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Navarrete-Perea J, Li J, Mitchell DC, Chi A. Synthetic Knockout Protein Standard for Evaluating Interference in Tandem Mass Tag-Based Proteomics. Anal Chem 2024; 96:6836-6846. [PMID: 38640495 DOI: 10.1021/acs.analchem.4c00871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/21/2024]
Abstract
Isobaric labeling is widely used for unbiased, proteome-wide studies, and it provides several advantages, such as fewer missing values among samples and higher quantitative precision. However, ion interference may lead to compressed or distorted observed ratios due to the coelution and coanalysis of peptides. Here, we introduced a synthetic KnockOut standard (sKO) for evaluating interference in tandem mass tags-based proteomics. sKO is made by mixing TMTpro-labeled tryptic peptides derived from four nonhuman proteins and a whole human proteome as background at different proportions. We showcased the utility of the sKO standard by exploring ion interference at different peptide concentrations (up to a 30-fold change in abundance) and using a variety of mass spectrometer data acquisition strategies. We also demonstrated that the sKO standard could provide valuable information for the rational design of acquisition strategies to achieve optimal data quality and discussed its potential applications for high-throughput proteomics workflows development.
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Affiliation(s)
| | - Jiaming Li
- Merck & Co., Inc., Cambridge, Massachusetts 02115, United States
| | | | - An Chi
- Merck & Co., Inc., Cambridge, Massachusetts 02115, United States
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Wu Z, Bonneil É, Belford M, Boeser C, Dunyach JJ, Thibault P. Targeted Mass Spectrometry Analyses of Somatic Mutations in Colorectal Cancer Specimens Using Differential Ion Mobility. J Proteome Res 2024; 23:644-652. [PMID: 38153093 DOI: 10.1021/acs.jproteome.3c00444] [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] [Indexed: 12/29/2023]
Abstract
Identification of K-Ras and B-Raf mutations in colorectal cancer (CRC) is essential to predict patients' response to anti-EGFR therapy and formulate appropriate therapeutic strategies to improve prognosis and survival. Here, we combined parallel reaction monitoring (PRM) with high-field asymmetric waveform ion mobility (FAIMS) to enhance mass spectrometry sensitivity and improve the identification of low-abundance K-Ras and B-Raf mutations in biological samples without immunoaffinity enrichment. In targeted LC-MS/MS analyses, FAIMS reduced the occurrence of interfering ions and enhanced precursor ion purity, resulting in a 3-fold improvement in the detection limit for K-Ras and B-Raf mutated peptides. In addition, the ion mobility separation of isomeric peptides using FAIMS facilitated the unambiguous identification of K-Ras G12D and G13D peptides. The application of targeted LC-MS/MS analyses using FAIMS is demonstrated for the detection and quantitation of B-Raf V600E, K-Ras G12D, G13D, and G12V in CRC cell lines and primary specimens.
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Affiliation(s)
- Zhaoguan Wu
- Institute for Research in Immunology and Cancer (IRIC) Université de Montréal, Montréal H3T 1J4, Canada
- Department of Chemistry, Université de Montréal, MIL Campus, Montréal H2 V 0B3, Canada
| | - Éric Bonneil
- Institute for Research in Immunology and Cancer (IRIC) Université de Montréal, Montréal H3T 1J4, Canada
| | - Michael Belford
- ThermoFisher Scientific, San Jose, California 95134, United States
| | - Cornelia Boeser
- ThermoFisher Scientific, San Jose, California 95134, United States
| | | | - Pierre Thibault
- Institute for Research in Immunology and Cancer (IRIC) Université de Montréal, Montréal H3T 1J4, Canada
- Department of Chemistry, Université de Montréal, MIL Campus, Montréal H2 V 0B3, Canada
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Dong KD, Schmid EW, Bomgarden RD, Choi JH, Gygi SP, Yu Q, Paulo JA. Adapting an Isobaric Tag-Labeled Yeast Peptide Standard to Develop Targeted Proteomics Assays. J Proteome Res 2024; 23:142-148. [PMID: 38009700 PMCID: PMC10777125 DOI: 10.1021/acs.jproteome.3c00493] [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: 11/29/2023]
Abstract
Targeted proteomics strategies present a streamlined hypothesis-driven approach to analyze specific sets of pathways or disease related proteins. goDig is a quantitative, targeted tandem mass tag (TMT)-based assay that can measure the relative abundance differences for hundreds of proteins directly from unfractionated mixtures. Specific protein groups or entire pathways of up to 200 proteins can be selected for quantitative profiling, while leveraging sample multiplexing permits the simultaneous analysis of up to 18 samples. Despite these benefits, implementing goDig is not without challenges, as it requires access to an instrument application programming interface (iAPI), an elution order and spectral library, a web-based method builder, and dedicated companion software. In addition, the absence of an example test assay may dissuade researchers from testing or implementing goDig. Here, we repurpose the TKO11 standard─which is commercially available but may also be assembled in-lab─and establish it as a de facto test assay for goDig. We build a proteome-wide goDig yeast library, quantify protein expression across several gene ontology (GO) categories, and compare these results to a fully fractionated yeast gold-standard data set. Essentially, we provide a guide detailing the goDig-based quantification of TKO11, which can also be used as a template for user-defined assays in other species.
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Affiliation(s)
- Kevin D Dong
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Ernst W Schmid
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Ryan D Bomgarden
- Thermo Fisher Scientific, Rockford, Illinois 61101, United States
| | - Jae H Choi
- Thermo Fisher Scientific, Rockford, Illinois 61101, United States
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Qing Yu
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Joao A Paulo
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, United States
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Madern M, Reiter W, Stanek F, Hartl N, Mechtler K, Hartl M. A Causal Model of Ion Interference Enables Assessment and Correction of Ratio Compression in Multiplex Proteomics. Mol Cell Proteomics 2024; 23:100694. [PMID: 38097181 PMCID: PMC10828822 DOI: 10.1016/j.mcpro.2023.100694] [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: 07/05/2023] [Revised: 12/01/2023] [Accepted: 12/11/2023] [Indexed: 01/29/2024] Open
Abstract
Multiplex proteomics using isobaric labeling tags has emerged as a powerful tool for the simultaneous relative quantification of peptides and proteins across multiple experimental conditions. However, the quantitative accuracy of the approach is largely compromised by ion interference, a phenomenon that causes fold changes to appear compressed. The degree of compression is generally unknown, and the contributing factors are poorly understood. In this study, we thoroughly characterized ion interference at the MS2 level using a defined two-proteome experimental system with known ground-truth. We discovered remarkably poor agreement between the apparent precursor purity in the isolation window and the actual level of observed reporter ion interference in MS2 scans-a discrepancy that we found resolved by considering cofragmentation of peptide ions hidden within the spectral "noise" of the MS1 isolation window. To address this issue, we developed a regression modeling strategy to accurately predict reporter ion interference in any dataset. Finally, we demonstrate the utility of our procedure for improved fold change estimation and unbiased PTM site-to-protein normalization. All computational tools and code required to apply this method to any MS2 TMT dataset are documented and freely available.
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Affiliation(s)
- Moritz Madern
- Max Perutz Labs, Mass Spectrometry Facility, Vienna Biocenter Campus (VBC), Vienna, Austria; Department for Biochemistry and Cell Biology, Center for Molecular Biology, University of Vienna, Vienna Biocenter Campus (VBC), Vienna, Austria
| | - Wolfgang Reiter
- Max Perutz Labs, Mass Spectrometry Facility, Vienna Biocenter Campus (VBC), Vienna, Austria; Department for Biochemistry and Cell Biology, Center for Molecular Biology, University of Vienna, Vienna Biocenter Campus (VBC), Vienna, Austria
| | - Florian Stanek
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter Campus (VBC), Vienna, Austria
| | - Natascha Hartl
- Max Perutz Labs, Mass Spectrometry Facility, Vienna Biocenter Campus (VBC), Vienna, Austria
| | - Karl Mechtler
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter Campus (VBC), Vienna, Austria
| | - Markus Hartl
- Max Perutz Labs, Mass Spectrometry Facility, Vienna Biocenter Campus (VBC), Vienna, Austria; Department for Biochemistry and Cell Biology, Center for Molecular Biology, University of Vienna, Vienna Biocenter Campus (VBC), Vienna, Austria.
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Ganji R, Paulo JA, Xi Y, Kline I, Zhu J, Clemen CS, Weihl CC, Purdy JG, Gygi SP, Raman M. The p97-UBXD8 complex regulates ER-Mitochondria contact sites by altering membrane lipid saturation and composition. Nat Commun 2023; 14:638. [PMID: 36746962 PMCID: PMC9902492 DOI: 10.1038/s41467-023-36298-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 01/25/2023] [Indexed: 02/08/2023] Open
Abstract
The intimate association between the endoplasmic reticulum (ER) and mitochondrial membranes at ER-Mitochondria contact sites (ERMCS) is a platform for critical cellular processes, particularly lipid synthesis. How contacts are remodeled and the impact of altered contacts on lipid metabolism remains poorly understood. We show that the p97 AAA-ATPase and its adaptor ubiquitin-X domain adaptor 8 (UBXD8) regulate ERMCS. The p97-UBXD8 complex localizes to contacts and its loss increases contacts in a manner that is dependent on p97 catalytic activity. Quantitative proteomics and lipidomics of ERMCS demonstrates alterations in proteins regulating lipid metabolism and a significant change in membrane lipid saturation upon UBXD8 deletion. Loss of p97-UBXD8 increased membrane lipid saturation via SREBP1 and the lipid desaturase SCD1. Aberrant contacts can be rescued by unsaturated fatty acids or overexpression of SCD1. We find that the SREBP1-SCD1 pathway is negatively impacted in the brains of mice with p97 mutations that cause neurodegeneration. We propose that contacts are exquisitely sensitive to alterations to membrane lipid composition and saturation.
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Affiliation(s)
- Rakesh Ganji
- Department of Developmental Molecular and Chemical Biology, Tufts University School of Medicine, Boston, MA, USA
| | - Joao A Paulo
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Yuecheng Xi
- Department of Immunobiology, BIO5 Institute, University of Arizona College of Medicine, Tucson, AZ, USA
| | - Ian Kline
- Department of Immunobiology, BIO5 Institute, University of Arizona College of Medicine, Tucson, AZ, USA
| | - Jiang Zhu
- Department of Neurology, Washington University School of Medicine, Saint Louis, MO, USA
- Ilumina Inc., San Diego, CA, USA
| | - Christoph S Clemen
- Institute of Aerospace Medicine, German Aerospace Center, Cologne, Germany
- Center for Physiology and Pathophysiology, Institute of Vegetative Physiology, Medical Faculty, University of Cologne, Cologne, Germany
| | - Conrad C Weihl
- Department of Neurology, Washington University School of Medicine, Saint Louis, MO, USA
| | - John G Purdy
- Department of Immunobiology, BIO5 Institute, University of Arizona College of Medicine, Tucson, AZ, USA
| | - Steve P Gygi
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Malavika Raman
- Department of Developmental Molecular and Chemical Biology, Tufts University School of Medicine, Boston, MA, USA.
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Paulo JA. Isobaric labeling: Expanding the breadth, accuracy, depth, and diversity of sample multiplexing. Proteomics 2022; 22:e2200328. [PMID: 36089831 PMCID: PMC10777124 DOI: 10.1002/pmic.202200328] [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: 08/25/2022] [Revised: 08/25/2022] [Accepted: 08/26/2022] [Indexed: 11/10/2022]
Abstract
Isobaric labeling has rapidly become a predominant strategy for proteome-wide abundance measurements. Coupled to mass spectrometry, sample multiplexing techniques using isobaric labeling are unparalleled for profiling proteins and posttranslational modifications across multiple samples in a single experiment. Here, I highlight aspects of isobaric labeling in the context of expanding the breadth of multiplexing, improving quantitative accuracy and proteome depth, and developing a wide range of diverse applications. I underscore two facets that enhance quantitative accuracy and reproducibility, specifically the availability of quality control standards for isobaric labeling experiments and the evolution of data acquisition methods. I also emphasize the necessity for standardized methodologies, particularly for emerging high-throughput workflows. Future developments in sample multiplexing will further strengthen the importance of isobaric labeling for comprehensive proteome profiling.
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Affiliation(s)
- Joao A Paulo
- Department of Cell Biology, Blavatnik Institute at Harvard Medical School, Boston, Massachusetts, USA
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