1
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Kumar S, Stover L, Wang L, Bahramimoghaddam H, Zhou M, Russell DH, Laganowsky A. Native mass spectrometry of membrane protein-lipid interactions in different detergent environments. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.27.601044. [PMID: 38979331 PMCID: PMC11230385 DOI: 10.1101/2024.06.27.601044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
Native mass spectrometry (MS) is revealing the role of specific lipids in modulating membrane protein structure and function. Membrane proteins solubilized in detergents are often introduced into the mass spectrometer; however, commonly used detergents for structural studies, such as dodecylmaltoside, tend to generate highly charged ions, leading to protein unfolding, thereby diminishing their utility for characterizing protein-lipid interactions. Thus, there is a critical need to develop approaches to investigate protein-lipid interactions in different detergents. Here, we demonstrate how charge-reducing molecules, such as spermine and trimethylamine-N-oxide, enable characterization of lipid binding to the bacterial water channel (AqpZ) and ammonia channel (AmtB) in complex with regulatory protein GlnK in different detergent environments. We find protein-lipid interactions are not only protein-dependent but can also be influenced by the detergent and type of charge-reducing molecule. AqpZ-lipid interactions are enhanced in LDAO (n-dodecyl-N,N-dimethylamine-N-oxide), whereas the interaction of AmtB-GlnK with lipids is comparable among different detergents. A fluorescent lipid binding assay also shows detergent dependence for AqpZ-lipid interactions, consistent with results from native MS. Taken together, native MS will play a pivotal role in establishing optimal experimental parameters that will be invaluable for various applications, such as drug discovery, as well as biochemical and structural investigations.
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Affiliation(s)
- Smriti Kumar
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Lauren Stover
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Lie Wang
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030, United States
| | | | - Ming Zhou
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030, United States
| | - David H. Russell
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Arthur Laganowsky
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
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2
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Shepherd SO, Green AW, Resendiz ES, Newton KR, Kurulugama RT, Prell JS. Effects of Nano-Electrospray Ionization Emitter Position on Unintentional In-Source Activation of Peptide and Protein Ions. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:498-507. [PMID: 38374644 PMCID: PMC11315166 DOI: 10.1021/jasms.3c00371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/21/2024]
Abstract
Native ion mobility-mass spectrometry (IM-MS) typically introduces protein ions into the gas phase through nano-electrospray ionization (nESI). Many nESI setups have mobile stages for tuning the ion signal and extent of co-solute and salt adduction. However, tuning the position of the emitter capillary in nESI can have unintended downstream consequences for collision-induced unfolding or collision-induced dissociation (CIU/D) experiments. Here, we show that relatively small variations in the nESI emitter position can shift the midpoint (commonly called the "CID50" or "CIU50") potential of CID breakdown curves and CIU transitions by as much as 8 V on commercial instruments. A spatial "map" of the shift in CID50 for the loss of heme from holomyoglobin onto the emitter position on a Waters Synapt G2-Si mass spectrometer shows that emitter positions closer to the instrument inlet can result in significantly greater in-source activation, whereas different effects are found on an Agilent 6545XT instrument for the ions studied. A similar effect is observed for CID of the singly protonated leucine enkephalin peptide and Shiga toxin 1 subunit B homopentamer on the Waters Synapt G2-Si instrument. In-source activation effects on a Waters Synapt G2-Si are also investigated by examining the RMSD between CIU fingerprints acquired at different emitter positions and the shifts in CIU50 for structural transitions of bovine serum albumin and NIST monoclonal antibody.
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Affiliation(s)
- Samantha O. Shepherd
- Department of Chemistry and Biochemistry, 1253 University of Oregon, Eugene, OR, USA, 97403-1253
| | - Austin W. Green
- Department of Chemistry and Biochemistry, 1253 University of Oregon, Eugene, OR, USA, 97403-1253
| | - Elizabeth S. Resendiz
- Department of Chemistry and Biochemistry, 1253 University of Oregon, Eugene, OR, USA, 97403-1253
| | - Kenneth R. Newton
- Department of Chemistry and Biochemistry, 1253 University of Oregon, Eugene, OR, USA, 97403-1253
- 5301 Stevens Creek Blvd, Agilent Technologies, Santa Clara, 95051, CA, USA
| | | | - James S. Prell
- Department of Chemistry and Biochemistry, 1253 University of Oregon, Eugene, OR, USA, 97403-1253
- Materials Science Institute, 1252 University of Oregon, Eugene, OR, USA, 97403-1252
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3
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Silva MP, Rodrigues CG, Machado DC, Nogueira RA. Long-term memory in Staphylococcus aureus α-hemolysin ion channel kinetics. EUROPEAN BIOPHYSICS JOURNAL : EBJ 2023; 52:661-671. [PMID: 37542583 DOI: 10.1007/s00249-023-01675-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 07/03/2023] [Accepted: 07/20/2023] [Indexed: 08/07/2023]
Abstract
The kinetics of an ion channel are classically understood as a random process. However, studies have shown that in complex ion channels, formed by multiple subunits, this process can be deterministic, presenting long-term memory. Staphylococcus aureus α-hemolysin (α-HL) is a toxin that acts as the major factor in Staphylococcus aureus virulence. α-HL is a water-soluble protein capable of forming ion channels into lipid bilayers, by insertion of an amphipathic β-barrel. Here, the α-HL was used as an experimental model to study memory in ion channel kinetics. We applied the approximate entropy (ApEn) approach to analyze randomness and the Detrended Fluctuation Analysis (DFA) to investigate the existence of long memory in α-HL channel kinetics. Single-channel currents were measured through experiments with α-HL channels incorporated in planar lipid bilayers. All experiments were carried out under the following conditions: 1 M NaCl solution, pH 4.5; transmembrane potential of + 40 mV and temperature 25 ± 1 °C. Single-channel currents were recorded in real-time in the memory of a microcomputer coupled to an A/D converter and a patch-clamp amplifier. The conductance value of the α-HL channels was 0.82 ± 0.0025 nS (n = 128). The DFA analysis showed that the kinetics of α-HL channels presents long-term memory ([Formula: see text] = 0.63 ± 0.04). The ApEn outcomes showed low complexity to dwell times when open (ApEno = 0.5514 ± 0.28) and closed (ApEnc = 0.1145 ± 0.08), corroborating the results of the DFA method.
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Affiliation(s)
- M P Silva
- Department of Animal Morphology and Physiology, Federal Rural University of Pernambuco, Recife, Pernambuco, Brazil
| | - C G Rodrigues
- Department of Biophysics and Radiobiology, Federal University of Pernambuco, Recife, Pernambuco, Brazil
| | - D C Machado
- Department of Biophysics and Radiobiology, Federal University of Pernambuco, Recife, Pernambuco, Brazil
| | - R A Nogueira
- Department of Animal Morphology and Physiology, Federal Rural University of Pernambuco, Recife, Pernambuco, Brazil.
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4
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Townsend JA, Marty MT. What's the defect? Using mass defects to study oligomerization of membrane proteins and peptides in nanodiscs with native mass spectrometry. Methods 2023; 218:1-13. [PMID: 37482149 PMCID: PMC10529358 DOI: 10.1016/j.ymeth.2023.07.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 06/20/2023] [Accepted: 07/03/2023] [Indexed: 07/25/2023] Open
Abstract
Many membrane proteins form functional complexes that are either homo- or hetero-oligomeric. However, it is challenging to characterize membrane protein oligomerization in intact lipid bilayers, especially for polydisperse mixtures. Native mass spectrometry of membrane proteins and peptides inserted in lipid nanodiscs provides a unique method to study the oligomeric state distribution and lipid preferences of oligomeric assemblies. To interpret these complex spectra, we developed novel data analysis methods using macromolecular mass defect analysis. Here, we provide an overview of how mass defect analysis can be used to study oligomerization in nanodiscs, discuss potential limitations in interpretation, and explore strategies to resolve these ambiguities. Finally, we review recent work applying this technique to studying formation of antimicrobial peptide, amyloid protein, and viroporin complexes with lipid membranes.
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Affiliation(s)
- Julia A Townsend
- Department of Chemistry and Biochemistry and Bio5 Institute, University of Arizona, Tucson, AZ 85721, USA
| | - Michael T Marty
- Department of Chemistry and Biochemistry and Bio5 Institute, University of Arizona, Tucson, AZ 85721, USA.
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5
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Abstract
Native mass spectrometry (MS) is aimed at preserving and determining the native structure, composition, and stoichiometry of biomolecules and their complexes from solution after they are transferred into the gas phase. Major improvements in native MS instrumentation and experimental methods over the past few decades have led to a concomitant increase in the complexity and heterogeneity of samples that can be analyzed, including protein-ligand complexes, protein complexes with multiple coexisting stoichiometries, and membrane protein-lipid assemblies. Heterogeneous features of these biomolecular samples can be important for understanding structure and function. However, sample heterogeneity can make assignment of ion mass, charge, composition, and structure very challenging due to the overlap of tens or even hundreds of peaks in the mass spectrum. In this review, we cover data analysis, experimental, and instrumental advances and strategies aimed at solving this problem, with an in-depth discussion of theoretical and practical aspects of the use of available deconvolution algorithms and tools. We also reflect upon current challenges and provide a view of the future of this exciting field.
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Affiliation(s)
- Amber D. Rolland
- Department of Chemistry and Biochemistry, 1253 University of Oregon, Eugene, OR, USA 97403-1253
| | - James S. Prell
- Department of Chemistry and Biochemistry, 1253 University of Oregon, Eugene, OR, USA 97403-1253
- Materials Science Institute, 1252 University of Oregon, Eugene, OR, USA 97403-1252
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6
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Waninger JJ, Beyett TS, Gadkari VV, Siebenaler RF, Kenum C, Shankar S, Ruotolo BT, Chinnaiyan AM, Tesmer JJ. Biochemical characterization of the interaction between KRAS and Argonaute 2. Biochem Biophys Rep 2022; 29:101191. [PMID: 34988297 PMCID: PMC8695255 DOI: 10.1016/j.bbrep.2021.101191] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 12/09/2021] [Accepted: 12/14/2021] [Indexed: 12/01/2022] Open
Abstract
Oncogenic mutations in KRAS result in a constitutively active, GTP-bound form that in turn activates many proliferative pathways. However, because of its compact and simple architecture, directly targeting KRAS with small molecule drugs has been challenging. Another approach is to identify targetable proteins that interact with KRAS. Argonaute 2 (AGO2) was recently identified as a protein that facilitates RAS-driven oncogenesis. Whereas previous studies described the in vivo effect of AGO2 on cancer progression in cells harboring mutated KRAS, here we sought to examine their direct interaction using purified proteins. We show that full length AGO2 co-immunoprecipitates with KRAS using purified components, however, a complex between FL AGO2 and KRAS could not be isolated. We also generated a smaller N-terminal fragment of AGO2 (NtAGO2) which is believed to represent the primary binding site of KRAS. A complex with NtAGO2 could be detected via ion-mobility mass spectrometry and size exclusion chromatography. However, the data suggest that the interaction of KRAS with purified AGO2 (NtAGO2 or FL AGO2) is weak and likely requires additional cellular components or proteo-forms of AGO2 that are not readily available in our purified assay systems. Future studies are needed to determine what conformation or modifications of AGO2 are necessary to enrich KRAS association and regulate its activities.
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Affiliation(s)
- Jessica J. Waninger
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, 48109, USA
- Department of Medical Education, University of Michigan, Ann Arbor, MI, USA
- Department of Cellular and Molecular Biology, University of Michigan, Ann Arbor, MI, USA
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA
| | - Tyler S. Beyett
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
| | - Varun V. Gadkari
- Department of Chemistry, University of Michigan, Ann Arbor, MI, USA
| | - Ronald F. Siebenaler
- Department of Medical Education, University of Michigan, Ann Arbor, MI, USA
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA
| | - Carson Kenum
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Sunita Shankar
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, 48109, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA
| | | | - Arul M. Chinnaiyan
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, 48109, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
- Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Urology, University of Michigan, Ann Arbor, MI, USA
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA
| | - John J.G. Tesmer
- Departments of Biological Sciences and Medicinal Chemistry & Molecular Pharmacology, Purdue University, Indiana, USA
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7
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Swansiger AK, Marty MT, Prell JS. Fourier-Transform Approach for Reconstructing Macromolecular Mass Defect Profiles. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:172-180. [PMID: 34913687 DOI: 10.1021/jasms.1c00317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
State-of-the-art native mass spectrometry (MS) methods have been developed for analysis of highly heterogeneous intact complexes and have provided much insight into the structure and properties of noncovalent assemblies that can be difficult to study using denatured proteins. These native MS methods can often be used to study even highly polydisperse membrane proteins embedded in detergent micelles, nanodiscs, and other membrane mimics. However, characterizing highly polydisperse native complexes which are also heterogeneous presents additional challenges for native MS. Macromolecular mass defect (MMD) analysis aims to characterize heterogeneous ion populations obfuscated by adduct polydispersity and reveal the distribution of "base" masses, and was recently implemented in the Bayesian analysis software UniDec. Here, we illustrate an alternative, orthogonal MMD analysis method implemented in the deconvolution program iFAMS, which takes advantage of Fourier transform (FT) to deconvolve low-resolution data with few user-input parameters and which can provide high quality results even for mass spectra with a signal-to-noise ratio of ∼5:1. Agreement between this method, which is based on frequency-domain data, and the mass-domain algorithm of UniDec provides strong evidence that both methods can accurately characterize highly polydisperse and heterogeneous ion populations. The FT algorithm is expected to be very useful in characterizing many types of analytes ranging from membrane proteins to polymer-conjugated proteins, branched polymers, and other large analytes, as well as for reconstructing isotope profiles for highly complex but still isotope-resolved mass spectra.
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Affiliation(s)
- Andrew K Swansiger
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon 97403-1253, United States
| | - Michael T Marty
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona 85721, United States
| | - James S Prell
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon 97403-1253, United States
- Materials Science Institute, University of Oregon, Eugene, Oregon 97403-1252, United States
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8
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Townsend JA, Sanders HM, Rolland AD, Park CK, Horton NC, Prell JS, Wang J, Marty MT. Influenza AM2 Channel Oligomerization Is Sensitive to Its Chemical Environment. Anal Chem 2021; 93:16273-16281. [PMID: 34813702 DOI: 10.1021/acs.analchem.1c04660] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Viroporins are small viral ion channels that play important roles in the viral infection cycle and are proven antiviral drug targets. Matrix protein 2 from influenza A (AM2) is the best-characterized viroporin, and the current paradigm is that AM2 forms monodisperse tetramers. Here, we used native mass spectrometry and other techniques to characterize the oligomeric state of both the full-length and transmembrane (TM) domain of AM2 in a variety of different pH and detergent conditions. Unexpectedly, we discovered that AM2 formed a range of different oligomeric complexes that were strongly influenced by the local chemical environment. Native mass spectrometry of AM2 in nanodiscs with different lipids showed that lipids also affected the oligomeric states of AM2. Finally, nanodiscs uniquely enabled the measurement of amantadine binding stoichiometries to AM2 in the intact lipid bilayer. These unexpected results reveal that AM2 can form a wider range of oligomeric states than previously thought possible, which may provide new potential mechanisms of influenza pathology and pharmacology.
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Affiliation(s)
- Julia A Townsend
- Department of Chemistry and Biochemistry, The University of Arizona, Tucson, Arizona 85721, United States
| | - Henry M Sanders
- Department of Chemistry and Biochemistry, The University of Arizona, Tucson, Arizona 85721, United States
| | - Amber D Rolland
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon 97403, United States.,Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403, United States
| | - Chad K Park
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona 85721, United States
| | - Nancy C Horton
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona 85721, United States
| | - James S Prell
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon 97403, United States.,Materials Science Institute, University of Oregon, Eugene, Oregon 97403, United States
| | - Jun Wang
- Department of Pharmacology and Toxicology, The University of Arizona, Tucson, Arizona 85721, United States.,Bio5 Institute, The University of Arizona, Tucson, Arizona 85721, United States
| | - Michael T Marty
- Department of Chemistry and Biochemistry, The University of Arizona, Tucson, Arizona 85721, United States.,Bio5 Institute, The University of Arizona, Tucson, Arizona 85721, United States
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9
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Donor MT, Wilson JW, Shepherd SO, Prell JS. Lipid Head Group Adduction to Soluble Proteins Follows Gas-Phase Basicity Predictions: Dissociation Barriers and Charge Abstraction. INTERNATIONAL JOURNAL OF MASS SPECTROMETRY 2021; 469:116670. [PMID: 34421332 PMCID: PMC8372978 DOI: 10.1016/j.ijms.2021.116670] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Native mass spectrometry analysis of membrane proteins has yielded many useful insights in recent years with respect to membrane protein-lipid interactions, including identifying specific interactions and even measuring binding affinities based on observed abundances of lipid-bound ions after collision-induced dissociation (CID). However, the behavior of non-covalent complexes subjected to extensive CID can in principle be affected by numerous factors related to gas-phase chemistry, including gas-phase basicity (GB) and acidity, shared-proton bonds, and other factors. A recent report from our group showed that common lipids span a wide range of GB values. Notably, phosphatidylcholine (PC) and sphingomyelin lipids are more basic than arginine, suggesting they may strip charge upon dissociation in positive ion mode, while phosphoserine lipids are slightly less basic than arginine and may form especially strong shared-proton bonds. Here, we use CID to probe the strength of non-specific gas-phase interactions between lipid head groups and several soluble proteins, used to deliberately avoid possible physiological protein-lipid interactions. The strengths of the protein-head group interactions follow the trend predicted based solely on lipid and amino acid GBs: phosphoserine (PS) head group forms the strongest bonds with these proteins and out-competes the other head groups studied, while glycerophosphocholine (GPC) head groups form the weakest interactions and dissociate carrying away a positive charge. These results indicate that gas-phase thermochemistry can play an important role in determining which head groups remain bound to protein ions with native-like structures and charge states in positive ion mode upon extensive collisional activation.
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Affiliation(s)
- Micah T. Donor
- Department of Chemistry and Biochemistry, 1253 University of Oregon, Eugene OR 97403-1253
| | - Jesse W. Wilson
- Department of Chemistry and Biochemistry, 1253 University of Oregon, Eugene OR 97403-1253
| | - Samantha O. Shepherd
- Department of Chemistry and Biochemistry, 1253 University of Oregon, Eugene OR 97403-1253
| | - James S. Prell
- Department of Chemistry and Biochemistry, 1253 University of Oregon, Eugene OR 97403-1253
- Materials Science Institute, University of Oregon, 1252 University of Oregon, Eugene, OR 97403-1252
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10
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Thirunavukarasu D, Cheng LY, Song P, Chen SX, Borad MJ, Kwong L, James P, Turner DJ, Zhang DY. Oncogene Concatenated Enriched Amplicon Nanopore Sequencing for rapid, accurate, and affordable somatic mutation detection. Genome Biol 2021; 22:227. [PMID: 34482832 PMCID: PMC8419911 DOI: 10.1186/s13059-021-02449-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 08/02/2021] [Indexed: 12/13/2022] Open
Abstract
We develop the Oncogene Concatenated Enriched Amplicon Nanopore Sequencing (OCEANS) method, in which variants with low variant allele frequency (VAFs) are amplified and subsequently concatenated for Nanopore Sequencing. OCEANS allows accurate detection of somatic mutations with VAF limits of detection between 0.05 and 1%. We construct 4 distinct multi-gene OCEANS panels targeting recurrent mutations in acute myeloid leukemia, melanoma, non-small- cell lung cancer, and hepatocellular carcinoma and validate them on clinical samples. By demonstrating detection of low VAF single nucleotide variant mutations using Nanopore Sequencing, OCEANS is poised to enable same-day clinical sequencing panels.
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Affiliation(s)
| | - Lauren Y Cheng
- Department of Bioengineering, Rice University, Houston, TX, USA
| | - Ping Song
- Department of Bioengineering, Rice University, Houston, TX, USA
| | | | | | - Lawrence Kwong
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | | | | | - David Yu Zhang
- NuProbe USA Inc, Houston, TX, USA.
- Department of Bioengineering, Rice University, Houston, TX, USA.
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11
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Ieritano C, Lee A, Crouse J, Bowman Z, Mashmoushi N, Crossley PM, Friebe BP, Campbell JL, Hopkins WS. Determining Collision Cross Sections from Differential Ion Mobility Spectrometry. Anal Chem 2021; 93:8937-8944. [PMID: 34132546 DOI: 10.1021/acs.analchem.1c01420] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The experimental determination of ion-neutral collision cross sections (CCSs) is generally confined to ion mobility spectrometry (IMS) technologies that operate under the so-called low-field limit or those that enable empirical calibration strategies (e.g., traveling wave IMS; TWIMS). Correlation of ion trajectories to CCS in other non-linear IMS techniques that employ dynamic electric fields, such as differential mobility spectrometry (DMS), has remained a challenge since its inception. Here, we describe how an ion's CCS can be measured from DMS experiments using a machine learning (ML)-based calibration. The differential mobility of 409 molecular cations (m/z: 86-683 Da and CCS 110-236 Å2) was measured in a N2 environment to train the ML framework. Several open-source ML routines were tested and trained using DMS-MS data in the form of the parent ion's m/z and the compensation voltage required for elution at specific separation voltages between 1500 and 4000 V. The best performing ML model, random forest regression, predicted CCSs with a mean absolute percent error of 2.6 ± 0.4% for analytes excluded from the training set (i.e., out-of-the-bag external validation). This accuracy approaches the inherent statistical error of ∼2.2% for the MobCal-MPI CCS calculations employed for training purposes and the <2% threshold for matching literature CCSs with those obtained on a TWIMS platform.
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Affiliation(s)
- Christian Ieritano
- Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo N2L 3G1, Ontario, Canada
- WaterMine Innovation, Inc., Waterloo N0B 2T0, Ontario, Canada
- Waterloo Institute for Nanotechnology, University of 200 University Avenue West, Waterloo N2L 3G1, Ontario, Canada
| | - Arthur Lee
- Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo N2L 3G1, Ontario, Canada
- WaterMine Innovation, Inc., Waterloo N0B 2T0, Ontario, Canada
- Waterloo Institute for Nanotechnology, University of 200 University Avenue West, Waterloo N2L 3G1, Ontario, Canada
| | - Jeff Crouse
- Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo N2L 3G1, Ontario, Canada
- WaterMine Innovation, Inc., Waterloo N0B 2T0, Ontario, Canada
| | - Zack Bowman
- Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo N2L 3G1, Ontario, Canada
| | - Nour Mashmoushi
- Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo N2L 3G1, Ontario, Canada
- Waterloo Institute for Nanotechnology, University of 200 University Avenue West, Waterloo N2L 3G1, Ontario, Canada
| | - Paige M Crossley
- Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo N2L 3G1, Ontario, Canada
| | - Benjamin P Friebe
- Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo N2L 3G1, Ontario, Canada
| | - J Larry Campbell
- Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo N2L 3G1, Ontario, Canada
- WaterMine Innovation, Inc., Waterloo N0B 2T0, Ontario, Canada
- Bedrock Scientific Inc., Milton, L6T 6J9, Ontario, Canada
| | - W Scott Hopkins
- Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo N2L 3G1, Ontario, Canada
- WaterMine Innovation, Inc., Waterloo N0B 2T0, Ontario, Canada
- Waterloo Institute for Nanotechnology, University of 200 University Avenue West, Waterloo N2L 3G1, Ontario, Canada
- Centre for Eye and Vision Research, Hong Kong Science Park, New Territories 999077, Hong Kong
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12
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Affiliation(s)
- James E. Keener
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85721, USA
| | - Guozhi Zhang
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85721, USA
| | - Michael T. Marty
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85721, USA
- Bio5 Institute, University of Arizona, Tucson, AZ 85721, USA
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13
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Baker K, Kwok E, Reardon P, Rodriguez DJ, Rolland AD, Wilson JW, Prell JS, Nyarko A. Yorkie-Warts Complexes are an Ensemble of Interconverting Conformers Formed by Multivalent Interactions. J Mol Biol 2020; 433:166776. [PMID: 33383033 DOI: 10.1016/j.jmb.2020.166776] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 11/18/2020] [Accepted: 12/16/2020] [Indexed: 11/17/2022]
Abstract
Multiple copies of WW domains and PPXY motif sequences are often reciprocally presented by regulatory proteins that interact at crucial regulatory steps in the cell life cycle. While biophysical studies of single WW domain-single PPXY motif complexes abound in the literature, the molecular mechanisms of multivalent WW domain-PPXY assemblies are still poorly understood. By way of investigating such assemblies, we characterized the multivalent association of the entire cognate binding domains, two WW sequences and five PPXY motifs respectively, of the Yorkie transcription coactivator and the Warts tumor suppressor. Isothermal titration calorimetry, sedimentation velocity, size-exclusion chromatography coupled to multi-angle light scattering and native-state mass spectrometry of Yorkie WW domains interactions with the full-length Warts PPXY domain, and numerous PPXY motif variants of Warts show that the two proteins assemble via binding of tandem WW domains to adjacent PPXY pairs to produce an ensemble of interconverting complexes of variable stoichiometries, binding energetics and WW domain occupancy. Apparently, the Yorkie tandem WW domains first target the two adjacent PPXY motifs at the C-terminus of the Warts polypeptide and additional WW domains bind unoccupied motifs. Similar ensembles of interconverting conformers may be common in multivalent WW domain-PPXY interactions to promote the adaptability and versatility of WW domain-PPXY mediated cellular processes.
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Affiliation(s)
- Kasie Baker
- Department of Biochemistry & Biophysics, Oregon State University, Corvallis, OR 97331, USA
| | - Ethiene Kwok
- Department of Biochemistry & Biophysics, Oregon State University, Corvallis, OR 97331, USA
| | - Patrick Reardon
- Department of Biochemistry & Biophysics, Oregon State University, Corvallis, OR 97331, USA
| | - Diego J Rodriguez
- Department of Biochemistry & Biophysics, Oregon State University, Corvallis, OR 97331, USA
| | - Amber D Rolland
- Department of Chemistry & Biochemistry, University of Oregon, Eugene, OR 97403, USA; Institute of Molecular Biology, University of Oregon, Eugene, OR 97403, USA
| | - Jesse W Wilson
- Department of Chemistry & Biochemistry, University of Oregon, Eugene, OR 97403, USA; Institute of Molecular Biology, University of Oregon, Eugene, OR 97403, USA
| | - James S Prell
- Department of Chemistry & Biochemistry, University of Oregon, Eugene, OR 97403, USA; Materials Science Institute, University of Oregon, Eugene, OR 97403, USA
| | - Afua Nyarko
- Department of Biochemistry & Biophysics, Oregon State University, Corvallis, OR 97331, USA.
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14
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Marty MT. Nanodiscs and Mass Spectrometry: Making Membranes Fly. INTERNATIONAL JOURNAL OF MASS SPECTROMETRY 2020; 458:116436. [PMID: 33100891 PMCID: PMC7584149 DOI: 10.1016/j.ijms.2020.116436] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Cells are surrounded by a protective lipid bilayer membrane, and membrane proteins in the bilayer control the flow of chemicals, information, and energy across this barrier. Many therapeutics target membrane proteins, and some directly target the lipid membrane itself. However, interactions within biological membranes are challenging to study due to their heterogeneity and insolubility. Mass spectrometry (MS) has become a powerful technique for studying membrane proteins, especially how membrane proteins interact with their surrounding lipid environment. Although detergent micelles are the most common membrane mimetic, nanodiscs are emerging as a promising platform for MS. Nanodiscs, nanoscale lipid bilayers encircled by two scaffold proteins, provide a controllable lipid bilayer for solubilizing membrane proteins. This Young Scientist Perspective focuses on native MS of intact nanodiscs and highlights the unique experiments enabled by making membranes fly, including studying membrane protein-lipid interactions and exploring the specificity of fragile transmembrane peptide complexes. It will also explore current challenges and future perspectives for interfacing nanodiscs with MS.
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Affiliation(s)
- Michael T Marty
- Department of Chemistry and Biochemistry and Bio5 Institute, University of Arizona, Tucson, AZ 85721
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15
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Logsdon GA, Vollger MR, Eichler EE. Long-read human genome sequencing and its applications. Nat Rev Genet 2020; 21:597-614. [PMID: 32504078 PMCID: PMC7877196 DOI: 10.1038/s41576-020-0236-x] [Citation(s) in RCA: 445] [Impact Index Per Article: 111.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/31/2020] [Indexed: 12/27/2022]
Abstract
Over the past decade, long-read, single-molecule DNA sequencing technologies have emerged as powerful players in genomics. With the ability to generate reads tens to thousands of kilobases in length with an accuracy approaching that of short-read sequencing technologies, these platforms have proven their ability to resolve some of the most challenging regions of the human genome, detect previously inaccessible structural variants and generate some of the first telomere-to-telomere assemblies of whole chromosomes. Long-read sequencing technologies will soon permit the routine assembly of diploid genomes, which will revolutionize genomics by revealing the full spectrum of human genetic variation, resolving some of the missing heritability and leading to the discovery of novel mechanisms of disease.
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Affiliation(s)
- Glennis A Logsdon
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Mitchell R Vollger
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA.
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA.
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16
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Li Z, Yu T, Paul R, Fan J, Yang Y, Wei Q. Agricultural nanodiagnostics for plant diseases: recent advances and challenges. NANOSCALE ADVANCES 2020; 2:3083-3094. [PMID: 36134297 PMCID: PMC9417629 DOI: 10.1039/c9na00724e] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2019] [Accepted: 07/06/2020] [Indexed: 05/18/2023]
Abstract
Crop diseases caused by pathogenic microorganisms pose severe threats to the global food supply. Effective diagnostic tools for timely determination of plant diseases become essential to the assurance of agricultural sustainability and global food security. Nucleic acid- and antibody-based molecular assays are gold-standard methodologies for the diagnosis of plant diseases, but the analyzing procedures are complex and laborious. The prominent physical or chemical properties of nanomaterials have enabled their use as innovative and high-performance diagnostic tools for numerous plant pathogens and other important disease biomarkers. Engineered nanomaterials have been incorporated into traditional laboratory molecular assays or sequencing technologies that offer notable enhancement in sensitivity and selectivity. Meanwhile, nanostructure-supported noninvasive detection tools combined with portable imaging devices (e.g., smartphones) have paved the way for fast and on-site diagnosis of plant diseases and long-term monitoring of plant health conditions, especially in resource-poor settings.
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Affiliation(s)
- Zheng Li
- Institute for Advanced Study, Shenzhen University Shenzhen 518060 P. R. China
- Department of Chemical and Biomolecular Engineering, North Carolina State University 911 Partners Way, Campus Box 7905 Raleigh NC 27695 USA
| | - Tao Yu
- Department of Chemical and Biomolecular Engineering, North Carolina State University 911 Partners Way, Campus Box 7905 Raleigh NC 27695 USA
| | - Rajesh Paul
- Department of Chemical and Biomolecular Engineering, North Carolina State University 911 Partners Way, Campus Box 7905 Raleigh NC 27695 USA
| | - Jingyuan Fan
- Department of Polymer Science and Engineering, Zhejiang University Hangzhou 310027 P. R. China
| | - Yuming Yang
- Department of Agrotechnology and Food Sciences, Wageningen University 6708 PB Wageningen The Netherlands
| | - Qingshan Wei
- Department of Chemical and Biomolecular Engineering, North Carolina State University 911 Partners Way, Campus Box 7905 Raleigh NC 27695 USA
- Emerging Plant Disease and Global Food Security Cluster, North Carolina State University USA
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17
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Wang M, Fu A, Hu B, Tong Y, Liu R, Liu Z, Gu J, Xiang B, Liu J, Jiang W, Shen G, Zhao W, Men D, Deng Z, Yu L, Wei W, Li Y, Liu T. Nanopore Targeted Sequencing for the Accurate and Comprehensive Detection of SARS-CoV-2 and Other Respiratory Viruses. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2020; 16:e2002169. [PMID: 32578378 PMCID: PMC7361204 DOI: 10.1002/smll.202002169] [Citation(s) in RCA: 126] [Impact Index Per Article: 31.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 05/27/2020] [Indexed: 05/17/2023]
Abstract
The ongoing global novel coronavirus pneumonia COVID-19 outbreak has engendered numerous cases of infection and death. COVID-19 diagnosis relies upon nucleic acid detection; however, currently recommended methods exhibit high false-negative rates and are unable to identify other respiratory virus infections, thereby resulting in patient misdiagnosis and impeding epidemic containment. Combining the advantages of targeted amplification and long-read, real-time nanopore sequencing, herein, nanopore targeted sequencing (NTS) is developed to detect SARS-CoV-2 and other respiratory viruses simultaneously within 6-10 h, with a limit of detection of ten standard plasmid copies per reaction. Compared with its specificity for five common respiratory viruses, the specificity of NTS for SARS-CoV-2 reaches 100%. Parallel testing with approved real-time reverse transcription-polymerase chain reaction kits for SARS-CoV-2 and NTS using 61 nucleic acid samples from suspected COVID-19 cases show that NTS identifies more infected patients (22/61) as positive, while also effectively monitoring for mutated nucleic acid sequences, categorizing types of SARS-CoV-2, and detecting other respiratory viruses in the test sample. NTS is thus suitable for COVID-19 diagnosis; moreover, this platform can be further extended for diagnosing other viruses and pathogens.
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Affiliation(s)
- Ming Wang
- Department of Clinical LaboratoryRenmin Hospital of Wuhan UniversityWuhan430060China
| | - Aisi Fu
- Key Laboratory of Combinatorial Biosynthesis and Drug DiscoveryMinistry of Education and Wuhan University School of Pharmaceutical SciencesWuhan430071China
| | - Ben Hu
- Key Laboratory of Combinatorial Biosynthesis and Drug DiscoveryMinistry of Education and Wuhan University School of Pharmaceutical SciencesWuhan430071China
| | - Yongqing Tong
- Department of Clinical LaboratoryRenmin Hospital of Wuhan UniversityWuhan430060China
| | - Ran Liu
- Key Laboratory of Combinatorial Biosynthesis and Drug DiscoveryMinistry of Education and Wuhan University School of Pharmaceutical SciencesWuhan430071China
| | - Zhen Liu
- CAS Key Laboratory of Computational BiologyCAS‐MPG Partner Institute for Computational BiologyShanghai Institute of Nutrition and HealthUniversity of Chinese Academy of SciencesChinese Academy of SciencesShanghai200031China
| | - Jiashuang Gu
- Wuhan Dgensee Clinical Laboratory Co., Ltd.Wuhan430075China
| | - Bin Xiang
- CAS Key Laboratory of Computational BiologyCAS‐MPG Partner Institute for Computational BiologyShanghai Institute of Nutrition and HealthUniversity of Chinese Academy of SciencesChinese Academy of SciencesShanghai200031China
| | - Jianghao Liu
- Wuhan Dgensee Clinical Laboratory Co., Ltd.Wuhan430075China
| | - Wen Jiang
- Wuhan Dgensee Clinical Laboratory Co., Ltd.Wuhan430075China
| | - Gaigai Shen
- Key Laboratory of Combinatorial Biosynthesis and Drug DiscoveryMinistry of Education and Wuhan University School of Pharmaceutical SciencesWuhan430071China
| | - Wanxu Zhao
- Key Laboratory of Combinatorial Biosynthesis and Drug DiscoveryMinistry of Education and Wuhan University School of Pharmaceutical SciencesWuhan430071China
| | - Dong Men
- Wuhan Institute of VirologyChinese Academy of SciencesWuhan430071China
| | - Zixin Deng
- Key Laboratory of Combinatorial Biosynthesis and Drug DiscoveryMinistry of Education and Wuhan University School of Pharmaceutical SciencesWuhan430071China
| | - Lilei Yu
- Department of Internal MedicineRenmin Hospital of Wuhan UniversityWuhan430060China
| | - Wu Wei
- CAS Key Laboratory of Computational BiologyCAS‐MPG Partner Institute for Computational BiologyShanghai Institute of Nutrition and HealthUniversity of Chinese Academy of SciencesChinese Academy of SciencesShanghai200031China
- Center for Biomedical InformaticsShanghai Engineering Research Center for Big Data in Pediatric Precision MedicineShanghai Children's HospitalShanghai Jiao Tong UniversityShanghai200040China
| | - Yan Li
- Department of Clinical LaboratoryRenmin Hospital of Wuhan UniversityWuhan430060China
| | - Tiangang Liu
- Key Laboratory of Combinatorial Biosynthesis and Drug DiscoveryMinistry of Education and Wuhan University School of Pharmaceutical SciencesWuhan430071China
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18
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Lyu J, Liu Y, McCabe JW, Schrecke S, Fang L, Russell DH, Laganowsky A. Discovery of Potent Charge-Reducing Molecules for Native Ion Mobility Mass Spectrometry Studies. Anal Chem 2020; 92:11242-11249. [PMID: 32672445 DOI: 10.1021/acs.analchem.0c01826] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
There is growing interest in the characterization of protein complexes and their interactions with ligands using native ion mobility mass spectrometry. A particular challenge, especially for membrane proteins, is preserving noncovalent interactions and maintaining native-like structures. Different approaches have been developed to minimize activation of protein complexes by manipulating charge on protein complexes in solution and the gas-phase. Here, we report the utility of polyamines that have exceptionally high charge-reducing potencies with some molecules requiring 5-fold less than trimethylamine oxide to elicit the same effect. The charge-reducing molecules do not adduct to membrane protein complexes and are also compatible with ion-mobility mass spectrometry, paving the way for improved methods of charge reduction.
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Affiliation(s)
- Jixing Lyu
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Yang Liu
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Jacob W McCabe
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Samantha Schrecke
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Lei Fang
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - David H Russell
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Arthur Laganowsky
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
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19
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Wilson JW, Donor MT, Shepherd SO, Prell JS. Increasing Collisional Activation of Protein Complexes Using Smaller Aperture Source Sampling Cones on a Synapt Q-IM-TOF Instrument with a Stepwave Source. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:10.1021/jasms.0c00117. [PMID: 32628844 PMCID: PMC7855748 DOI: 10.1021/jasms.0c00117] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Quadrupole ion mobility time-of-flight (Q-IM-TOF) mass spectrometers have revolutionized investigation of native biomolecular complexes. High pressures in the sources of these instruments aid transmission of protein complexes through damping of kinetic energy by collisional cooling. As adducts are removed through collisional heating (declustering), excessive collisional cooling can prevent removal of nonspecific adducts from protein ions, leading to inaccurate mass measurements, broad mass spectral peaks, and obfuscation of ligand binding. We show that reducing the source pressure using smaller aperture source sampling cones (SC) in a Waters Synapt G2-Si instrument increases protein ion heating by decreasing collisional cooling, providing a simple way to enhance removal of adducted salts from soluble proteins (GroEL 14-mer) and detergents from a transmembrane protein complex (heptameric Staphylococcus aureus α-hemolysin, αHL). These experiments are supported by ion heating and cooling simulations which demonstrate reduced collisional cooling at lower source pressures. Using these easily swapped sample cones of different apertures is a facile approach to reproducibly extend the range of activation in Synapt-type instruments.
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Affiliation(s)
- Jesse W. Wilson
- Department of Chemistry and Biochemistry, University of Oregon, 1253 University of Oregon Eugene, OR, USA, 97403-1253
| | - Micah T. Donor
- Department of Chemistry and Biochemistry, University of Oregon, 1253 University of Oregon Eugene, OR, USA, 97403-1253
| | - Samantha O. Shepherd
- Department of Chemistry and Biochemistry, University of Oregon, 1253 University of Oregon Eugene, OR, USA, 97403-1253
| | - James S. Prell
- Department of Chemistry and Biochemistry, University of Oregon, 1253 University of Oregon Eugene, OR, USA, 97403-1253
- Materials Science Institute, University of Oregon, 1252 University of Oregon, OR, USA, 97403-1252
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20
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Cleary SP, Prell JS. Distinct classes of multi-subunit heterogeneity: analysis using Fourier Transform methods and native mass spectrometry. Analyst 2020; 145:4688-4697. [PMID: 32459233 PMCID: PMC8483610 DOI: 10.1039/d0an00726a] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Native electrospray mass spectrometry is a powerful method for determining the native stoichiometry of many polydisperse multi-subunit biological complexes, including multi-subunit protein complexes and lipid-bound transmembrane proteins. However, when polydispersity results from incorporation of multiple copies of two or more different subunits, it can be difficult to analyze subunit stoichiometry using conventional mass spectrometry analysis methods, especially when m/z distributions for different charge states overlap in the mass spectrum. It was recently demonstrated by Marty and co-workers (K. K. Hoi, et al., Anal. Chem., 2016, 88, 6199-6204) that Fourier Transform (FT)-based methods can determine the bulk average lipid composition of protein-lipid Nanodiscs assembled with two different lipids, but a detailed statistical description of the composition of more general polydisperse two-subunit populations is still difficult to achieve. This results from the vast number of ways in which the two types of subunit can be distributed within the analyte ensemble. Here, we present a theoretical description of three common classes of heterogeneity for mixed-subunit analytes and demonstrate how to differentiate and analyze them using mass spectrometry and FT methods. First, we first describe FT-based analysis of mass spectra corresponding to simple superpositions, convolutions, and multinomial distributions for two or more different subunit types using model data sets. We then apply these principles with real samples, including mixtures of single-lipid Nanodiscs in the same solution (superposition), mixed-lipid Nanodiscs and copolymers (convolutions), and isotope distribution for ubiquitin (multinomial distribution). This classification scheme and the FT method used to study these analyte classes should be broadly useful in mass spectrometry as well as other techniques where overlapping, periodic signals arising from analyte mixtures are common.
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Affiliation(s)
- Sean P Cleary
- Department of Chemistry and Biochemistry, 1253 University of Oregon, Eugene, OR 97403-1253, USA.
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21
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Amarasinghe SL, Su S, Dong X, Zappia L, Ritchie ME, Gouil Q. Opportunities and challenges in long-read sequencing data analysis. Genome Biol 2020; 21:30. [PMID: 32033565 PMCID: PMC7006217 DOI: 10.1186/s13059-020-1935-5] [Citation(s) in RCA: 737] [Impact Index Per Article: 184.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Accepted: 01/15/2020] [Indexed: 12/11/2022] Open
Abstract
Long-read technologies are overcoming early limitations in accuracy and throughput, broadening their application domains in genomics. Dedicated analysis tools that take into account the characteristics of long-read data are thus required, but the fast pace of development of such tools can be overwhelming. To assist in the design and analysis of long-read sequencing projects, we review the current landscape of available tools and present an online interactive database, long-read-tools.org, to facilitate their browsing. We further focus on the principles of error correction, base modification detection, and long-read transcriptomics analysis and highlight the challenges that remain.
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Affiliation(s)
- Shanika L. Amarasinghe
- Epigenetics and Development Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, 3052 Australia
- Department of Medical Biology, The University of Melbourne, Parkville, 3010 Australia
| | - Shian Su
- Epigenetics and Development Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, 3052 Australia
- Department of Medical Biology, The University of Melbourne, Parkville, 3010 Australia
| | - Xueyi Dong
- Epigenetics and Development Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, 3052 Australia
- Department of Medical Biology, The University of Melbourne, Parkville, 3010 Australia
| | - Luke Zappia
- Bioinformatics, Murdoch Children’s Research Institute, Parkville, 3052 Australia
- School of Biosciences, Faculty of Science, The University of Melbourne, Parkville, 3010 Australia
| | - Matthew E. Ritchie
- Epigenetics and Development Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, 3052 Australia
- Department of Medical Biology, The University of Melbourne, Parkville, 3010 Australia
- School of Mathematics and StatisticsThe University of Melbourne, Parkville, 3010 Australia
| | - Quentin Gouil
- Epigenetics and Development Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, 3052 Australia
- Department of Medical Biology, The University of Melbourne, Parkville, 3010 Australia
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