Subjects -> PHYSICS (Total: 857 journals)
    - ELECTRICITY AND MAGNETISM (10 journals)
    - MECHANICS (22 journals)
    - NUCLEAR PHYSICS (53 journals)
    - OPTICS (92 journals)
    - PHYSICS (625 journals)
    - SOUND (25 journals)
    - THERMODYNAMICS (30 journals)

PHYSICS (625 journals)            First | 1 2 3 4 | Last

Showing 201 - 400 of 741 Journals sorted alphabetically
International Journal of Astronomy and Astrophysics     Open Access   (Followers: 36)
International Journal of Biological, Physical and Chemical Studies     Open Access  
International Journal of Computational Materials Science and Surface Engineering     Hybrid Journal   (Followers: 7)
International Journal of Damage Mechanics     Hybrid Journal   (Followers: 5)
International Journal of Engineering and Applied Physics     Open Access  
International Journal of Fatigue     Hybrid Journal   (Followers: 41)
International Journal of Fracture     Hybrid Journal   (Followers: 14)
International Journal of Geometric Methods in Modern Physics     Hybrid Journal   (Followers: 2)
International Journal of Geophysics     Open Access   (Followers: 5)
International Journal of Heat and Fluid Flow     Hybrid Journal   (Followers: 41)
International Journal of Low Radiation     Hybrid Journal  
International Journal of Low-Carbon Technologies     Open Access   (Followers: 1)
International Journal of Mass Spectrometry     Hybrid Journal   (Followers: 17)
International Journal of Material Forming     Hybrid Journal   (Followers: 1)
International Journal of Materials and Product Technology     Hybrid Journal   (Followers: 2)
International Journal of Mechanical Sciences     Hybrid Journal   (Followers: 14)
International Journal of Mechanics and Materials in Design     Hybrid Journal   (Followers: 7)
International Journal of Medical Physics, Clinical Engineering and Radiation Oncology     Open Access   (Followers: 11)
International Journal of Microstructure and Materials Properties     Hybrid Journal   (Followers: 7)
International Journal of Microwave Science and Technology     Open Access   (Followers: 12)
International Journal of Modeling, Simulation, and Scientific Computing     Hybrid Journal   (Followers: 3)
International Journal of Modern Physics A     Hybrid Journal   (Followers: 15)
International Journal of Modern Physics B     Hybrid Journal   (Followers: 12)
International Journal of Modern Physics C     Hybrid Journal   (Followers: 14)
International Journal of Modern Physics D     Hybrid Journal   (Followers: 13)
International Journal of Modern Physics E     Hybrid Journal   (Followers: 13)
International Journal of Multiphysics     Open Access  
International Journal of Nanomanufacturing     Hybrid Journal  
International Journal of Nanoscience     Hybrid Journal  
International Journal of Nanotechnology     Hybrid Journal   (Followers: 9)
International Journal of Non-Linear Mechanics     Hybrid Journal   (Followers: 8)
International Journal of Nonlinear Dynamics and Control     Hybrid Journal   (Followers: 6)
International Journal of Physics     Open Access   (Followers: 10)
International Journal of PIXE     Hybrid Journal  
International Journal of Plasticity     Hybrid Journal   (Followers: 7)
International Journal of Quantum Information     Hybrid Journal   (Followers: 6)
International Journal of Self-Propagating High-Temperature Synthesis     Hybrid Journal  
International Journal of Solids and Structures     Hybrid Journal   (Followers: 14)
International Journal of Surface Science and Engineering     Hybrid Journal   (Followers: 6)
International Journal of Theoretical and Applied Multiscale Mechanics     Hybrid Journal   (Followers: 3)
International Journal of Theoretical and Mathematical Physics     Open Access   (Followers: 13)
International Journal of Theoretical Physics     Hybrid Journal   (Followers: 17)
International Journal of Thermal Sciences     Hybrid Journal   (Followers: 18)
International Journal on Smart Sensing and Intelligent Systems     Open Access  
International Letters of Chemistry, Physics and Astronomy     Open Access   (Followers: 8)
International Materials Reviews     Hybrid Journal   (Followers: 15)
Iranian Journal of Medical Physics     Open Access  
Iranian Journal of Science and Technology, Transactions A : Science     Hybrid Journal  
Ironmaking & Steelmaking     Hybrid Journal   (Followers: 4)
Izvestiya, Atmospheric and Oceanic Physics     Full-text available via subscription   (Followers: 1)
Izvestiya, Physics of the Solid Earth     Hybrid Journal   (Followers: 2)
Jambura Physics Journal     Open Access  
JETP Letters     Hybrid Journal   (Followers: 3)
Journal of Adhesion Science and Technology     Hybrid Journal   (Followers: 10)
Journal of Advanced Physics     Full-text available via subscription   (Followers: 13)
Journal of Advances in Physics     Open Access   (Followers: 13)
Journal of Applied Mathematics and Physics     Open Access   (Followers: 9)
Journal of Applied Mechanics and Technical Physics     Hybrid Journal   (Followers: 7)
Journal of Applied Physics     Hybrid Journal   (Followers: 69)
Journal of Applied Spectroscopy     Hybrid Journal   (Followers: 9)
Journal of Astrophysics     Open Access   (Followers: 33)
Journal of Astrophysics and Astronomy     Open Access   (Followers: 58)
Journal of Building Physics     Hybrid Journal   (Followers: 1)
Journal of Chromatographic Science     Hybrid Journal   (Followers: 15)
Journal of Complex Networks     Hybrid Journal   (Followers: 1)
Journal of Composite Materials     Hybrid Journal   (Followers: 242)
Journal of Computational and Theoretical Transport     Hybrid Journal   (Followers: 2)
Journal of Computational Methods in Physics     Open Access   (Followers: 8)
Journal of Computational Physics     Hybrid Journal   (Followers: 59)
Journal of Computational Physics : X     Open Access   (Followers: 1)
Journal of Contemporary Physics (Armenian Academy of Sciences)     Hybrid Journal   (Followers: 9)
Journal of Dynamic Systems, Measurement, and Control     Full-text available via subscription   (Followers: 14)
Journal of Elasticity     Hybrid Journal   (Followers: 7)
Journal of Electron Spectroscopy and Related Phenomena     Hybrid Journal   (Followers: 3)
Journal of Electronic Materials     Hybrid Journal   (Followers: 3)
Journal of Electronics Cooling and Thermal Control     Open Access   (Followers: 9)
Journal of Engineering Materials and Technology     Full-text available via subscription   (Followers: 17)
Journal of Engineering Physics and Thermophysics     Hybrid Journal   (Followers: 2)
Journal of Experimental and Theoretical Physics     Hybrid Journal   (Followers: 4)
Journal of Experimental Physics     Open Access   (Followers: 3)
Journal of Fire Sciences     Hybrid Journal   (Followers: 6)
Journal of Geometry and Physics     Full-text available via subscription   (Followers: 2)
Journal of Geophysical Research : Space Physics     Full-text available via subscription   (Followers: 134)
Journal of Gravity     Open Access   (Followers: 4)
Journal of High Energy Astrophysics     Full-text available via subscription   (Followers: 25)
Journal of High Energy Physics     Hybrid Journal   (Followers: 17)
Journal of High Energy Physics, Gravitation and Cosmology     Open Access   (Followers: 2)
Journal of Hydrogels     Full-text available via subscription  
Journal of Hyperspectral Remote Sensing     Open Access   (Followers: 23)
Journal of Imaging     Open Access   (Followers: 3)
Journal of Information Display     Open Access   (Followers: 1)
Journal of Intelligent Material Systems and Structures     Hybrid Journal   (Followers: 8)
Journal of Lightwave Technology     Hybrid Journal   (Followers: 14)
Journal of Low Frequency Noise, Vibration and Active Control     Open Access   (Followers: 8)
Journal of Luminescence     Hybrid Journal   (Followers: 2)
Journal of Materials Engineering and Performance     Hybrid Journal   (Followers: 22)
Journal of Materials Physics and Chemistry     Open Access   (Followers: 7)
Journal of Materials Science     Hybrid Journal   (Followers: 25)
Journal of Materials Science : Materials in Electronics     Hybrid Journal   (Followers: 2)
Journal of Materials Science : Materials in Medicine     Hybrid Journal   (Followers: 1)
Journal of Mathematical Fluid Mechanics     Hybrid Journal   (Followers: 10)
Journal of Mathematical Physics     Hybrid Journal   (Followers: 25)
Journal of Medical Imaging and Health Informatics     Full-text available via subscription  
Journal of Medical Ultrasonics     Hybrid Journal   (Followers: 2)
Journal of Micro/Nanolithography MEMS and MOEMS     Hybrid Journal   (Followers: 24)
Journal of Molecular Spectroscopy     Hybrid Journal   (Followers: 6)
Journal of Motor Behavior     Hybrid Journal   (Followers: 8)
Journal of Multiscale Modeling     Hybrid Journal   (Followers: 1)
Journal of Nepal Physical Society     Open Access  
Journal of Nondestructive Evaluation     Hybrid Journal   (Followers: 11)
Journal of Nonlinear Dynamics     Open Access   (Followers: 6)
Journal of Nonlinear Mathematical Physics     Hybrid Journal   (Followers: 2)
Journal of Nuclear Physics, Material Sciences, Radiation and Applications     Open Access   (Followers: 6)
Journal of Optics     Hybrid Journal   (Followers: 17)
Journal of Photonics for Energy     Hybrid Journal   (Followers: 2)
Journal of Physical and Chemical Reference Data     Hybrid Journal   (Followers: 4)
Journal of Physical Chemistry B     Hybrid Journal   (Followers: 48)
Journal of Physical Chemistry C     Hybrid Journal   (Followers: 36)
Journal of Physical Oceanography     Hybrid Journal   (Followers: 18, SJR: 2.461, CiteScore: 3)
Journal of Physical Organic Chemistry     Hybrid Journal   (Followers: 8)
Journal of Physics and Chemistry of Solids     Hybrid Journal   (Followers: 3)
Journal of Plasma Physics     Hybrid Journal   (Followers: 21)
Journal of Polymer Science Part B: Polymer Physics     Hybrid Journal   (Followers: 22)
Journal of Porous Materials     Hybrid Journal   (Followers: 4)
Journal of Porphyrins and Phthalocyanines     Hybrid Journal   (Followers: 1)
Journal of Quantitative Spectroscopy and Radiative Transfer     Hybrid Journal   (Followers: 3)
Journal of Reinforced Plastics and Composites     Hybrid Journal   (Followers: 30)
Journal of Rheology     Full-text available via subscription   (Followers: 7)
Journal of Sandwich Structures and Materials     Hybrid Journal   (Followers: 4)
Journal of Scientific Research     Open Access  
Journal of Sensors     Open Access   (Followers: 25)
Journal of Sol-Gel Science and Technology     Hybrid Journal  
Journal of Solid State Physics     Open Access   (Followers: 8)
Journal of Spectroscopy     Open Access   (Followers: 6)
Journal of Superconductivity and Novel Magnetism     Partially Free   (Followers: 1)
Journal of Synchrotron Radiation     Open Access   (Followers: 3)
Journal of the American Society for Mass Spectrometry     Hybrid Journal   (Followers: 32)
Journal of the ICRU     Hybrid Journal  
Journal of the Korean Physical Society     Partially Free  
Journal of the Physical Society of Japan     Hybrid Journal   (Followers: 2)
Journal of Theoretical and Applied Physics     Open Access   (Followers: 9)
Journal of Tissue Engineering     Open Access   (Followers: 6)
Journal of Ultrasound in Medicine     Full-text available via subscription   (Followers: 11)
Journal of Vibration and Control     Hybrid Journal   (Followers: 42)
Journal of Visualization     Hybrid Journal   (Followers: 3)
Journal of Zhejiang University : Sceince A     Hybrid Journal  
JPSE (Journal of Physical Science and Engineering)     Open Access  
Jurnal Fisika     Open Access  
Jurnal Ilmiah Pendidikan Fisika Al-Biruni     Open Access  
Jurnal NEUTRINO     Open Access  
Jurnal Online of Physics     Open Access  
Jurnal Pendidikan Fisika Indonesia (Indonesian Journal of Physics Education)     Open Access  
Jurnal Penelitian Fisika dan Aplikasinya     Open Access  
Jurnal Penelitian Sains (JPS)     Open Access  
Karbala International Journal of Modern Science     Open Access  
Kasuari : Physics Education Journal     Open Access  
La Rivista del Nuovo Cimento     Hybrid Journal  
Lasers in Surgery and Medicine     Hybrid Journal   (Followers: 1)
Latvian Journal of Physics and Technical Sciences     Open Access  
Letters in High Energy Physics     Open Access  
Letters in Mathematical Physics     Hybrid Journal   (Followers: 4)
Light : Science & Applications     Open Access   (Followers: 3)
Living Reviews in Computational Astrophysics     Open Access   (Followers: 3)
Living Reviews in Relativity     Open Access  
Living Reviews in Solar Physics     Open Access   (Followers: 1)
Lubrication Science     Hybrid Journal   (Followers: 2)
Macalester Journal of Physics and Astronomy     Open Access   (Followers: 5)
Machining Science and Technology: An International Journal     Hybrid Journal   (Followers: 2)
Magnetic Resonance     Open Access  
Magnetic Resonance Letters     Open Access  
Magnetic Resonance Materials in Physics, Biology and Medicine     Hybrid Journal   (Followers: 3)
MAPAN     Hybrid Journal  
Mass Spectrometry Reviews     Hybrid Journal   (Followers: 31)
Matéria (Rio de Janeiro)     Open Access  
Materials and Design     Open Access   (Followers: 47)
Materials at High Temperatures     Full-text available via subscription   (Followers: 3)
Materials Chemistry and Physics     Full-text available via subscription   (Followers: 15)
Materials Research Bulletin     Hybrid Journal   (Followers: 25)
Materials Research Innovations     Hybrid Journal   (Followers: 1)
Materials Science     Hybrid Journal   (Followers: 7)
Materials Science and Engineering: A     Hybrid Journal   (Followers: 44)
Materials Science and Engineering: B     Hybrid Journal   (Followers: 22)
Materials Science and Engineering: R: Reports     Hybrid Journal   (Followers: 15)
Materials Science and Technology     Hybrid Journal   (Followers: 40)
Materials Today Physics     Hybrid Journal   (Followers: 1)
Matériaux & Techniques     Full-text available via subscription   (Followers: 2)
Mathematical Physics, Analysis and Geometry     Hybrid Journal   (Followers: 3)
Mathematics and Mechanics of Solids     Hybrid Journal   (Followers: 3)
Matter and Radiation at Extremes     Open Access   (Followers: 1)
Matters Select     Open Access  
Meccanica     Hybrid Journal   (Followers: 1)
Mechanics of Advanced Materials and Structures     Hybrid Journal   (Followers: 6)
Mechanics of Materials     Hybrid Journal   (Followers: 25)
Mechanics of Time-Dependent Materials     Hybrid Journal   (Followers: 2)
Mechanics Research Communications     Hybrid Journal   (Followers: 4)
Medical Physics     Hybrid Journal   (Followers: 17)
Micro and Nano Systems Letters     Open Access   (Followers: 6)
Microfluidics and Nanofluidics     Hybrid Journal   (Followers: 11)
Microporous and Mesoporous Materials     Hybrid Journal   (Followers: 9)
Modern Instrumentation     Open Access   (Followers: 57)

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Similar Journals
Journal Cover
Journal of the American Society for Mass Spectrometry
Journal Prestige (SJR): 1.058
Citation Impact (citeScore): 3
Number of Followers: 32  
 
  Hybrid Journal Hybrid journal (It can contain Open Access articles)
ISSN (Print) 1044-0305 - ISSN (Online) 1879-1123
Published by Springer-Verlag Homepage  [2469 journals]
  • 34th ASMS Asilomar Conference on Quantitative Analysis of
           Posttranslational Modifications by Mass Spectrometry

    • Free pre-print version: Loading...

      PubDate: 2019-12-01
      DOI: 10.1007/s13361-019-02351-y
       
  • Focus in Honor of Benjamin A. Garcia, Recipient of the 2018 ASMS Biemann
           Medal

    • Free pre-print version: Loading...

      PubDate: 2019-12-01
      DOI: 10.1007/s13361-019-02320-5
       
  • Deep Intact Proteoform Characterization in Human Cell Lysate Using High-pH
           and Low-pH Reversed-Phase Liquid Chromatography

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      Abstract: Abstract Post-translational modifications (PTMs) play critical roles in biological processes and have significant effects on the structures and dynamics of proteins. Top-down proteomics methods were developed for and applied to the study of intact proteins and their PTMs in human samples. However, the large dynamic range and complexity of human samples makes the study of human proteins challenging. To address these challenges, we developed a 2D pH RP/RPLC-MS/MS technique that fuses high-resolution separation and intact protein characterization to study the human proteins in HeLa cell lysate. Our results provide a deep coverage of soluble proteins in human cancer cells. Compared to 225 proteoforms from 124 proteins identified when 1D separation was used, 2778 proteoforms from 628 proteins were detected and characterized using our 2D separation method. Many proteoforms with critically functional PTMs including phosphorylation were characterized. Additionally, we present the first detection of intact human GcvH proteoforms with rare modifications such as octanoylation and lipoylation. Overall, the increase in the number of proteoforms identified using 2DLC separation is largely due to the reduction in sample complexity through improved separation resolution, which enables the detection of low-abundance PTM-modified proteoforms. We demonstrate here that 2D pH RP/RPLC is an effective technique to analyze complex protein samples using top-down proteomics.
      PubDate: 2019-12-01
      DOI: 10.1007/s13361-019-02315-2
       
  • Ion-Ion Interactions in Charge Detection Mass Spectrometry

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      Abstract: Abstract Charge detection mass spectrometry (CDMS) is a single-particle technique where the masses of individual ions are determined by simultaneously measuring their mass-to-charge ratio (m/z) and charge. Ions are usually trapped inside an electrostatic linear ion trap (ELIT) where they oscillate back and forth through a detection cylinder, generating a periodic signal that is analyzed by fast Fourier transforms. The oscillation frequency is related to the ion’s m/z, and the magnitude is related to the ion’s charge. In early work, multiple ion trapping events were discarded because there was a question about whether ion-ion interactions affected the results. Here, we report trajectory calculations performed to assess the influence of ion-ion interactions when multiple highly charged ions are simultaneously trapped in an ELIT. Ion-ion interactions cause trajectory and energy fluctuations that lead to variations in the oscillation frequencies that in turn degrade the precision and accuracy of the m/z measurements. The peak shapes acquire substantial high and low m/z tails, and the average m/z shifts to a higher value as the number of trapped ions increases. The effects of the ion-ion interactions are proportional to the product of the charges and the square root of the number of trapped ions and depend on the ions’ m/z distribution. For the ELIT design examined here, ion-ion interactions limit the m/z resolving power to several hundred for a typical homogeneous ion population.
      PubDate: 2019-12-01
      DOI: 10.1007/s13361-019-02343-y
       
  • Fragmentation Spectra Prediction and DNA Adducts Structural Determination

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      Abstract: Abstract In this work, chemical dynamics simulations were optimized and used to predict fragmentation mass spectra for DNA adduct structural determination. O6-methylguanine (O6-Me-G) was used as a simple model adduct to calculate theoretical spectra for comparison with measured high-resolution fragmentation data. An automatic protocol was established to consider the different tautomers accessible at a given energy and obtain final theoretical spectra by insertion of an initial tautomer. In the work reported here, the most stable tautomer was chosen as the initial structure, but in general, any structure could be considered. Allowing for the formation of the various possible tautomers during simulation calculations was found to be important to getting a more complete fragmentation spectrum. The calculated theoretical results reproduce the experimental peaks such that it was possible to determine reaction pathways and product structures. The calculated tautomerization network was crucial to correctly identifying all the observed ion peaks, showing that a mobile proton model holds not only for peptide fragmentation but also for nucleobases. Finally, first principles results were compared to simple machine learning fragmentation models.
      PubDate: 2019-12-01
      DOI: 10.1007/s13361-019-02348-7
       
  • Quantitation of Single and Combinatorial Histone Modifications by
           Integrated Chromatography of Bottom-up Peptides and Middle-down
           Polypeptide Tails

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      Abstract: Abstract The analysis of histone post-translational modifications (PTMs) by mass spectrometry (MS) has been critical to the advancement of the field of epigenetics. The most sensitive and accurate workflow is similar to the canonical proteomics analysis workflow (bottom-up MS), where histones are digested into short peptides (4-20 aa) and quantitated in extracted ion chromatograms. However, this limits the ability to detect even very common co-occurrences of modifications on histone proteins, preventing biological interpretation of PTM crosstalk. By digesting with GluC rather than trypsin, it is possible to produce long polypeptides corresponding to intact histone N-terminal tails (50-60 aa), where most modifications reside. This middle-down MS approach is used to study distant PTM co-existence. However, the most sensitive middle-down workflow uses weak cation exchange-hydrophilic interaction chromatography (WCX-HILIC), which is less robust than conventional reversed-phase chromatography. Additionally, since the buffer systems for middle-down and bottom-up proteomics differ substantially, it is cumbersome to toggle back and forth between both experimental setups on the same LC system. Here, we present a new workflow using porous graphitic carbon (PGC) as a stationary phase for histone analysis where bottom-up and middle-down sized histone peptides can be analyzed simultaneously using the same reversed-phase buffer setup. By using this protocol for middle-down sized peptides, we identified 406 uniquely modified intact histone tails and achieved a correlation of 0.85 between PGC and WCX-HILIC LC methods. Together, our method facilitates the analysis of single and combinatorial histone PTMs with much simpler applicability for conventional proteomics labs than the state-of-the-art middle-down MS.
      PubDate: 2019-12-01
      DOI: 10.1007/s13361-019-02303-6
       
  • High-Throughput Quantitative Top-Down Proteomics: Histone H4

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      Abstract: Abstract Proteins physiologically exist as “proteoforms” that arise from one gene and acquire additional function by post-translational modifications (PTM). When multiple PTMs coexist on single protein molecules, top-down proteomics becomes the only feasible method of characterization; however, most top-down methods have limited quantitative capacity and insufficient throughput to truly address proteoform biology. Here we demonstrate that top-down proteomics can be quantitative, reproducible, sensitive, and high throughput. The proteoforms of histone H4 are well studied both as a challenging proteoform identification problem and due to their essential role in the regulation of all eukaryotic DNA-templated processes. Much of histone H4’s function is obfuscated from prevailing methods due to combinatorial mechanisms. Starting from cells or tissues, after an optimized protein purification process, the H4 proteoforms are physically separated by on-line C3 chromatography, narrowly isolated in MS1 and sequenced with ETD fragmentation. We achieve more than 30 replicates from a single 35-mm tissue culture dish by loading 55 ng of H4 on column. Parallelization and automation yield a sustained throughput of 12 replicates per day. We achieve reproducible quantitation (average biological Pearson correlations of 0.89) of hundreds of proteoforms (about 200–300) over almost six orders of magnitude and an estimated LLoQ of 0.001% abundance. We demonstrate the capacity of the method to precisely measure well-established changes with sodium butyrate treatment of SUM159 cells. We show that the data produced by a quantitative top-down method can be amenable to parametric statistical comparisons and is capable of delineating relevant biological changes at the full proteoform level.
      PubDate: 2019-12-01
      DOI: 10.1007/s13361-019-02350-z
       
  • Comprehensive Characterization of the Recombinant Catalytic Subunit of
           cAMP-Dependent Protein Kinase by Top-Down Mass Spectrometry

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      Abstract: Abstract Reversible phosphorylation plays critical roles in cell growth, division, and signal transduction. Kinases which catalyze the transfer of γ-phosphate groups of nucleotide triphosphates to their substrates are central to the regulation of protein phosphorylation and are therefore important therapeutic targets. Top-down mass spectrometry (MS) presents unique opportunities to study protein kinases owing to its capabilities in comprehensive characterization of proteoforms that arise from alternative splicing, sequence variations, and post-translational modifications. Here, for the first time, we developed a top-down MS method to characterize the catalytic subunit (C-subunit) of an important kinase, cAMP-dependent protein kinase (PKA). The recombinant PKA C-subunit was expressed in Escherichia coli and successfully purified via his-tag affinity purification. By intact mass analysis with high resolution and high accuracy, four different proteoforms of the affinity-purified PKA C-subunit were detected, and the most abundant proteoform was found containing seven phosphorylations with the removal of N-terminal methionine. Subsequently, the seven phosphorylation sites of the most abundant PKA C-subunit proteoform were characterized simultaneously using tandem MS methods. Four sites were unambiguously identified as Ser10, Ser11, Ser18, and Ser30, and the remaining phosphorylation sites were localized to Ser2/Ser3, Ser358/Thr368, and Thr[215-224]Tyr in the PKA C-subunit sequence with a 20mer 6xHis-tag added at the N-terminus. Interestingly, four of these seven phosphorylation sites were located at the 6xHis-tag. Furthermore, we have performed dephosphorylation reaction by Lambda protein phosphatase and showed that all phosphorylations of the recombinant PKA C-subunit phosphoproteoforms were removed by this phosphatase.
      PubDate: 2019-12-01
      DOI: 10.1007/s13361-019-02341-0
       
  • Discovery of Missing Methylation Sites on Endogenous Peptides of Human
           Cell Lines

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      Abstract: Abstract Methylation of proteins has considerable impacts on physiological processes including signal transduction, DNA damage repair, transcriptional regulation, gene activation, and inhibition of gene expression. However, the traditional proteomics-based approach suffers from limited identification rates of these critical methylation sites on endogenous peptides. In this work, a peptidomics-based workflow was established to discover and characterize the global methylome of endogenous peptides in human cells. The reliability of our strategy was validated by methyl-SILAC labeling, resulting in 83% true-positive identifications in the HeLa cell line. We applied this approach to seven human cell lines, and 700 methylated forms on 646 putative methylation sites were identified in total, with over 61% of the methylation sites being newly identified. This study provides a complementary strategy for a traditional proteomics-based approach that enables identification of missing methylation sites and creates a first methylome draft of endogenous peptides of human cell lines, offering a valuable resource for in-depth studies of biological functions of methylated endogenous peptides.
      PubDate: 2019-12-01
      DOI: 10.1007/s13361-019-02270-y
       
  • One-Pot Quantitative Top- and Middle-Down Analysis of GluC-Digested
           Histone H4

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      Abstract: Abstract Histone post-translational modifications (PTMs) have been intensively investigated due to their essential function in eukaryotic genome regulation. Histone modifications have been effectively studied using modified bottom-up proteomics approaches; however, the methods often do not capture single-molecule combinations of PTMs (proteoforms) that mediate known and expected biochemical mechanisms. Both middle-down mass spectrometry (MS) and top-down MS quantitation of H4 proteoforms present viable access to this important information. Histone H4 middle-down has previously avoided GluC digestion due to complex digestion products and interferences; however, the common AspN digestion cleaves at amino acid 23, disconnecting K31ac from other PTMs. Here, we demonstrate the effective use of GluC-based middle-down quantitation and compare it to top-down-based quantitation of proteoforms. Despite potential interferences in the m/z space, the proteoforms arising from all three GluC products (E52, E53, and E63) and intact H4 are chromatographically resolved and successfully analyzed in a single LC–MS analysis. Quantitative results and associated analytical metrics are compared between the different analytes of a single sample digested to different extents to reveal general concordance as well as the relative biases and complementarity of each approach. There is moderate proteoform discordance between digestion products (e.g., E52 and E53); however, each digestion product exhibits high concordance, regardless of digestion time. Under the conditions used, the GluC products are better chromatographically resolved yet show greater variance than the top-down quantitation that are more extensively sampled for MS2. GluC-based middle-down of H4 is thus viable. Both top-down and middle-down approaches have comparable quantitation capacity and are complementary.
      PubDate: 2019-12-01
      DOI: 10.1007/s13361-019-02219-1
       
  • Finding the Sweet Spot in ERLIC Mobile Phase for Simultaneous Enrichment
           of N-Glyco and Phosphopeptides

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      Abstract: Abstract Simultaneous enrichment of glyco- and phosphopeptides will benefit the studies of biological processes regulated by these posttranslational modifications (PTMs). It will also reveal potential crosstalk between these two ubiquitous PTMs. Unlike custom-designed multifunctional solid phase extraction (SPE) materials, operating strong anion exchange (SAX) resin in electrostatic repulsion-hydrophilic interaction chromatography (ERLIC) mode provides a readily available strategy to analytical labs for enrichment of these PTMs for subsequent mass spectrometry (MS)-based characterization. However, the choice of mobile phase has largely relied on empirical rules from hydrophilic interaction chromatography (HILIC) or ion-exchange chromatography (IEX) without further optimization and adjustments. In this study, ten mobile phase compositions of ERLIC were systematically compared; the impact of multiple factors including organic phase proportion, ion pairing reagent, pH, and salt on the retention of glycosylated and phosphorylated peptides was evaluated. This study demonstrated good enrichment of glyco- and phosphopeptides from the nonmodified peptides in a complex tryptic digest. Moreover, the enriched glyco- and phosphopeptides elute in different fractions by orthogonal retention mechanisms of hydrophilic interaction and electrostatic interaction in ERLIC, maximizing the LC-MS identification of each PTM. The optimized mobile phase can be adapted to the ERLIC HPLC system, where the high resolution in separating multiple PTMs will benefit large-scale MS-based PTM profiling and in-depth characterization.
      PubDate: 2019-12-01
      DOI: 10.1007/s13361-019-02230-6
       
  • Top-down Mass Spectrometry of Sarcomeric Protein Post-translational
           Modifications from Non-human Primate Skeletal Muscle

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      Abstract: Abstract Sarcomeric proteins, including myofilament and Z-disk proteins, play critical roles in regulating muscle contractile properties. A variety of isoforms and post-translational modifications (PTMs) of sarcomeric proteins have been shown to be associated with modulation of muscle functions and the occurrence of muscle diseases. Non-human primates (NHPs) are excellent research models for sarcopenia, a disease associated with alterations in sarcomeric proteins, due to their marked similarities to humans. However, the sarcomeric proteins in NHP skeletal muscle have not been well characterized. To gain a deeper understanding of sarcomeric proteins in NHP skeletal muscle, we employed top-down mass spectrometry (MS) to conduct a comprehensive analysis on isoforms and PTMs of sarcomeric proteins in rhesus macaque skeletal muscle. We identified 23 protein isoforms with 46 proteoforms of sarcomeric proteins, including 6 isoforms with 18 proteoforms from fast skeletal troponin T. Particularly, for the first time, a novel PDZ/LIM domain protein isoform, PDLIM7, was characterized with a newly identified protein sequence. Moreover, we also identified multiple PTMs on these proteins, including deamidation, methylation, acetylation, tri-methylation, phosphorylation, and S-glutathionylation. Most PTM sites were localized, including Asn13 deamidation on MLC-2S; His73 methylation on αactin; N-terminal acetylation on most identified proteins; N-terminal tri-methylation on MLC-1S, MLC-1F, MLC-2S, and MLC-2F; Ser14 phosphorylation on MLC-2S; and Ser15 and Ser16 phosphorylation on MLC-2F. In summary, a comprehensive characterization of sarcomeric proteins including multiple isoforms and PTMs in NHP skeletal muscle was achieved by analyzing intact proteins in the top-down MS approach.
      PubDate: 2019-12-01
      DOI: 10.1007/s13361-019-02139-0
       
  • Lipid Alterations during Zebrafish Embryogenesis Revealed by Dynamic Mass
           Spectrometry Profiling with C=C Specificity

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      Abstract: Abstract Lipids exert substantial influences on vertebrate embryogenesis, but their metabolic dynamics at detailed structural levels remains elusive, primarily owing to the lack of a tool capable of resolving their huge structural diversity. Herein, we present the first large-scale and spatiotemporal monitoring of unsaturated lipids with C=C specificity in single developing zebrafish embryos enabled by photochemical derivatization and tandem mass spectrometry (MS). The lipid isomer composition was found extremely stable in yolk throughout embryogenesis, while notable differences in ratios of C=C location (e.g., PC 16:0_16:1 (7) vs. 16:0_16:1 (9)) and fatty acyl composition isomers (e.g., PC 16:1_18:1 vs. 16:0_18:2) were unveiled between blastomeres and yolk from zygote to 4 h post fertilization (hpf). From 24 hpf onwards, lipid isomer compositions in embryo head and tail evolved distinctively with development, suggesting a meticulously regulated lipid remodeling essential for cell division and differentiation. This work has laid the foundation for functional studies of structurally defined lipids in vertebrate embryology.
      PubDate: 2019-12-01
      DOI: 10.1007/s13361-019-02334-z
       
  • 1,4-Benzoquinone as a Highly Efficient Dopant for Enhanced Ionization and
           Detection of Nitramine Explosives on a Single-Quadrupole Mass Spectrometer
           Fitted with a Helium-Plasma Ionization (HePI) Source

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      Abstract: Abstract Previous investigations have evaluated the efficacy of anions such as NO3−, Cl−, Br−, CH3COO−, and CF3COO− as additives to generate or enhance mass spectrometric signals from explosives under plasma ionization conditions. The results of this study demonstrate that for detecting nitramine-class explosives, such as 1,3,5-trinitroperhydro-1,3,5-triazine (RDX) and 1,3,5,7-tetranitro-1,3,5,7-tetrazacyclooctane (HMX), 1,4-benzoquinone (BQ) is a highly effective and efficient dopant. When used in conjunction with ambient-pressure negative-ion helium-plasma ionization (HePI), 1,4-benzoquinone readily captures an electron, forming an abundant molecular anion (m/z 108), which upon exposure to vapors of RDX and HMX generates adduct ions of m/z 330 and 404, respectively. The signal level recorded for RDX upon adduction to the radical anion of 1,4-benzoquinone under our experimental conditions was significantly higher than that realized by chloride adduction using dichloromethane (DCM) as the dopant.
      PubDate: 2019-12-01
      DOI: 10.1007/s13361-019-02339-8
       
  • Comparison of Clusters Produced from Sb2Se3 Homemade Polycrystalline
           Material, Thin Films, and Commercial Polycrystalline Bulk Using Laser
           Desorption Ionization with Time of Flight Quadrupole Ion Trap Mass
           Spectrometry

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      Abstract: Abstract This study compared Sb2Se3 material in the form of commercial polycrystalline bulk, sputtered thin film, and homemade polycrystalline material using laser desorption ionization (LDI) time of flight mass spectrometry with quadrupole ion trap mass spectrometry. It also analyzed the stoichiometry of the SbmSen clusters formed. The results showed that homemade Sb2Se3 bulk was more stable compared to thin film; its mass spectra showed the expected cluster formation. The use of materials for surface-assisted LDI (SALDI), i.e., graphene, graphene oxide, and C60, significantly increased the mass spectra intensity. In total, 19 SbmSen clusters were observed. Six novel, high-mass clusters—Sb4Se4+, Sb5Se3-6+, and Sb7Se4+—were observed for the first time when using paraffin as a protective agent.
      PubDate: 2019-12-01
      DOI: 10.1007/s13361-019-02346-9
       
  • Using LC-MS to Identify Clipping in Self-Assembled Nanoparticles During
           Vaccine Development

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      Abstract: Abstract A hemagglutinin stabilized stem nanoparticle (HA-SS-np) that is designed to provide broad protection against influenza is being developed as a potential vaccine. During an early formulation screening study, reducing gel (rCGE) analysis indicated product degradation in a few candidate buffers at the first-week accelerated stability point, whereas no change was shown in the size exclusion chromatography (SEC) measurement. A LC-MS workflow was therefore applied to investigate the integrity of this large HA-SS-np vaccine molecule (≈ 1 MDa). Application of LC-MS was critical to rationalize the conflicting results from the rCGE and SEC assays and led to the discovery that (1) an unexpected sequence clipping in the HA-SS-np subunits occurred, explaining the atypical reducing gel profile, and (2) an undisrupted disulfide bond held the two fragments together, explaining the unchanged SEC profile. This analytical case study led to a formulation buffer redesign, which mitigated the issue.
      PubDate: 2019-12-01
      DOI: 10.1007/s13361-019-02318-z
       
  • Electron Ionization of Imidazole and Its Derivative 2-Nitroimidazole

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      Abstract: Abstract Imidazole (IMI) is a basic building block of many biologically important compounds. Thus, its electron ionization properties are of major interest and essential for the comparison with other molecular targets containing its elemental structure. 2-Nitroimidazole (2NI) contains the imidazole ring together with nitrogen dioxide bound to the C2 position, making it a radiosensitizing compound in hypoxic tumors. In the present study, we investigated electron ionization of IMI and 2NI and determined the mass spectra, the ionization energies, and appearance energies of the most abundant fragment cations. The experiments were complemented by quantum chemical calculations on the thermodynamic thresholds and potential energy surfaces, with particular attention to the calculated transition states for the most important dissociation reactions. In the case of IMI, substantially lower threshold values (up to ~ 1.5 eV) were obtained in the present work compared to the only available previous electron ionization study. Closer agreement was found with recent photon ionization values, albeit the general trend of slightly higher values for the case of electron ionization. The only exception for imidazole was found in the molecular cation at m/z 40 which is tentatively assigned to the quasi-linear HCCNH+/ HCNCH+. Electron ionization of 2NI leads to analogous fragment cations as in imidazole, yet different dissociation pathways must be operative due to the presence of the NO2 group. Regarding the potential radiosensitization properties of 2NI, electron ionization is characterized by dominant parent cation formation and release of the neutral NO radical.
      PubDate: 2019-12-01
      DOI: 10.1007/s13361-019-02337-w
       
  • Hydrogen-Deuterium Exchange and Hydroxyl Radical Footprinting for Mapping
           Hydrophobic Interactions of Human Bromodomain with a Small Molecule
           Inhibitor

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      Abstract: Abstract Mass spectrometry (MS)–based protein footprinting, a valuable structural tool in mapping protein-ligand interaction, has been extensively applied to protein-protein complexes, showing success in mapping large interfaces. Here, we utilized an integrated footprinting strategy incorporating both hydrogen-deuterium exchange (HDX) and hydroxyl radical footprinting (i.e., fast photochemical oxidation of proteins (FPOP)) for molecular-level characterization of the interaction of human bromodomain-containing protein 4 (BRD4) with a hydrophobic benzodiazepine inhibitor. HDX does not provide strong evidence for the location of the binding interface, possibly because the shielding of solvent by the small molecule is not large. Instead, HDX suggests that BRD4 appears to be stabilized by showing a modest decrease in dynamics caused by binding. In contrast, FPOP points to a critical binding region in the hydrophobic cavity, also identified by crystallography, and, therefore, exhibits higher sensitivity than HDX in mapping the interaction of BRD4 with compound 1. In the absence or under low concentrations of the radical scavenger, FPOP modifications on Met residues show significant differences that reflect the minor change in protein conformation. This problem can be avoided by using a sufficient amount of proper scavenger, as suggested by the FPOP kinetics directed by a dosimeter of the hydroxyl radical.
      PubDate: 2019-12-01
      DOI: 10.1007/s13361-019-02316-1
       
  • Ion-Neutral Collision Effects on Ion Trapping and Pseudopotential Depth in
           Ion Trap Mass Spectrometry

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      Abstract: Abstract Ion trapping using radio-frequency (RF) devices has been widely used in mass spectrometry (MS). The pseudopotential well (PW) model enables the use of a pseudopotential depth, D, to evaluate the ion trapping capability of the RF devices in the pure electric field. It remains unclear how gas pressures regulate the ion trapping and D. Here, we calculated the D of a linear ion trap (LIT) from 1 mTorr to 2 Torr, a pressure range critical for the operation of the RF devices, through ion cloud simulations. Compared with the case of pure electric field, ion-neutral collision effects at pressures of 1 to 100 mTorr were beneficial for the ion trapping and revealed an optimal trapping depth, D, at around 10 mTorr. We explained the mechanism and validated the observation via ion trapping experiments performed in a home-made dual LIT mass spectrometer. We also showed that near the stability boundary, the RF heating became comparable with the D, which led to the decrement of ion trapping capability characterized by the available D.
      PubDate: 2019-12-01
      DOI: 10.1007/s13361-019-02344-x
       
  • Compositional Analysis of Heavy Petroleum Distillates by Comprehensive
           Two-dimensional Gas Chromatography, Field Ionization and High-resolution
           Mass Spectrometry

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      Abstract: Abstract We report recent progresses of combining comprehensive two-dimensional gas chromatography (2DGC or GC × GC) separation, field ionization (FI), and time-of-flight mass spectrometry (TOF MS) for the detailed analysis of vacuum gas oil distillation (VGO) cuts. 2DGC separates petroleum molecules by the combination of boiling point and polarity. FI generates molecule ions-only mass spectra. TOF MS allows accurate mass analysis of hydrocarbon molecules. A new data analysis strategy is implemented for compositional analysis. First, all masses were separated into nominal mass classes. Since petroleum homologues have unique Kendrick mass defects (KMD), KMD plots were generated for easy recognition of homologues series within each nominal mass class. Finally, KMD windows were imposed for complete resolution of petroleum molecules. Using this approach, a total of 16 hydrocarbon types, 14 sulfur types, and their carbon number distributions were determined in the three VGO distillation cuts. Two series of geological biomarkers were also revealed by the analysis.
      PubDate: 2019-12-01
      DOI: 10.1007/s13361-019-02349-6
       
 
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