AILNYVANK, and TELAEPTSTR) and one peptide specific to both rabbit offal and skeletal muscle tissue (AFFGHYLYEVAR) were monitored. Analyses were performed using peptides labelled with stable isotopes (13C and 15N) as internal standards. Fifteen food samples containing rabbit meat and/or liver were analysed to verify compliance of the rabbit meat and liver composition with product labelling. One sample was adulterated with undeclared rabbit liver. The limit of detection and limit of quantification for the selected peptides of interest were in the range of 0.17 to 0.35 ng/mg and 0.57 to 1.17 ng/mg, respectively. The method may be useful for the determination of rabbit meat and liver tissue in highly processed food samples.
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Affiliation(s)
- Anna Stachniuk
- Department of Bioanalytics, Medical University of Lublin, ul. Jaczewskiego 8b, 20-090 Lublin, Poland.
| | - Alicja Trzpil
- Department of Bioanalytics, Medical University of Lublin, ul. Jaczewskiego 8b, 20-090 Lublin, Poland
| | - Renata Czeczko
- Department of Chemistry, University of Live Sciences in Lublin, ul. Akademicka 15, 20-950 Lublin, Poland
| | - Łukasz Nowicki
- Altium International Sp. z o.o, ul. Puławska 303, 02-785 Warszawa, Poland
| | | | - Emilia Fornal
- Department of Bioanalytics, Medical University of Lublin, ul. Jaczewskiego 8b, 20-090 Lublin, Poland
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Lundeen RA, Kennedy JJ, Murillo OD, Ivey RG, Zhao L, Schoenherr RM, Hoofnagle AN, Wang P, Whiteaker JR, Paulovich AG. Monitoring Both Extended and Tryptic Forms of Stable Isotope-Labeled Standard Peptides Provides an Internal Quality Control of Proteolytic Digestion in Targeted Mass Spectrometry-Based Assays. Mol Cell Proteomics 2023; 22:100621. [PMID: 37478973 PMCID: PMC10458721 DOI: 10.1016/j.mcpro.2023.100621] [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: 04/20/2023] [Revised: 07/10/2023] [Accepted: 07/17/2023] [Indexed: 07/23/2023] Open
Abstract
Targeted mass spectrometry (MS)-based proteomic assays, such as multiplexed multiple reaction monitoring (MRM)-MS assays, enable sensitive and specific quantification of proteotypic peptides as stoichiometric surrogates for proteins. Efforts are underway to expand the use of MRM-MS assays in clinical environments, which requires a reliable strategy to monitor proteolytic digestion efficiency within individual samples. Towards this goal, extended stable isotope-labeled standard (SIS) peptides (hE), which incorporate native proteolytic cleavage sites, can be spiked into protein lysates prior to proteolytic (trypsin) digestion, and release of the tryptic SIS peptide (hT) can be monitored. However, hT measurements alone cannot monitor the extent of digestion and may be confounded by matrix effects specific to individual patient samples; therefore, they are not sufficient to monitor sample-to-sample digestion variability. We hypothesized that measuring undigested hE, along with its paired hT, would improve detection of digestion issues compared to only measuring hT. We tested the ratio of the SIS pair measurements, or hE/hT, as a quality control (QC) metric of trypsin digestion for two MRM assays: a direct-MRM (398 targets) and an immuno-MRM (126 targets requiring immunoaffinity peptide enrichment) assay, with extended SIS peptides observable for 54% (216) and 62% (78) of the targets, respectively. We evaluated the quantitative bias for each target in a series of experiments that adversely affected proteolytic digestion (e.g., variable digestion times, pH, and temperature). We identified a subset of SIS pairs (36 for the direct-MRM, 7 for the immuno-MRM assay) for which the hE/hT ratio reliably detected inefficient digestion that resulted in decreased assay sensitivity and unreliable endogenous quantification. The hE/hT ratio was more responsive to a decrease in digestion efficiency than a metric based on hT measurements alone. For clinical-grade MRM-MS assays, this study describes a ready-to-use QC panel and also provides a road map for designing custom QC panels.
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Affiliation(s)
- Rachel A Lundeen
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Jacob J Kennedy
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Oscar D Murillo
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Richard G Ivey
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Lei Zhao
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Regine M Schoenherr
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Andrew N Hoofnagle
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA; Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Pei Wang
- Department of Genetics and Genomic Sciences, Mount Sinai Hospital, New York, New York, USA
| | - Jeffrey R Whiteaker
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA.
| | - Amanda G Paulovich
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA.
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Guo D, Deng X, Gu S, Chen N, Zhang X, Wang S. Online trypsin digestion coupled with LC-MS/MS for detecting of A1 and A2 types of β-casein proteins in pasteurized milk using biomarker peptides. JOURNAL OF FOOD SCIENCE AND TECHNOLOGY 2022; 59:2983-2991. [PMID: 35872738 PMCID: PMC9304457 DOI: 10.1007/s13197-022-05376-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Revised: 01/04/2022] [Accepted: 01/14/2022] [Indexed: 06/15/2023]
Abstract
UNLABELLED Bovine A1-or A2-type β-caseins have attracted a growing interest due to their variation in beta-casomorphin-7 (BCM-7) formation, which may affect health. In the present work, identification and quantification of A1 and A2 types of β-casein proteins at the peptide level was achieved for the first time. An automated and online immobilized trypsin digestion system was employed for high throughput digesting of proteins into peptides. Tryptic peptides were separated and analyzed subsequently by liquid chromatography coupled to mass spectrometry platform. Two specific peptides ranging from the position of 49 to 97 in the peptide chain were selected for the identification and quantification of A1 and A2 β-casein, which covered the different amino acids between them. Synthetic isotopically labeled winged peptides were used for absolute quantification. Compared with traditional in-solution digestion, online digestion shortens digestion times from 2 to 24 h to 4 min. The limits of quantification (LOQ) of A1 and A2 β-casein in pasteurized milk are 0.8 and 2.4 µg/g, respectively. To further demonstrate the applicability of the proposed method, commercial pasteurized milk tests were performed with satisfactory results. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s13197-022-05376-6.
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Affiliation(s)
- Dehua Guo
- Technical Center for Animal, Plant and Food Inspection and Quarantine of Shanghai Customs, 200135 Shanghai, China
| | - Xiaojun Deng
- Technical Center for Animal, Plant and Food Inspection and Quarantine of Shanghai Customs, 200135 Shanghai, China
| | - Shuqing Gu
- Technical Center for Animal, Plant and Food Inspection and Quarantine of Shanghai Customs, 200135 Shanghai, China
| | - Niannian Chen
- Technical Center for Animal, Plant and Food Inspection and Quarantine of Shanghai Customs, 200135 Shanghai, China
| | - Xiaomei Zhang
- Technology Center of Qingdao Customs District, 266002 Qingdao, China
| | - Shuo Wang
- School of Medicine, NanKai University, 300071 Tianjin, China
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Fernández-Metzler C, Ackermann B, Garofolo F, Arnold ME, DeSilva B, Gu H, Laterza O, Mao Y, Rose M, Vazvaei-Smith F, Steenwyk R. Biomarker Assay Validation by Mass Spectrometry. AAPS J 2022; 24:66. [PMID: 35534647 DOI: 10.1208/s12248-022-00707-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 03/31/2022] [Indexed: 11/30/2022] Open
Abstract
Decades of discussion and publication have gone into the guidance from the scientific community and the regulatory agencies on the use and validation of pharmacokinetic and toxicokinetic assays by chromatographic and ligand binding assays for the measurement of drugs and metabolites. These assay validations are well described in the FDA Guidance on Bioanalytical Methods Validation (BMV, 2018). While the BMV included biomarker assay validation, the focus was on understanding the challenges posed in validating biomarker assays and the importance of having reliable biomarker assays when used for regulatory submissions, rather than definition of the appropriate experiments to be performed. Different from PK bioanalysis, analysis of biomarkers can be challenging due to the presence of target analyte(s) in the control matrices used for calibrator and quality control sample preparation, and greater difficulty in procuring appropriate reference standards representative of the endogenous molecule. Several papers have been published offering recommendations for biomarker assay validation. The situational nature of biomarker applications necessitates fit-for-purpose (FFP) assay validation. A unifying theme for FFP analysis is that method validation requirements be consistent with the proposed context of use (COU) for any given biomarker. This communication provides specific recommendations for biomarker assay validation (BAV) by LC-MS, for both small and large molecule biomarkers. The consensus recommendations include creation of a validation plan that contains definition of the COU of the assay, use of the PK assay validation elements that support the COU, and definition of assay validation elements adapted to fit biomarker assays and the acceptance criteria for both.
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Affiliation(s)
| | - Brad Ackermann
- Eli Lilly & Company, Lilly Corporate Center, Indianapolis, IN, 46285, USA
| | - Fabio Garofolo
- BRI - a Frontage Company, 8898 Heather St, Vancouver, British Columbia, V6P 3S8, Canada
| | - Mark E Arnold
- Labcorp Drug Development, 221 Tulip Tree Drive, Westampton, NJ, 08060-5511, USA
| | - Binodh DeSilva
- Bristol-Myers Squibb Co., Route 206 & Province Line Road, Princeton, NJ, 08543, USA
| | - Huidong Gu
- Bristol-Myers Squibb Co., Route 206 & Province Line Road, Princeton, NJ, 08543, USA
| | - Omar Laterza
- Merck and Co Inc., 90 E Scott Ave, Rahway, NJ, 07065, USA
| | - Yan Mao
- Boehringer-Ingelheim Pharmaceuticals, 900 Ridgebury Road, Ridgefield, CT, 06877, USA
| | - Mark Rose
- Gossamer Bio Inc., 3013 Science Park Road, Suite 200, San Diego, CA, 92121, USA
| | | | - Rick Steenwyk
- Pfizer-Retired, 8739 N Homestead Circle, Irons, MI, 49644, USA
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