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Shi M, Huang C, Chen R, Chen DDY, Yan B. A New Evaluation Metric for Quantitative Accuracy of LC-MS/MS-Based Proteomics with Data-Independent Acquisition. J Proteome Res 2024; 23:3780-3790. [PMID: 39193824 DOI: 10.1021/acs.jproteome.4c00088] [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: 08/29/2024]
Abstract
Data-independent acquisition (DIA) has improved the identification and quantitation coverage of peptides and proteins in liquid chromatography-tandem mass spectrometry-based proteomics. However, different DIA data-processing tools can produce very different identification and quantitation results for the same data set. Currently, benchmarking studies of DIA tools are predominantly focused on comparing the identification results, while the quantitative accuracy of DIA measurements is acknowledged to be important but insufficiently investigated, and the absence of suitable metrics for comparing quantitative accuracy is one of the reasons. A new metric is proposed for the evaluation of quantitative accuracy to avoid the influence of differences in false discovery rate control stringency. The part of the quantitation results with high reliability was acquired from each DIA tool first, and the quantitative accuracy was evaluated by comparing quantification error rates at the same number of accurate ratios. From the results of four benchmark data sets, the proposed metric was shown to be more sensitive to discriminating the quantitative performance of DIA tools. Moreover, the DIA tools with advantages in quantitative accuracy were consistently revealed by this metric. The proposed metric can also help researchers in optimizing algorithms of the same DIA tool and sample preprocessing methods to enhance quantitative accuracy.
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Affiliation(s)
- Mengtian Shi
- College of Pharmaceutical Science, Zhejiang Chinese Medical University, Hangzhou 310053, China
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Hangzhou 310024, China
| | - Chiyuan Huang
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Hangzhou 310024, China
| | - Renhui Chen
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Hangzhou 310024, China
| | - David Da Yong Chen
- Department of Chemistry, University of British Columbia, Vancouver, BC V6T 1Z1, Canada
| | - Binjun Yan
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Hangzhou 310024, China
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2
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Searle B, Shannon A, Teodorescu R, Song NJ, Heil L, Jacob C, Remes P, Li Z, Rubinstein M. Rapid assay development for low input targeted proteomics using a versatile linear ion trap. RESEARCH SQUARE 2024:rs.3.rs-4702746. [PMID: 39070662 PMCID: PMC11275998 DOI: 10.21203/rs.3.rs-4702746/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
Advances in proteomics and mass spectrometry enable the study of limited cell populations, where high-mass accuracy instruments are typically required. While triple quadrupoles offer fast and sensitive low-mass accuracy measurements, these instruments are effectively restricted to targeted proteomics. Linear ion traps (LITs) offer a versatile, cost-effective alternative capable of both targeted and global proteomics. Here, we describe a workflow using a new hybrid quadrupole-LIT instrument that rapidly develops targeted proteomics assays from global data-independent acquisition (DIA) measurements without needing high-mass accuracy. Using an automated software approach for scheduling parallel reaction monitoring assays (PRM), we show consistent quantification across three orders of magnitude in a matched-matrix background. We demonstrate measuring low-level proteins such as transcription factors and cytokines with quantitative linearity below two orders of magnitude in a 1 ng background proteome without requiring stable isotope-labeled standards. From a 1 ng sample, we found clear consistency between proteins in subsets of CD4+ and CD8+ T cells measured using high dimensional flow cytometry and LIT-based proteomics. Based on these results, we believe hybrid quadrupole-LIT instruments represent an economical solution to democratizing mass spectrometry in a wide variety of laboratory settings.
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Affiliation(s)
| | | | | | | | | | | | | | - Zihai Li
- The Ohio State University Comprehensive Cancer Center - James Cancer Hospital and Solove Research Institute
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3
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Plubell DL, Remes PM, Wu CC, Jacob CC, Merrihew GE, Hsu C, Shulman N, MacLean BX, Heil L, Poston K, Montine T, MacCoss MJ. Development of highly multiplex targeted proteomics assays in biofluids using the Stellar mass spectrometer. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.04.597431. [PMID: 38895256 PMCID: PMC11185584 DOI: 10.1101/2024.06.04.597431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
The development of targeted assays that monitor biomedically relevant proteins is an important step in bridging discovery experiments to large scale clinical studies. Targeted assays are currently unable to scale to hundreds or thousands of targets. We demonstrate the generation of large-scale assays using a novel hybrid nominal mass instrument. The scale of these assays is achievable with the Stellar™ mass spectrometer through the accommodation of shifting retention times by real-time alignment, while being sensitive and fast enough to handle many concurrent targets. Assays were constructed using precursor information from gas-phase fractionated (GPF) data-independent acquisition (DIA). We demonstrate the ability to schedule methods from an orbitrap and linear ion trap acquired GPF DIA library and compare the quantification of a matrix-matched calibration curve from orbitrap DIA and linear ion trap parallel reaction monitoring (PRM). Two applications of these proposed workflows are shown with a cerebrospinal fluid (CSF) neurodegenerative disease protein PRM assay and with a Mag-Net enriched plasma extracellular vesicle (EV) protein survey PRM assay.
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Affiliation(s)
- Deanna L Plubell
- Department of Genome Sciences, University of Washington, Seattle WA
| | | | - Christine C Wu
- Department of Genome Sciences, University of Washington, Seattle WA
| | | | | | - Chris Hsu
- Department of Genome Sciences, University of Washington, Seattle WA
| | - Nick Shulman
- Department of Genome Sciences, University of Washington, Seattle WA
| | | | | | - Kathleen Poston
- Department of Neurology & Neurological Sciences, Stanford University, Palo Alto CA, USA
| | - Tom Montine
- Department of Pathology, Stanford University, Palo Alto CA, USA
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4
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Shannon AE, Teodorescu RN, Soon N, Heil LR, Jacob CC, Remes PM, Rubinstein MP, Searle BC. A workflow for targeted proteomics assay development using a versatile linear ion trap. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.31.596891. [PMID: 38853838 PMCID: PMC11160733 DOI: 10.1101/2024.05.31.596891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Advances in proteomics and mass spectrometry have enabled the study of limited cell populations, such as single-cell proteomics, where high-mass accuracy instruments are typically required. While triple quadrupoles offer fast and sensitive nominal resolution measurements, these instruments are effectively limited to targeted proteomics. Linear ion traps (LITs) offer a versatile, cost-effective alternative capable of both targeted and global proteomics. We demonstrate a workflow using a newly released, hybrid quadrupole-LIT instrument for developing targeted proteomics assays from global data-independent acquisition (DIA) measurements without needing high-mass accuracy. Gas-phase fraction-based DIA enables rapid target library generation in the same background chemical matrix as each quantitative injection. Using a new software tool embedded within EncyclopeDIA for scheduling parallel reaction monitoring assays, we show consistent quantification across three orders of magnitude of input material. Using this approach, we demonstrate measuring peptide quantitative linearity down to 25x dilution in a background of only a 1 ng proteome without requiring stable isotope labeled standards. At 1 ng total protein on column, we found clear consistency between immune cell populations measured using flow cytometry and immune markers measured using LIT-based proteomics. We believe hybrid quadrupole-LIT instruments represent an economic solution to democratizing mass spectrometry in a wide variety of laboratory settings.
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5
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Plubell DL, Huang E, Spencer SE, Poston K, Montine TJ, MacCoss MJ. Data Independent Acquisition to Inform the Development of Targeted Proteomics Assays Using a Triple Quadrupole Mass Spectrometer. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.29.596554. [PMID: 38853953 PMCID: PMC11160738 DOI: 10.1101/2024.05.29.596554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Mass spectrometry based targeted proteomics methods provide sensitive and high-throughput analysis of selected proteins. To develop a targeted bottom-up proteomics assay, peptides must be evaluated as proxies for the measurement of a protein or proteoform in a biological matrix. Candidate peptide selection typically relies on predetermined biochemical properties, data from semi-stochastic sampling, or by empirical measurements. These strategies require extensive testing and method refinement due to the difficulties associated with prediction of peptide response in the biological matrix of interest. Gas-phase fractionated (GPF) narrow window data-independent acquisition (DIA) aids in the development of reproducible selected reaction monitoring (SRM) assays by providing matrix-specific information on peptide detectability and quantification by mass spectrometry. To demonstrate the suitability of DIA data for selecting peptide targets, we reimplement a portion of an existing assay to measure 98 Alzheimer's disease proteins in cerebrospinal fluid (CSF). Peptides were selected from GPF-DIA based on signal intensity and reproducibility. The resulting SRM assay exhibits similar quantitative precision to published data, despite the inclusion of different peptides between the assays. This workflow enables development of new assays without additional up-front data acquisition, demonstrated here through generation of a separate assay for an unrelated set of proteins in CSF from the same dataset.
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Affiliation(s)
- Deanna L Plubell
- University of Washington, Department of Genome Sciences, Seattle, WA, 98195, USA
| | - Eric Huang
- University of Washington, Department of Genome Sciences, Seattle, WA, 98195, USA
| | - Sandra E Spencer
- University of Washington, Department of Genome Sciences, Seattle, WA, 98195, USA
| | - Kathleen Poston
- Stanford University, Department of Neurology & Neurological Sciences, Stanford, CA, 94305, USA
| | - Thomas J Montine
- Stanford University, Department of Pathology, Stanford, CA, 94305, USA
| | - Michael J MacCoss
- University of Washington, Department of Genome Sciences, Seattle, WA, 98195, USA
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6
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Wu CC, Tsantilas KA, Park J, Plubell D, Sanders JA, Naicker P, Govender I, Buthelezi S, Stoychev S, Jordaan J, Merrihew G, Huang E, Parker ED, Riffle M, Hoofnagle AN, Noble WS, Poston KL, Montine TJ, MacCoss MJ. Mag-Net: Rapid enrichment of membrane-bound particles enables high coverage quantitative analysis of the plasma proteome. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.06.10.544439. [PMID: 38617345 PMCID: PMC11014469 DOI: 10.1101/2023.06.10.544439] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
Membrane-bound particles in plasma are composed of exosomes, microvesicles, and apoptotic bodies and represent ~1-2% of the total protein composition. Proteomic interrogation of this subset of plasma proteins augments the representation of tissue-specific proteins, representing a "liquid biopsy," while enabling the detection of proteins that would otherwise be beyond the dynamic range of liquid chromatography-tandem mass spectrometry of unfractionated plasma. We have developed an enrichment strategy (Mag-Net) using hyper-porous strong-anion exchange magnetic microparticles to sieve membrane-bound particles from plasma. The Mag-Net method is robust, reproducible, inexpensive, and requires <100 μL plasma input. Coupled to a quantitative data-independent mass spectrometry analytical strategy, we demonstrate that we can collect results for >37,000 peptides from >4,000 plasma proteins with high precision. Using this analytical pipeline on a small cohort of patients with neurodegenerative disease and healthy age-matched controls, we discovered 204 proteins that differentiate (q-value < 0.05) patients with Alzheimer's disease dementia (ADD) from those without ADD. Our method also discovered 310 proteins that were different between Parkinson's disease and those with either ADD or healthy cognitively normal individuals. Using machine learning we were able to distinguish between ADD and not ADD with a mean ROC AUC = 0.98 ± 0.06.
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Affiliation(s)
- Christine C. Wu
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | | | - Jea Park
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Deanna Plubell
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Justin A. Sanders
- Department of Computer Science, University of Washington, Seattle, WA, USA
| | | | | | | | | | | | - Gennifer Merrihew
- Department of Computer Science, University of Washington, Seattle, WA, USA
| | - Eric Huang
- Department of Computer Science, University of Washington, Seattle, WA, USA
| | - Edward D. Parker
- Vision Core Lab, Department of Ophthalmology, University of Washington, Seattle, WA, USA
| | - Michael Riffle
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Andrew N. Hoofnagle
- Department of Lab Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - William S. Noble
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Department of Computer Science, University of Washington, Seattle, WA, USA
| | - Kathleen L. Poston
- Department of Neurology & Neurological Sciences, Stanford University, Palo Alto CA, USA
| | | | - Michael J. MacCoss
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
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7
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Saul MC, Litkowski EM, Hadad N, Dunn AR, Boas SM, Wilcox JAL, Robbins JE, Wu Y, Philip VM, Merrihew GE, Park J, De Jager PL, Bridges DE, Menon V, Bennett DA, Hohman TJ, MacCoss MJ, Kaczorowski CC. Hippocampus Glutathione S Reductase Potentially Confers Genetic Resilience to Cognitive Decline in the AD-BXD Mouse Population. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.09.574219. [PMID: 38260300 PMCID: PMC10802440 DOI: 10.1101/2024.01.09.574219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Alzheimer's disease (AD) is a prevalent and costly age-related dementia. Heritable factors account for 58-79% of variation in late-onset AD, but substantial variation remains in age-of- onset, disease severity, and whether those with high-risk genotypes acquire AD. To emulate the diversity of human populations, we utilized the AD-BXD mouse panel. This genetically diverse resource combines AD genotypes with multiple BXD strains to discover new genetic drivers of AD resilience. Comparing AD-BXD carriers to noncarrier littermates, we computed a novel quantitative metric for resilience to cognitive decline in the AD-BXDs. Our quantitative AD resilience trait was heritable and genetic mapping identified a locus on chr8 associated with resilience to AD mutations that resulted in amyloid brain pathology. Using a hippocampus proteomics dataset, we nominated the mitochondrial glutathione S reductase protein (GR or GSHR) as a resilience factor, finding that the DBA/2J genotype was associated with substantially higher GR abundance. By mapping protein QTLs (pQTLs), we identified synaptic organization and mitochondrial proteins coregulated in trans with a cis-pQTL for GR. We found four coexpression modules correlated with the quantitative resilience score in aged 5XFAD mice using paracliques, which were related to cell structure, protein folding, and postsynaptic densities. Finally, we found significant positive associations between human GSR transcript abundance in the brain and better outcomes on AD-related cognitive and pathology traits in the Religious Orders Study/Memory and Aging project (ROSMAP). Taken together, these data support a framework for resilience in which neuronal antioxidant pathway activity provides for stability of synapses within the hippocampus.
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8
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Harris L, Fondrie WE, Oh S, Noble WS. Evaluating Proteomics Imputation Methods with Improved Criteria. J Proteome Res 2023; 22:3427-3438. [PMID: 37861703 PMCID: PMC10949645 DOI: 10.1021/acs.jproteome.3c00205] [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: 10/21/2023]
Abstract
Quantitative measurements produced by tandem mass spectrometry proteomics experiments typically contain a large proportion of missing values. Missing values hinder reproducibility, reduce statistical power, and make it difficult to compare across samples or experiments. Although many methods exist for imputing missing values, in practice, the most commonly used methods are among the worst performing. Furthermore, previous benchmarking studies have focused on relatively simple measurements of error such as the mean-squared error between imputed and held-out values. Here we evaluate the performance of commonly used imputation methods using three practical, "downstream-centric" criteria. These criteria measure the ability to identify differentially expressed peptides, generate new quantitative peptides, and improve the peptide lower limit of quantification. Our evaluation comprises several experiment types and acquisition strategies, including data-dependent and data-independent acquisition. We find that imputation does not necessarily improve the ability to identify differentially expressed peptides but that it can identify new quantitative peptides and improve the peptide lower limit of quantification. We find that MissForest is generally the best performing method per our downstream-centric criteria. We also argue that existing imputation methods do not properly account for the variance of peptide quantifications and highlight the need for methods that do.
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Affiliation(s)
- Lincoln Harris
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, United States
| | | | - Sewoong Oh
- Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, Washington 98195, United States
| | - William S Noble
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, United States
- Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, Washington 98195, United States
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9
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Heil L, Damoc E, Arrey TN, Pashkova A, Denisov E, Petzoldt J, Peterson AC, Hsu C, Searle BC, Shulman N, Riffle M, Connolly B, MacLean BX, Remes PM, Senko MW, Stewart HI, Hock C, Makarov AA, Hermanson D, Zabrouskov V, Wu CC, MacCoss MJ. Evaluating the Performance of the Astral Mass Analyzer for Quantitative Proteomics Using Data-Independent Acquisition. J Proteome Res 2023; 22:3290-3300. [PMID: 37683181 PMCID: PMC10563156 DOI: 10.1021/acs.jproteome.3c00357] [Citation(s) in RCA: 31] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Indexed: 09/10/2023]
Abstract
We evaluate the quantitative performance of the newly released Asymmetric Track Lossless (Astral) analyzer. Using data-independent acquisition, the Thermo Scientific Orbitrap Astral mass spectrometer quantifies 5 times more peptides per unit time than state-of-the-art Thermo Scientific Orbitrap mass spectrometers, which have long been the gold standard for high-resolution quantitative proteomics. Our results demonstrate that the Orbitrap Astral mass spectrometer can produce high-quality quantitative measurements across a wide dynamic range. We also use a newly developed extracellular vesicle enrichment protocol to reach new depths of coverage in the plasma proteome, quantifying over 5000 plasma proteins in a 60 min gradient with the Orbitrap Astral mass spectrometer.
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Affiliation(s)
- Lilian
R. Heil
- Department
of Genome Sciences, University of Washington, 3720 15th Street NE, Seattle, Washington 98195, United States
| | - Eugen Damoc
- Thermo
Fisher Scientific, Hanna-Kunath
Ste. 11, 28199 Bremen, Germany
| | - Tabiwang N. Arrey
- Thermo
Fisher Scientific, Hanna-Kunath
Ste. 11, 28199 Bremen, Germany
| | - Anna Pashkova
- Thermo
Fisher Scientific, Hanna-Kunath
Ste. 11, 28199 Bremen, Germany
| | - Eduard Denisov
- Thermo
Fisher Scientific, Hanna-Kunath
Ste. 11, 28199 Bremen, Germany
| | - Johannes Petzoldt
- Thermo
Fisher Scientific, Hanna-Kunath
Ste. 11, 28199 Bremen, Germany
| | | | - Chris Hsu
- Department
of Genome Sciences, University of Washington, 3720 15th Street NE, Seattle, Washington 98195, United States
| | - 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
| | - Nicholas Shulman
- Department
of Genome Sciences, University of Washington, 3720 15th Street NE, Seattle, Washington 98195, United States
| | - Michael Riffle
- Department
of Genome Sciences, University of Washington, 3720 15th Street NE, Seattle, Washington 98195, United States
| | - Brian Connolly
- Department
of Genome Sciences, University of Washington, 3720 15th Street NE, Seattle, Washington 98195, United States
| | - Brendan X. MacLean
- Department
of Genome Sciences, University of Washington, 3720 15th Street NE, Seattle, Washington 98195, United States
| | - Philip M. Remes
- Thermo
Fisher Scientific, 355 River Oaks Parkway, San Jose, California 95134, United States
| | - Michael W. Senko
- Thermo
Fisher Scientific, 355 River Oaks Parkway, San Jose, California 95134, United States
| | - Hamish I. Stewart
- Thermo
Fisher Scientific, Hanna-Kunath
Ste. 11, 28199 Bremen, Germany
| | - Christian Hock
- Thermo
Fisher Scientific, Hanna-Kunath
Ste. 11, 28199 Bremen, Germany
| | | | - Daniel Hermanson
- Thermo
Fisher Scientific, 355 River Oaks Parkway, San Jose, California 95134, United States
| | - Vlad Zabrouskov
- Thermo
Fisher Scientific, 355 River Oaks Parkway, San Jose, California 95134, United States
| | - Christine C. Wu
- Department
of Genome Sciences, University of Washington, 3720 15th Street NE, Seattle, Washington 98195, United States
| | - Michael J. MacCoss
- Department
of Genome Sciences, University of Washington, 3720 15th Street NE, Seattle, Washington 98195, United States
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10
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Huang T, Wang J, Stukalov A, Donovan MKR, Ferdosi S, Williamson L, Just S, Castro G, Cantrell LS, Elgierari E, Benz RW, Huang Y, Motamedchaboki K, Hakimi A, Arrey T, Damoc E, Kreimer S, Farokhzad OC, Batzoglou S, Siddiqui A, Van Eyk JE, Hornburg D. Protein Coronas on Functionalized Nanoparticles Enable Quantitative and Precise Large-Scale Deep Plasma Proteomics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.28.555225. [PMID: 37693476 PMCID: PMC10491250 DOI: 10.1101/2023.08.28.555225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
Background The wide dynamic range of circulating proteins coupled with the diversity of proteoforms present in plasma has historically impeded comprehensive and quantitative characterization of the plasma proteome at scale. Automated nanoparticle (NP) protein corona-based proteomics workflows can efficiently compress the dynamic range of protein abundances into a mass spectrometry (MS)-accessible detection range. This enhances the depth and scalability of quantitative MS-based methods, which can elucidate the molecular mechanisms of biological processes, discover new protein biomarkers, and improve comprehensiveness of MS-based diagnostics. Methods Investigating multi-species spike-in experiments and a cohort, we investigated fold-change accuracy, linearity, precision, and statistical power for the using the Proteograph™ Product Suite, a deep plasma proteomics workflow, in conjunction with multiple MS instruments. Results We show that NP-based workflows enable accurate identification (false discovery rate of 1%) of more than 6,000 proteins from plasma (Orbitrap Astral) and, compared to a gold standard neat plasma workflow that is limited to the detection of hundreds of plasma proteins, facilitate quantification of more proteins with accurate fold-changes, high linearity, and precision. Furthermore, we demonstrate high statistical power for the discovery of biomarkers in small- and large-scale cohorts. Conclusions The automated NP workflow enables high-throughput, deep, and quantitative plasma proteomics investigation with sufficient power to discover new biomarker signatures with a peptide level resolution.
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Affiliation(s)
| | - Jian Wang
- Seer, Inc., Redwood City, CA, 94065 USA
| | | | | | | | | | - Seth Just
- Seer, Inc., Redwood City, CA, 94065 USA
| | | | | | | | | | | | | | | | | | - Eugen Damoc
- Thermo Fisher Scientific, (Bremen) GmbH, Germany
| | - Simion Kreimer
- Advanced Clinical Biosystems Research Institute, Precision Health, Barbra Streisand Women’s Heart Center at the Smidt Heart Institute, Cedars-Sinai Medical Center, 127 S. San Vicente Blvd., Los Angeles, CA, 90048, USA
| | | | | | | | - Jennifer E. Van Eyk
- Advanced Clinical Biosystems Research Institute, Precision Health, Barbra Streisand Women’s Heart Center at the Smidt Heart Institute, Cedars-Sinai Medical Center, 127 S. San Vicente Blvd., Los Angeles, CA, 90048, USA
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11
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Alberti G, Magnaghi LR, Iurato M, Zanoni C, Biesuz R. Colorimetric Paper-Based Analytical Devices (PADs) Backed by Chemometrics for Pd(II) Detection. SENSORS (BASEL, SWITZERLAND) 2023; 23:7425. [PMID: 37687882 PMCID: PMC10490827 DOI: 10.3390/s23177425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 08/23/2023] [Accepted: 08/24/2023] [Indexed: 09/10/2023]
Abstract
This paper presents the development of cheap and selective Paper-based Analytical Devices (PADs) for selective Pd(II) determination from very acidic aqueous solutions. The PADs were obtained by impregnating two cm-side squares of filter paper with an azoic ligand, (2-(tetrazolylazo)-1,8 dihydroxy naphthalene-3,6,-disulphonic acid), termed TazoC. The so-obtained orange TazoC-PADs interact quickly with Pd(II) in aqueous solutions by forming a complex purple-blue-colored already at pH lower than 2. The dye complexes no other metal ions at such an acidic media, making TazoC-PADs highly selective to Pd(II) detection. Besides, at higher pH values, other cations, for example, Cu(II) and Ni(II), can interact with TazoC through the formation of stable and pink-magenta-colored complexes; however, it is possible to quantify Pd(II) in the presence of other cations using a multivariate approach. To this end, UV-vis spectra of the TazoC-PADs after equilibration with the metal ions solutions were registered in the 300-800 nm wavelength range. By applying Partial Least Square regression (PLS), the whole UV-vis spectra of the TazoC-PADs were related to the Pd(II) concentrations both when present alone in solution and also in the presence of Cu(II) and Ni(II). Tailored PLS models obtained with matrix-matched standard solutions correctly predicted Pd(II) concentrations in unknown samples and tap water spiked with the metal cation, making the method promising for quick and economical sensing of Pd(II).
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Affiliation(s)
- Giancarla Alberti
- Department of Chemistry, University of Pavia, Via Taramelli 12, 27100 Pavia, Italy; (L.R.M.); (R.B.)
| | - Lisa Rita Magnaghi
- Department of Chemistry, University of Pavia, Via Taramelli 12, 27100 Pavia, Italy; (L.R.M.); (R.B.)
- Unità di Ricerca di Pavia, Consorzio Interuniversitario Nazionale per la Scienza e Tecnologia dei Materiali (INSTM), Via G. Giusti 9, 50121 Firenze, Italy
| | - Marzia Iurato
- Department of Chemistry, University of Pavia, Via Taramelli 12, 27100 Pavia, Italy; (L.R.M.); (R.B.)
| | - Camilla Zanoni
- Department of Chemistry, University of Pavia, Via Taramelli 12, 27100 Pavia, Italy; (L.R.M.); (R.B.)
| | - Raffaela Biesuz
- Department of Chemistry, University of Pavia, Via Taramelli 12, 27100 Pavia, Italy; (L.R.M.); (R.B.)
- Unità di Ricerca di Pavia, Consorzio Interuniversitario Nazionale per la Scienza e Tecnologia dei Materiali (INSTM), Via G. Giusti 9, 50121 Firenze, Italy
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12
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Heil LR, Remes PM, Canterbury JD, Yip P, Barshop WD, Wu CC, MacCoss MJ. Dynamic Data-Independent Acquisition Mass Spectrometry with Real-Time Retrospective Alignment. Anal Chem 2023; 95:11854-11858. [PMID: 37527417 PMCID: PMC10517878 DOI: 10.1021/acs.analchem.3c00903] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/03/2023]
Abstract
Data-independent acquisition (DIA) mass spectrometry has grown in popularity in recent years, because of the reproducibility and quantitative rigor of a systematic tandem mass spectrometry (MS/MS) sampling method. However, traditional DIA methods may spend valuable instrument time acquiring MS/MS spectra with no usable information in them, affecting sensitivity and quantitative performance. We developed a DIA strategy that dynamically adjusts the MS/MS windows during the chromatographic separation. The method focuses MS/MS acquisition on the most relevant mass range at each point in time─increasing the quantitative sensitivity by increasing the time spent on each DIA window. We demonstrate an improved lower limit of quantification, on average, without sacrificing the number of peptides detected.
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Affiliation(s)
- Lilian R Heil
- Department of Genome Sciences, University of Washington, 3720 15th Street NE, Seattle, Washington 98195, United States
| | - Philip M Remes
- Thermo Fisher Scientific, 355 River Oaks Parkway, San Jose, California 95134, United States
| | - Jesse D Canterbury
- Thermo Fisher Scientific, 355 River Oaks Parkway, San Jose, California 95134, United States
| | - Ping Yip
- Thermo Fisher Scientific, 355 River Oaks Parkway, San Jose, California 95134, United States
| | - William D Barshop
- Thermo Fisher Scientific, 355 River Oaks Parkway, San Jose, California 95134, United States
| | - Christine C Wu
- Department of Genome Sciences, University of Washington, 3720 15th Street NE, Seattle, Washington 98195, United States
| | - Michael J MacCoss
- Department of Genome Sciences, University of Washington, 3720 15th Street NE, Seattle, Washington 98195, United States
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13
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Heil LR, Damoc E, Arrey TN, Pashkova A, Denisov E, Petzoldt J, Peterson AC, Hsu C, Searle BC, Shulman N, Riffle M, Connolly B, MacLean BX, Remes PM, Senko MW, Stewart HI, Hock C, Makarov AA, Hermanson D, Zabrouskov V, Wu CC, MacCoss MJ. Evaluating the Performance of the Astral Mass Analyzer for Quantitative Proteomics Using Data Independent Acquisition. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.03.543570. [PMID: 37398334 PMCID: PMC10312564 DOI: 10.1101/2023.06.03.543570] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
We evaluate the quantitative performance of the newly released Asymmetric Track Lossless (Astral) analyzer. Using data independent acquisition, the Thermo Scientific™ Orbitrap™ Astral™ mass spectrometer quantifies 5 times more peptides per unit time than state-of-the-art Thermo Scientific™ Orbitrap™ mass spectrometers, which have long been the gold standard for high resolution quantitative proteomics. Our results demonstrate that the Orbitrap Astral mass spectrometer can produce high quality quantitative measurements across a wide dynamic range. We also use a newly developed extra-cellular vesicle enrichment protocol to reach new depths of coverage in the plasma proteome, quantifying over 5,000 plasma proteins in a 60-minute gradient with the Orbitrap Astral mass spectrometer.
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Affiliation(s)
- Lilian R. Heil
- Department of Genome Sciences, University of Washington, 3720 15th Street NE, Seattle, Washington 98195, United States
| | - Eugen Damoc
- Thermo Fisher Scientific, Hanna-Kunath Ste. 11, 28199 Bremen, Germany
| | - Tabiwang N. Arrey
- Thermo Fisher Scientific, Hanna-Kunath Ste. 11, 28199 Bremen, Germany
| | - Anna Pashkova
- Thermo Fisher Scientific, Hanna-Kunath Ste. 11, 28199 Bremen, Germany
| | - Eduard Denisov
- Thermo Fisher Scientific, Hanna-Kunath Ste. 11, 28199 Bremen, Germany
| | - Johannes Petzoldt
- Thermo Fisher Scientific, Hanna-Kunath Ste. 11, 28199 Bremen, Germany
| | | | - Chris Hsu
- Department of Genome Sciences, University of Washington, 3720 15th Street NE, Seattle, Washington 98195, United States
| | - 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
| | - Nicholas Shulman
- Department of Genome Sciences, University of Washington, 3720 15th Street NE, Seattle, Washington 98195, United States
| | - Michael Riffle
- Department of Genome Sciences, University of Washington, 3720 15th Street NE, Seattle, Washington 98195, United States
| | - Brian Connolly
- Department of Genome Sciences, University of Washington, 3720 15th Street NE, Seattle, Washington 98195, United States
| | - Brendan X. MacLean
- Department of Genome Sciences, University of Washington, 3720 15th Street NE, Seattle, Washington 98195, United States
| | - Philip M. Remes
- Thermo Fisher Scientific, 355 River Oaks Parkway, San Jose, California 95134, United States
| | - Michael W. Senko
- Thermo Fisher Scientific, 355 River Oaks Parkway, San Jose, California 95134, United States
| | - Hamish I. Stewart
- Thermo Fisher Scientific, Hanna-Kunath Ste. 11, 28199 Bremen, Germany
| | - Christian Hock
- Thermo Fisher Scientific, Hanna-Kunath Ste. 11, 28199 Bremen, Germany
| | | | - Daniel Hermanson
- Thermo Fisher Scientific, 355 River Oaks Parkway, San Jose, California 95134, United States
| | - Vlad Zabrouskov
- Thermo Fisher Scientific, 355 River Oaks Parkway, San Jose, California 95134, United States
| | - Christine C. Wu
- Department of Genome Sciences, University of Washington, 3720 15th Street NE, Seattle, Washington 98195, United States
| | - Michael J. MacCoss
- Department of Genome Sciences, University of Washington, 3720 15th Street NE, Seattle, Washington 98195, United States
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14
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Allen C, Meinl R, Paez JS, Searle BC, Just S, Pino LK, Fondrie WE. nf-encyclopedia: A Cloud-Ready Pipeline for Chromatogram Library Data-Independent Acquisition Proteomics Workflows. J Proteome Res 2023; 22:2743-2749. [PMID: 37417926 DOI: 10.1021/acs.jproteome.2c00613] [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: 07/08/2023]
Abstract
Data-independent acquisition (DIA) mass spectrometry methods provide systematic and comprehensive quantification of the proteome; yet, relatively few open-source tools are available to analyze DIA proteomics experiments. Fewer still are tools that can leverage gas phase fractionated (GPF) chromatogram libraries to enhance the detection and quantification of peptides in these experiments. Here, we present nf-encyclopedia, an open-source NextFlow pipeline that connects three open-source tools, MSConvert, EncyclopeDIA, and MSstats, to analyze DIA proteomics experiments with or without chromatogram libraries. We demonstrate that nf-encyclopedia is reproducible when run on either a cloud platform or a local workstation and provides robust peptide and protein quantification. Additionally, we found that MSstats enhances protein-level quantitative performance over EncyclopeDIA alone. Finally, we benchmarked the ability of nf-encyclopedia to scale to large experiments in the cloud by leveraging the parallelization of compute resources. The nf-encyclopedia pipeline is available under a permissive Apache 2.0 license; run it on your desktop, cluster, or in the cloud: https://github.com/TalusBio/nf-encyclopedia.
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Affiliation(s)
- Carolyn Allen
- Talus Bioscience, Seattle, Washington 98122, United States
| | - Rico Meinl
- Talus Bioscience, Seattle, Washington 98122, United States
| | | | - Brian C Searle
- Department of Biomedical Informatics, The Ohio State University, Columbus, Ohio 43210, United States
- Pelotonia Institute for Immuno-Oncology, The Ohio State University Comprehensive Cancer Center, Columbus, Ohio 43210, United States
- Proteome Software, Inc., Portland, Oregon 97219, United States
| | - Seth Just
- Proteome Software, Inc., Portland, Oregon 97219, United States
| | - Lindsay K Pino
- Talus Bioscience, Seattle, Washington 98122, United States
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15
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Cao Q, Han M, Zhang Z, Yu C, Xu L, Shi T, Zheng P, Sun J. Novel 15N Metabolic Labeling-Based Large-Scale Absolute Quantitative Proteomics Method for Corynebacterium glutamicum. Anal Chem 2023; 95:4829-4833. [PMID: 36897266 DOI: 10.1021/acs.analchem.2c05524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/11/2023]
Abstract
With fast growth, synthetic biology powers us with the capability to produce high commercial value products in an efficient resource/energy-consuming manner. Comprehensive knowledge of the protein regulatory network of a bacterial host chassis, e.g., the actual amount of the given proteins, is the key to building cell factories for certain target hyperproduction. Many talent methods have been introduced for absolute quantitative proteomics. However, for most cases, a set of reference peptides with isotopic labeling (e.g., SIL, AQUA, QconCAT) or a set of reference proteins (e.g., commercial UPS2 kit) needs to be prepared. The higher cost hinders these methods for large sample research. In this work, we proposed a novel metabolic labeling-based absolute quantification approach (termed nMAQ). The reference Corynebacterium glutamicum strain is metabolically labeled with 15N, and a set of endogenous anchor proteins of the reference proteome is quantified by chemically synthesized light (14N) peptides. The prequantified reference proteome was then utilized as an internal standard (IS) and spiked into the target (14N) samples. SWATH-MS analysis is performed to obtain the absolute expression levels of the proteins from the target cells. The cost for nMAQ is estimated to be less than 10 dollars per sample. We have benchmarked the quantitative performance of the novel method. We believe this method will help with the deep understanding of the intrinsic regulatory mechanism of C. glutamicum during bioengineering and will promote the process of building cell factories for synthetic biology.
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Affiliation(s)
- Qichen Cao
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Systems Biology Centre, Technical Support Core Facilities, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Manman Han
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Systems Biology Centre, Technical Support Core Facilities, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Zuoqing Zhang
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Systems Biology Centre, Technical Support Core Facilities, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Chang Yu
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Systems Biology Centre, Technical Support Core Facilities, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- College of Life Sciences, Nankai University, Tianjin 300350, China
| | - Lida Xu
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Systems Biology Centre, Technical Support Core Facilities, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Tuo Shi
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Ping Zheng
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Jibin Sun
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Systems Biology Centre, Technical Support Core Facilities, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
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16
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Neely BA, Dorfer V, Martens L, Bludau I, Bouwmeester R, Degroeve S, Deutsch EW, Gessulat S, Käll L, Palczynski P, Payne SH, Rehfeldt TG, Schmidt T, Schwämmle V, Uszkoreit J, Vizcaíno JA, Wilhelm M, Palmblad M. Toward an Integrated Machine Learning Model of a Proteomics Experiment. J Proteome Res 2023; 22:681-696. [PMID: 36744821 PMCID: PMC9990124 DOI: 10.1021/acs.jproteome.2c00711] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
In recent years machine learning has made extensive progress in modeling many aspects of mass spectrometry data. We brought together proteomics data generators, repository managers, and machine learning experts in a workshop with the goals to evaluate and explore machine learning applications for realistic modeling of data from multidimensional mass spectrometry-based proteomics analysis of any sample or organism. Following this sample-to-data roadmap helped identify knowledge gaps and define needs. Being able to generate bespoke and realistic synthetic data has legitimate and important uses in system suitability, method development, and algorithm benchmarking, while also posing critical ethical questions. The interdisciplinary nature of the workshop informed discussions of what is currently possible and future opportunities and challenges. In the following perspective we summarize these discussions in the hope of conveying our excitement about the potential of machine learning in proteomics and to inspire future research.
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Affiliation(s)
- Benjamin A Neely
- National Institute of Standards and Technology, Charleston, South Carolina 29412, United States
| | - Viktoria Dorfer
- Bioinformatics Research Group, University of Applied Sciences Upper Austria, Softwarepark 11, 4232 Hagenberg, Austria
| | - Lennart Martens
- VIB-UGent Center for Medical Biotechnology, VIB, 9000 Ghent, Belgium.,Department of Biomolecular Medicine, Faculty of Health Sciences and Medicine, Ghent University, 9000 Ghent, Belgium
| | - Isabell Bludau
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Robbin Bouwmeester
- VIB-UGent Center for Medical Biotechnology, VIB, 9000 Ghent, Belgium.,Department of Biomolecular Medicine, Faculty of Health Sciences and Medicine, Ghent University, 9000 Ghent, Belgium
| | - Sven Degroeve
- VIB-UGent Center for Medical Biotechnology, VIB, 9000 Ghent, Belgium.,Department of Biomolecular Medicine, Faculty of Health Sciences and Medicine, Ghent University, 9000 Ghent, Belgium
| | - Eric W Deutsch
- Institute for Systems Biology, Seattle, Washington 98109, United States
| | | | - Lukas Käll
- Science for Life Laboratory, KTH - Royal Institute of Technology, 171 21 Solna, Sweden
| | - Pawel Palczynski
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense, Denmark
| | - Samuel H Payne
- Department of Biology, Brigham Young University, Provo, Utah 84602, United States
| | - Tobias Greisager Rehfeldt
- Institute for Mathematics and Computer Science, University of Southern Denmark, 5230 Odense, Denmark
| | | | - Veit Schwämmle
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense, Denmark
| | - Julian Uszkoreit
- Medical Proteome Analysis, Center for Protein Diagnostics (ProDi), Ruhr University Bochum, 44801 Bochum, Germany.,Medizinisches Proteom-Center, Medical Faculty, Ruhr University Bochum, 44801 Bochum, Germany
| | - Juan Antonio Vizcaíno
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - Mathias Wilhelm
- Computational Mass Spectrometry, Technical University of Munich (TUM), 85354 Freising, Germany
| | - Magnus Palmblad
- Leiden University Medical Center, Postbus 9600, 2300 RC Leiden, The Netherlands
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17
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Phlairaharn T, Ye Z, Krismer E, Pedersen AK, Pietzner M, Olsen JV, Schoof EM, Searle BC. Optimizing linear ion trap data independent acquisition towards single cell proteomics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.21.529444. [PMID: 36865114 PMCID: PMC9980145 DOI: 10.1101/2023.02.21.529444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/23/2023]
Abstract
A linear ion trap (LIT) is an affordable, robust mass spectrometer that proves fast scanning speed and high sensitivity, where its primary disadvantage is inferior mass accuracy compared to more commonly used time-of-flight (TOF) or orbitrap (OT) mass analyzers. Previous efforts to utilize the LIT for low-input proteomics analysis still rely on either built-in OTs for collecting precursor data or OT-based library generation. Here, we demonstrate the potential versatility of the LIT for low-input proteomics as a stand-alone mass analyzer for all mass spectrometry measurements, including library generation. To test this approach, we first optimized LIT data acquisition methods and performed library-free searches with and without entrapment peptides to evaluate both the detection and quantification accuracy. We then generated matrix-matched calibration curves to estimate the lower limit of quantification using only 10 ng of starting material. While LIT-MS1 measurements provided poor quantitative accuracy, LIT-MS2 measurements were quantitatively accurate down to 0.5 ng on column. Finally, we optimized a suitable strategy for spectral library generation from low-input material, which we used to analyze single-cell samples by LIT-DIA using LIT-based libraries generated from as few as 40 cells.
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18
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Searle BC, Shannon AE, Wilburn DB. Scribe: Next Generation Library Searching for DDA Experiments. J Proteome Res 2023; 22:482-490. [PMID: 36695531 DOI: 10.1021/acs.jproteome.2c00672] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Spectrum library searching is a powerful alternative to database searching for data dependent acquisition experiments, but has been historically limited to identifying previously observed peptides in libraries. Here we present Scribe, a new library search engine designed to leverage deep learning fragmentation prediction software such as Prosit. Rather than relying on highly curated DDA libraries, this approach predicts fragmentation and retention times for every peptide in a FASTA database. Scribe embeds Percolator for false discovery rate correction and an interference tolerant, label-free quantification integrator for an end-to-end proteomics workflow. By leveraging expected relative fragmentation and retention time values, we find that library searching with Scribe can outperform traditional database searching tools both in terms of sensitivity and quantitative precision. Scribe and its graphical interface are easy to use, freely accessible, and fully open source.
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Affiliation(s)
- Brian C Searle
- Department of Biomedical Informatics, The Ohio State University Medical Center, Columbus, Ohio43210, United States.,Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio43210, United States.,Pelotonia Institute for Immuno-Oncology, The Ohio State University Comprehensive Cancer Center, Columbus, Ohio43210, United States.,Proteome Software Inc., Portland, Oregon97219, United States
| | - Ariana E Shannon
- Department of Biomedical Informatics, The Ohio State University Medical Center, Columbus, Ohio43210, United States.,Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio43210, United States.,Pelotonia Institute for Immuno-Oncology, The Ohio State University Comprehensive Cancer Center, Columbus, Ohio43210, United States
| | - Damien Beau Wilburn
- Department of Biomedical Informatics, The Ohio State University Medical Center, Columbus, Ohio43210, United States.,Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio43210, United States.,Pelotonia Institute for Immuno-Oncology, The Ohio State University Comprehensive Cancer Center, Columbus, Ohio43210, United States
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19
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Rusilowicz M, Newman DW, Creamer DR, Johnson J, Adair K, Harman VM, Grant CM, Beynon RJ, Hubbard SJ. AlacatDesigner─Computational Design of Peptide Concatamers for Protein Quantitation. J Proteome Res 2023; 22:594-604. [PMID: 36688735 PMCID: PMC9903321 DOI: 10.1021/acs.jproteome.2c00608] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Protein quantitation via mass spectrometry relies on peptide proxies for the parent protein from which abundances are estimated. Owing to the variability in signal from individual peptides, accurate absolute quantitation usually relies on the addition of an external standard. Typically, this involves stable isotope-labeled peptides, delivered singly or as a concatenated recombinant protein. Consequently, the selection of the most appropriate surrogate peptides and the attendant design in recombinant proteins termed QconCATs are challenges for proteome science. QconCATs can now be built in a "a-la-carte" assembly method using synthetic biology: ALACATs. To assist their design, we present "AlacatDesigner", a tool that supports the peptide selection for recombinant protein standards based on the user's target protein. The user-customizable tool considers existing databases, occurrence in the literature, potential post-translational modifications, predicted miscleavage, predicted divergence of the peptide and protein quantifications, and ionization potential within the mass spectrometer. We show that peptide selections are enriched for good proteotypic and quantotypic candidates compared to empirical data. The software is freely available to use either via a web interface AlacatDesigner, downloaded as a Desktop application or imported as a Python package for the command line interface or in scripts.
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Affiliation(s)
- Martin Rusilowicz
- Division
of Evolution, Infection and Genomics, School of Biological Sciences,
Faculty of Biology, Medicine and Health, Manchester Academic Health
Science Centre, University of Manchester, Manchester M13 9PT, United Kingdom
| | - David W. Newman
- Division
of Evolution, Infection and Genomics, School of Biological Sciences,
Faculty of Biology, Medicine and Health, Manchester Academic Health
Science Centre, University of Manchester, Manchester M13 9PT, United Kingdom
| | - Declan R. Creamer
- Division
of Molecular and Cellular Function, School of Biological Sciences,
Faculty of Biology, Medicine and Health, Manchester Academic Health
Science Centre, University of Manchester, Manchester M13 9PT, United Kingdom
| | - James Johnson
- GeneMill,
Institute of Systems Molecular and Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, United
Kingdom
| | - Kareena Adair
- Centre
for Proteome Research, Institute of Systems and Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, United
Kingdom
| | - Victoria M. Harman
- Centre
for Proteome Research, Institute of Systems and Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, United
Kingdom
| | - Chris M. Grant
- Division
of Molecular and Cellular Function, School of Biological Sciences,
Faculty of Biology, Medicine and Health, Manchester Academic Health
Science Centre, University of Manchester, Manchester M13 9PT, United Kingdom
| | - Robert J. Beynon
- Centre
for Proteome Research, Institute of Systems and Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, United
Kingdom
| | - Simon J. Hubbard
- Division
of Evolution, Infection and Genomics, School of Biological Sciences,
Faculty of Biology, Medicine and Health, Manchester Academic Health
Science Centre, University of Manchester, Manchester M13 9PT, United Kingdom,
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20
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Ponce S, Zhang H. Developing quantitative assays for six urinary glycoproteins using parallel reaction monitoring, data-independent acquisition, and TMT-based data-dependent acquisition. Proteomics 2023; 23:e2200072. [PMID: 36592098 DOI: 10.1002/pmic.202200072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Revised: 12/21/2022] [Accepted: 12/22/2022] [Indexed: 01/03/2023]
Abstract
Quantitative approaches encompassing parallel reaction monitoring (PRM), data-independent acquisition (DIA), and data-dependent acquisition (DDA) are commonly used to investigate protein expression profiles. However, analytical performances of assays developed using PRM, DIA, and Tandem Mass Tag (TMT)-based DDA for quantitative proteomics have yet not been investigated. Here, we developed assays for glycopeptides identified from six glycoproteins, including Leucine-rich alpha-2-glycoprotein (LRG1), Prostaglandin-H2 D-isomerase (PTGDS), Aminopeptidase N (ANPEP), CD63 antigen (CD63), Clusterin (CLU), and Prostatic acid phosphatase (ACPP), using PRM, DDA, and DIA and evaluated the analytical performances of each assay using the different acquisition modes. We also compared assays in each acquisition mode on three different orbitrap instruments: Thermo Fisher Q Exactive, Exploris 480, and Lumos. We found that DIA showed the largest linear range, highest sensitivity, and most reproducibility. We then applied our developed DIA assays to urine samples from non-aggressive (n = 48) and aggressive (n = 35) prostate cancer patients. In conclusion, we developed assays for the six glycoproteins, evaluated the analytical performances of each assay in DIA, PRM, and PRM acquisition modes on three types of mass spectrometry instruments, and chose the DIA assays for the quantitative analysis of urine samples from patients with aggressive and non-aggressive prostate cancer.
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Affiliation(s)
- Sean Ponce
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland, USA
| | - Hui Zhang
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland, USA.,Department of Pathology, Johns Hopkins University, Baltimore, Maryland, USA
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21
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Casavant EP, Liang J, Sankhe S, Mathews WR, Anania VG. Using SILAC to Develop Quantitative Data-Independent Acquisition (DIA) Proteomic Methods. Methods Mol Biol 2023; 2603:245-257. [PMID: 36370285 DOI: 10.1007/978-1-0716-2863-8_20] [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: 06/16/2023]
Abstract
Proteins are integral to biological systems and functions. Identifying and quantifying proteins can therefore offer systems-wide insights into protein-protein interactions, cellular signaling, and biological pathway activity. The use of quantitative proteomics has become a method of choice for identifying and quantifying proteins in complex matrices. Proteomics allows researchers to survey hundreds to thousands of proteins in a less biased manner than classical antibody-based protein capture strategies. Typically, discovery approaches have used data-dependent acquisition (DDA) methods, but this approach suffers from stochasticity that compromises quantitation. Recent developments in data-independent acquisition (DIA) proteomics workflows enable proteomic profiling of thousands of samples with increased peak picking consistency making it an excellent candidate for discovering and assessing biomarkers in clinical samples. However, quantitation of peptides from DIA datasets is computationally intensive, and guidelines on how to establish DIA methods are lacking. Method development and optimization require novel tools to visualize and filter DIA datasets appropriately. Here, a protocol and novel script workflow for the optimization of quantitative DIA methods using stable isotope labeling of amino acids in culture (SILAC) are presented. This protocol includes steps for cell growth and labeling, peptide digestion and preparation, and optimization of quantitative DIA methods. In addition, important steps for (1) computational analysis to identify and quantify peptides, (2) data visualizations to identify the linear abundance ranges for all peptides in the sample, and (3) descriptions of how to find high confidence quantitation abundance thresholds are described herein.
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22
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Strzepek RF, Nunn BL, Bach LT, Berges JA, Young EB, Boyd PW. The ongoing need for rates: can physiology and omics come together to co-design the measurements needed to understand complex ocean biogeochemistry? JOURNAL OF PLANKTON RESEARCH 2022; 44:485-495. [PMID: 35898813 PMCID: PMC9310281 DOI: 10.1093/plankt/fbac026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 05/05/2022] [Indexed: 05/16/2023]
Abstract
The necessity to understand the influence of global ocean change on biota has exposed wide-ranging gaps in our knowledge of the fundamental principles that underpin marine life. Concurrently, physiological research has stagnated, in part driven by the advent and rapid evolution of molecular biological techniques, such that they now influence all lines of enquiry in biological oceanography. This dominance has led to an implicit assumption that physiology is outmoded, and advocacy that ecological and biogeochemical models can be directly informed by omics. However, the main modeling currencies are biological rates and biogeochemical fluxes. Here, we ask: how do we translate the wealth of information on physiological potential from omics-based studies to quantifiable physiological rates and, ultimately, to biogeochemical fluxes? Based on the trajectory of the state-of-the-art in biomedical sciences, along with case-studies from ocean sciences, we conclude that it is unlikely that omics can provide such rates in the coming decade. Thus, while physiological rates will continue to be central to providing projections of global change biology, we must revisit the metrics we rely upon. We advocate for the co-design of a new generation of rate measurements that better link the benefits of omics and physiology.
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Affiliation(s)
- Robert F Strzepek
- Australian Antarctic Program Partnership (AAPP), Institute for Marine and Antarctic Studies, University of Tasmania, 20 Castray Esplanade, Hobart, TAS 7004, Australia
| | - Brook L Nunn
- Department of Genome Sciences, University of Washington, Foege Building S113 3720 15th Ave NE, Seattle, WA 98195, USA
| | - Lennart T Bach
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, TAS 7004, Australia
| | - John A Berges
- Department of Biological Sciences and School of Freshwater Sciences, University of Wisconsin-Milwaukee, 3209 N. Maryland Avenue, Milwaukee, WI 53211, USA
| | - Erica B Young
- Department of Biological Sciences and School of Freshwater Sciences, University of Wisconsin-Milwaukee, 3209 N. Maryland Avenue, Milwaukee, WI 53211, USA
| | - Philip W Boyd
- Australian Antarctic Program Partnership (AAPP), Institute for Marine and Antarctic Studies, University of Tasmania, 20 Castray Esplanade, Hobart, TAS 7004, Australia
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, TAS 7004, Australia
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23
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Wang Z, Cryar A, Lemke O, Tober-Lau P, Ludwig D, Helbig ET, Hippenstiel S, Sander LE, Blake D, Lane CS, Sayers RL, Mueller C, Zeiser J, Townsend S, Demichev V, Mülleder M, Kurth F, Sirka E, Hartl J, Ralser M. A multiplex protein panel assay for severity prediction and outcome prognosis in patients with COVID-19: An observational multi-cohort study. EClinicalMedicine 2022; 49:101495. [PMID: 35702332 PMCID: PMC9181834 DOI: 10.1016/j.eclinm.2022.101495] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 05/11/2022] [Accepted: 05/17/2022] [Indexed: 12/15/2022] Open
Abstract
Background Global healthcare systems continue to be challenged by the COVID-19 pandemic, and there is a need for clinical assays that can help optimise resource allocation, support treatment decisions, and accelerate the development and evaluation of new therapies. Methods We developed a multiplexed proteomics assay for determining disease severity and prognosis in COVID-19. The assay quantifies up to 50 peptides, derived from 30 known and newly introduced COVID-19-related protein markers, in a single measurement using routine-lab compatible analytical flow rate liquid chromatography and multiple reaction monitoring (LC-MRM). We conducted two observational studies in patients with COVID-19 hospitalised at Charité - Universitätsmedizin Berlin, Germany before (from March 1 to 26, 2020, n=30) and after (from April 4 to November 19, 2020, n=164) dexamethasone became standard of care. The study is registered in the German and the WHO International Clinical Trials Registry (DRKS00021688). Findings The assay produces reproducible (median inter-batch CV of 10.9%) absolute quantification of 47 peptides with high sensitivity (median LLOQ of 143 ng/ml) and accuracy (median 96.8%). In both studies, the assay reproducibly captured hallmarks of COVID-19 infection and severity, as it distinguished healthy individuals, mild, moderate, and severe COVID-19. In the post-dexamethasone cohort, the assay predicted survival with an accuracy of 0.83 (108/130), and death with an accuracy of 0.76 (26/34) in the median 2.5 weeks before the outcome, thereby outperforming compound clinical risk assessments such as SOFA, APACHE II, and ABCS scores. Interpretation Disease severity and clinical outcomes of patients with COVID-19 can be stratified and predicted by the routine-applicable panel assay that combines known and novel COVID-19 biomarkers. The prognostic value of this assay should be prospectively assessed in larger patient cohorts for future support of clinical decisions, including evaluation of sample flow in routine setting. The possibility to objectively classify COVID-19 severity can be helpful for monitoring of novel therapies, especially in early clinical trials. Funding This research was funded in part by the European Research Council (ERC) under grant agreement ERC-SyG-2020 951475 (to M.R) and by the Wellcome Trust (IA 200829/Z/16/Z to M.R.). The work was further supported by the Ministry of Education and Research (BMBF) as part of the National Research Node 'Mass Spectrometry in Systems Medicine (MSCoresys)', under grant agreements 031L0220 and 161L0221. J.H. was supported by a Swiss National Science Foundation (SNSF) Postdoc Mobility fellowship (project number 191052). This study was further supported by the BMBF grant NaFoUniMedCOVID-19 - NUM-NAPKON, FKZ: 01KX2021. The study was co-funded by the UK's innovation agency, Innovate UK, under project numbers 75594 and 56328.
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Affiliation(s)
- Ziyue Wang
- Department of Biochemistry, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Am Chariteplatz 1, 10117 Berlin, Germany
| | - Adam Cryar
- Inoviv, Mappin House, 4 Winsley St, London, United Kingdom
| | - Oliver Lemke
- Department of Biochemistry, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Am Chariteplatz 1, 10117 Berlin, Germany
| | - Pinkus Tober-Lau
- Department of Infectious Diseases and Respiratory Medicine, Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Augustenburger Platz 1, 13353 Berlin, Germany
| | - Daniela Ludwig
- Department of Biochemistry, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Am Chariteplatz 1, 10117 Berlin, Germany
| | - Elisa Theresa Helbig
- Department of Infectious Diseases and Respiratory Medicine, Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Augustenburger Platz 1, 13353 Berlin, Germany
| | - Stefan Hippenstiel
- Department of Infectious Diseases and Respiratory Medicine, Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Augustenburger Platz 1, 13353 Berlin, Germany
| | - Leif-Erik Sander
- Department of Infectious Diseases and Respiratory Medicine, Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Augustenburger Platz 1, 13353 Berlin, Germany
- Berlin Institute of Health at the Charité - Universitätsmedizin Berlin, Berlin, Germany
| | | | | | | | - Christoph Mueller
- Agilent Technologies Sales & Services GmbH & Co. KG, Waldbronn, Germany
| | - Johannes Zeiser
- Agilent Technologies Sales & Services GmbH & Co. KG, Waldbronn, Germany
| | - StJohn Townsend
- Department of Biochemistry, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Am Chariteplatz 1, 10117 Berlin, Germany
| | - Vadim Demichev
- Department of Biochemistry, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Am Chariteplatz 1, 10117 Berlin, Germany
| | - Michael Mülleder
- Core Facility – High-Throughput Mass Spectrometry, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Am Chariteplatz 1, 10117 Berlin, Germany
| | - Florian Kurth
- Department of Infectious Diseases and Respiratory Medicine, Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Augustenburger Platz 1, 13353 Berlin, Germany
- Department of Tropical Medicine, Bernhard Nocht Institute for Tropical Medicine, and Department of Medicine I, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany
| | - Ernestas Sirka
- Inoviv, Mappin House, 4 Winsley St, London, United Kingdom
| | - Johannes Hartl
- Department of Biochemistry, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Am Chariteplatz 1, 10117 Berlin, Germany
| | - Markus Ralser
- Department of Biochemistry, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Am Chariteplatz 1, 10117 Berlin, Germany
- The Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, UK
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24
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Heil LR, Fondrie WE, McGann CD, Federation AJ, Noble WS, MacCoss MJ, Keich U. Building Spectral Libraries from Narrow-Window Data-Independent Acquisition Mass Spectrometry Data. J Proteome Res 2022; 21:1382-1391. [PMID: 35549345 DOI: 10.1021/acs.jproteome.1c00895] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Advances in library-based methods for peptide detection from data-independent acquisition (DIA) mass spectrometry have made it possible to detect and quantify tens of thousands of peptides in a single mass spectrometry run. However, many of these methods rely on a comprehensive, high-quality spectral library containing information about the expected retention time and fragmentation patterns of peptides in the sample. Empirical spectral libraries are often generated through data-dependent acquisition and may suffer from biases as a result. Spectral libraries can be generated in silico, but these models are not trained to handle all possible post-translational modifications. Here, we propose a false discovery rate-controlled spectrum-centric search workflow to generate spectral libraries directly from gas-phase fractionated DIA tandem mass spectrometry data. We demonstrate that this strategy is able to detect phosphorylated peptides and can be used to generate a spectral library for accurate peptide detection and quantitation in wide-window DIA data. We compare the results of this search workflow to other library-free approaches and demonstrate that our search is competitive in terms of accuracy and sensitivity. These results demonstrate that the proposed workflow has the capacity to generate spectral libraries while avoiding the limitations of other methods.
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Affiliation(s)
- Lilian R Heil
- Department of Genome Sciences, University of Washington, Seattle, Washington 98105, United States
| | - William E Fondrie
- Department of Genome Sciences, University of Washington, Seattle, Washington 98105, United States
| | - Christopher D McGann
- Department of Genome Sciences, University of Washington, Seattle, Washington 98105, United States
| | - Alexander J Federation
- Department of Genome Sciences, University of Washington, Seattle, Washington 98105, United States
| | - William S Noble
- Department of Genome Sciences, University of Washington, Seattle, Washington 98105, United States.,Paul G. Allen School for Computer Science and Engineering, University of Washington, Seattle, Washington 98105, United States
| | - Michael J MacCoss
- Department of Genome Sciences, University of Washington, Seattle, Washington 98105, United States
| | - Uri Keich
- School of Mathematics and Statistics, University of Sydney, Sydney, NSW 2006, Australia
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25
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Gotti C, Roux-Dalvai F, Joly-Beauparlant C, Mangnier L, Leclercq M, Droit A. Extensive and Accurate Benchmarking of DIA Acquisition Methods and Software Tools Using a Complex Proteomic Standard. J Proteome Res 2021; 20:4801-4814. [PMID: 34472865 DOI: 10.1021/acs.jproteome.1c00490] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Over the past decade, the data-independent acquisition mode has gained popularity for broad coverage of complex proteomes by LC-MS/MS and quantification of low-abundance proteins. However, there is no consensus in the literature on the best data acquisition parameters and processing tools to use for this specific application. Here, we present the most comprehensive comparison of DIA workflows on Orbitrap instruments published so far in the field of proteomics. Using a standard human 48 proteins mixture (UPS1-Sigma) at 8 different concentrations in an E. coli proteome background, we tested 36 workflows including 4 different DIA window acquisition schemes and 6 different software tools (DIA-NN, DIA-Umpire, OpenSWATH, ScaffoldDIA, Skyline, and Spectronaut) with or without the use of a DDA spectral library. On the basis of the number of proteins identified, quantification linearity and reproducibility, as well as sensitivity and specificity in 28 pairwise comparisons of different UPS1 concentrations, we summarize the major considerations and propose guidelines for choosing the DIA workflow best suited for LC-MS/MS proteomic analyses. Our 96 DIA raw files and software outputs have been deposited on ProteomeXchange for testing or developing new DIA processing tools.
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Affiliation(s)
- Clarisse Gotti
- Proteomics Platform, CHU de Québec - Université Laval Research Centre, Québec City, Québec G1V 4G2, Canada.,Computational Biology Laboratory, CHU de Québec - Université Laval Research Centre, Québec City, Québec G1V 4G2, Canada
| | - Florence Roux-Dalvai
- Proteomics Platform, CHU de Québec - Université Laval Research Centre, Québec City, Québec G1V 4G2, Canada.,Computational Biology Laboratory, CHU de Québec - Université Laval Research Centre, Québec City, Québec G1V 4G2, Canada
| | - Charles Joly-Beauparlant
- Computational Biology Laboratory, CHU de Québec - Université Laval Research Centre, Québec City, Québec G1V 4G2, Canada
| | - Loïc Mangnier
- Computational Biology Laboratory, CHU de Québec - Université Laval Research Centre, Québec City, Québec G1V 4G2, Canada
| | - Mickaël Leclercq
- Computational Biology Laboratory, CHU de Québec - Université Laval Research Centre, Québec City, Québec G1V 4G2, Canada
| | - Arnaud Droit
- Proteomics Platform, CHU de Québec - Université Laval Research Centre, Québec City, Québec G1V 4G2, Canada.,Computational Biology Laboratory, CHU de Québec - Université Laval Research Centre, Québec City, Québec G1V 4G2, Canada
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26
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Kulyyassov A, Fresnais M, Longuespée R. Targeted liquid chromatography-tandem mass spectrometry analysis of proteins: Basic principles, applications, and perspectives. Proteomics 2021; 21:e2100153. [PMID: 34591362 DOI: 10.1002/pmic.202100153] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 09/08/2021] [Accepted: 09/24/2021] [Indexed: 12/25/2022]
Abstract
Liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) is now the main analytical method for the identification and quantification of peptides and proteins in biological samples. In modern research, identification of biomarkers and their quantitative comparison between samples are becoming increasingly important for discovery, validation, and monitoring. Such data can be obtained following specific signals after fragmentation of peptides using multiple reaction monitoring (MRM) and parallel reaction monitoring (PRM) methods, with high specificity, accuracy, and reproducibility. In addition, these methods allow measurement of the amount of post-translationally modified forms and isoforms of proteins. This review article describes the basic principles of MRM assays, guidelines for sample preparation, recent advanced MRM-based strategies, applications and illustrative perspectives of MRM/PRM methods in clinical research and molecular biology.
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Affiliation(s)
| | - Margaux Fresnais
- Department of Clinical Pharmacology and Pharmacoepidemiology, Heidelberg University Hospital, Heidelberg, Germany
| | - Rémi Longuespée
- Department of Clinical Pharmacology and Pharmacoepidemiology, Heidelberg University Hospital, Heidelberg, Germany
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27
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Lill JR, Mathews WR, Rose CM, Schirle M. Proteomics in the pharmaceutical and biotechnology industry: a look to the next decade. Expert Rev Proteomics 2021; 18:503-526. [PMID: 34320887 DOI: 10.1080/14789450.2021.1962300] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
INTRODUCTION Pioneering technologies such as proteomics have helped fuel the biotechnology and pharmaceutical industry with the discovery of novel targets and an intricate understanding of the activity of therapeutics and their various activities in vitro and in vivo. The field of proteomics is undergoing an inflection point, where new sensitive technologies are allowing intricate biological pathways to be better understood, and novel biochemical tools are pivoting us into a new era of chemical proteomics and biomarker discovery. In this review, we describe these areas of innovation, and discuss where the fields are headed in terms of fueling biotechnological and pharmacological research and discuss current gaps in the proteomic technology landscape. AREAS COVERED Single cell sequencing and single molecule sequencing. Chemoproteomics. Biological matrices and clinical samples including biomarkers. Computational tools including instrument control software, data analysis. EXPERT OPINION Proteomics will likely remain a key technology in the coming decade, but will have to evolve with respect to type and granularity of data, cost and throughput of data generation as well as integration with other technologies to fulfill its promise in drug discovery.
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Affiliation(s)
- Jennie R Lill
- Department of Microchemistry, Lipidomics and Next Generation Sequencing, Genentech Inc. DNA Way, South San Francisco, CA, USA
| | - William R Mathews
- OMNI Department, Genentech Inc. 1 DNA Way, South San Francisco, CA, USA
| | - Christopher M Rose
- Department of Microchemistry, Lipidomics and Next Generation Sequencing, Genentech Inc. DNA Way, South San Francisco, CA, USA
| | - Markus Schirle
- Chemical Biology and Therapeutics Department, Novartis Institutes for Biomedical Research, Cambridge, MA, USA
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28
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Nakayasu ES, Gritsenko M, Piehowski PD, Gao Y, Orton DJ, Schepmoes AA, Fillmore TL, Frohnert BI, Rewers M, Krischer JP, Ansong C, Suchy-Dicey AM, Evans-Molina C, Qian WJ, Webb-Robertson BJM, Metz TO. Tutorial: best practices and considerations for mass-spectrometry-based protein biomarker discovery and validation. Nat Protoc 2021; 16:3737-3760. [PMID: 34244696 PMCID: PMC8830262 DOI: 10.1038/s41596-021-00566-6] [Citation(s) in RCA: 93] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 04/26/2021] [Indexed: 02/06/2023]
Abstract
Mass-spectrometry-based proteomic analysis is a powerful approach for discovering new disease biomarkers. However, certain critical steps of study design such as cohort selection, evaluation of statistical power, sample blinding and randomization, and sample/data quality control are often neglected or underappreciated during experimental design and execution. This tutorial discusses important steps for designing and implementing a liquid-chromatography-mass-spectrometry-based biomarker discovery study. We describe the rationale, considerations and possible failures in each step of such studies, including experimental design, sample collection and processing, and data collection. We also provide guidance for major steps of data processing and final statistical analysis for meaningful biological interpretations along with highlights of several successful biomarker studies. The provided guidelines from study design to implementation to data interpretation serve as a reference for improving rigor and reproducibility of biomarker development studies.
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Affiliation(s)
- Ernesto S Nakayasu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA.
| | - Marina Gritsenko
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Paul D Piehowski
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Yuqian Gao
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Daniel J Orton
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Athena A Schepmoes
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Thomas L Fillmore
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Brigitte I Frohnert
- Barbara Davis Center for Diabetes, School of Medicine, University of Colorado, Aurora, CO, USA
| | - Marian Rewers
- Barbara Davis Center for Diabetes, School of Medicine, University of Colorado, Aurora, CO, USA
| | - Jeffrey P Krischer
- Morsani College of Medicine, University of South Florida, Tampa, FL, USA
| | - Charles Ansong
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Astrid M Suchy-Dicey
- Elson S. Floyd College of Medicine, Washington State University, Seattle, WA, USA
| | - Carmella Evans-Molina
- Center for Diabetes and Metabolic Diseases and the Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Wei-Jun Qian
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Bobbie-Jo M Webb-Robertson
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
- Department of Biostatistics and Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Thomas O Metz
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA.
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29
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Heil LR, Remes PM, MacCoss MJ. Comparison of Unit Resolution Versus High-Resolution Accurate Mass for Parallel Reaction Monitoring. J Proteome Res 2021; 20:4435-4442. [PMID: 34319745 DOI: 10.1021/acs.jproteome.1c00377] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Parallel reaction monitoring (PRM) is an increasingly popular alternative to selected reaction monitoring (SRM) for targeted proteomics. PRM's strengths over SRM are that it monitors all product ions in a single spectrum, thus eliminating the need to select interference-free product ions prior to data acquisition, and that it is most frequently performed on high-resolution instruments, such as quadrupole-orbitrap and quadrupole-time-of-flight instruments. Here, we show that the primary advantage of PRM is the ability to monitor all transitions in parallel and that high-resolution data are not necessary to obtain high-quality quantitative data. We run the same scheduled PRM assay, measuring 432 peptides from 126 plasma proteins, multiple times on an Orbitrap Eclipse Tribrid mass spectrometer, alternating separate liquid chromatography-tandem mass spectrometry runs between the high-resolution Orbitrap and the unit resolution linear ion trap for PRM. We find that both mass analyzers have similar technical precision and that the linear ion trap's superior sensitivity gives it better lower limits of quantitation for over 62% of peptides in the assay.
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Affiliation(s)
- Lilian R Heil
- Department of Genome Sciences, University of Washington, 3720 15th Street NE, Seattle, Washington 98195, United States
| | - Philip M Remes
- Thermo Fisher Scientific, 355 River Oaks Parkway, San Jose, California 95134, United States
| | - Michael J MacCoss
- Department of Genome Sciences, University of Washington, 3720 15th Street NE, Seattle, Washington 98195, United States
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30
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Remes PM, Yip P, MacCoss MJ. Highly Multiplex Targeted Proteomics Enabled by Real-Time Chromatographic Alignment. Anal Chem 2020; 92:11809-11817. [PMID: 32867497 DOI: 10.1021/acs.analchem.0c02075] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Targeted mass spectrometry methods produce high-quality quantitative data in terms of limits of detection and dynamic range, at the cost of a substantial compromise in throughput compared to methods such as data independent and data dependent acquisition. The logistical and experimental issues inherent to maintaining assays of even several hundred targets are significant. Prominent among these issues is the drift in analyte retention time as liquid chromatography (LC) columns wear, forcing targeted scheduling windows to be much larger than LC peak widths. If these problems could be solved, proteomics assays would be capable of targeting thousands of peptides in an hour-long experiment, enabling large cohort studies to be performed without sacrificing sensitivity and specificity. We describe a solution in the form of a new method for real-time chromatographic alignment and demonstrate its application to a 56 min LC-gradient HeLa digest assay with 1489 targets. The method is based on the periodic acquisition of untargeted survey scans in a reference experiment and alignment to those scans during subsequent experiments. We describe how the method enables narrower scheduled retention time windows to be used. The narrower scheduling windows enables more targets to be included in the assay or proportionally more time to be allocated to each target, improving the sensitivity. Finally, we point out how the procedure could be improved and how much additional target multiplexing could be gained in the future.
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Affiliation(s)
- Philip M Remes
- Thermo Fisher Scientific, 355 River Oaks Parkway, San Jose, California 95134, United States
| | - Ping Yip
- Thermo Fisher Scientific, 355 River Oaks Parkway, San Jose, California 95134, United States
| | - Michael J MacCoss
- Department of Genome Sciences, University of Washington, 3720 15th Street NE, Seattle, Washington 98195, United States
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31
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Pino LK, Just SC, MacCoss MJ, Searle BC. Acquiring and Analyzing Data Independent Acquisition Proteomics Experiments without Spectrum Libraries. Mol Cell Proteomics 2020; 19:1088-1103. [PMID: 32312845 PMCID: PMC7338082 DOI: 10.1074/mcp.p119.001913] [Citation(s) in RCA: 135] [Impact Index Per Article: 33.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 04/14/2020] [Indexed: 11/06/2022] Open
Abstract
Data independent acquisition (DIA) is an attractive alternative to standard shotgun proteomics methods for quantitative experiments. However, most DIA methods require collecting exhaustive, sample-specific spectrum libraries with data dependent acquisition (DDA) to detect and quantify peptides. In addition to working with non-human samples, studies of splice junctions, sequence variants, or simply working with small sample yields can make developing DDA-based spectrum libraries impractical. Here we illustrate how to acquire, queue, and validate DIA data without spectrum libraries, and provide a workflow to efficiently generate DIA-only chromatogram libraries using gas-phase fractionation (GPF). We present best-practice methods for collecting DIA data using Orbitrap-based instruments and develop an understanding for why DIA using an Orbitrap mass spectrometer should be approached differently than when using time-of-flight instruments. Finally, we discuss several methods for analyzing DIA data without libraries.
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Affiliation(s)
- Lindsay K Pino
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Seth C Just
- Proteome Software, Inc. Portland, Oregon, USA
| | - Michael J MacCoss
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Brian C Searle
- Institute for Systems Biology, Seattle, Washington, USA.
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32
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Searle BC, Swearingen KE, Barnes CA, Schmidt T, Gessulat S, Küster B, Wilhelm M. Generating high quality libraries for DIA MS with empirically corrected peptide predictions. Nat Commun 2020; 11:1548. [PMID: 32214105 PMCID: PMC7096433 DOI: 10.1038/s41467-020-15346-1] [Citation(s) in RCA: 131] [Impact Index Per Article: 32.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Accepted: 02/28/2020] [Indexed: 11/09/2022] Open
Abstract
Data-independent acquisition approaches typically rely on experiment-specific spectrum libraries, requiring offline fractionation and tens to hundreds of injections. We demonstrate a library generation workflow that leverages fragmentation and retention time prediction to build libraries containing every peptide in a proteome, and then refines those libraries with empirical data. Our method specifically enables rapid, experiment-specific library generation for non-model organisms, which we demonstrate using the malaria parasite Plasmodium falciparum, and non-canonical databases, which we show by detecting missense variants in HeLa.
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Affiliation(s)
- Brian C Searle
- Institute for Systems Biology, Seattle, WA, USA.
- Proteome Software, Inc., Portland, OR, USA.
| | | | | | | | - Siegfried Gessulat
- Technical University of Munich, Freising, Germany
- SAP SE, Potsdam, Germany
| | - Bernhard Küster
- Technical University of Munich, Freising, Germany
- Bavarian Center for Biomolecular Mass Spectrometry, Freising, Germany
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