Journal: bioRxiv

Article Title: Covalent Protein Painting Reveals Structural Changes in the Proteome in Alzheimer Disease

doi: 10.1101/2020.01.31.929117

Figure Lengend Snippet: Schematic of the CPP method. CPP includes in vivo chemical methylation of lysine residues at the surface of proteins and its detection with mass spectrometry. The flow chart shows each labeling step and the resultant relative measurement of surface accessibility for chemical modification based on mass spectrometric quantification of isotope labeled peptides. Proteins are labeled with isotope defined reagents at solvent exposed lysine residues (K) with two methyl moieties ( 13 CD 3 , heavy) in vivo . Protein are then digested in peptides with the endoproteinase Chymotrypsin, and all newly accessible primary amines labeled with two methyl moieties (CH 3 , light). Peptides are separated by liquid chromatography (LC) and transferred into gas phase by electrospray ionization (nano ESI). High mass resolution (Orbitrap) mass spectra (MS) and fragment ion mass spectra (MS/MS) are acquired. Peptides are identified with a database search using ProLuCID and quantified with Census. The “surfaces of all protein complexes” (SoPaX) algorithm within ProteinClusterQuant (PCQ) determines and compares the relative surface accessibility of lysine residues.

Article Snippet: Following chromatographic separation, peptides were transferred into an Orbitrap Lumos mass spectrometer by electrospray ionization (nanoEasy, Thermo Fisher Scientific).

Techniques: In Vivo, Methylation, Mass Spectrometry, Labeling, Modification, Liquid Chromatography, Tandem Mass Spectroscopy

Journal: Analytical Chemistry

Article Title: MS2Analyzer: A Software for Small Molecule Substructure Annotations from Accurate Tandem Mass Spectra

doi: 10.1021/ac502818e

Figure Lengend Snippet: Annotations of lipids by MS2Analyzer. (a) QTOF MS/MS of digalactosyldiacylglycerol 18:3/16:0 in positive electrospray mode, indicating the neutral loss of the DGDG headgroup from the [M + NH 4 ] + adduct precursor ion as well as m / z differences for product ions indicating both acyl side chains. Note that positional isomers of acyl groups cannot be determined with this method. (b) QTOF MS/MS of phosphatidylglycerol 16:0/16:0 in negative electrospray mode, indicating the characteristic product ions of the phosphatidylglycerol headgroup ( m / z 152.995) and the acyl side chains ( m / z 255.233).

Article Snippet: In order to reduce the impact from different instruments, ionizations, and adducts, only [M + H]+ spectra acquired under positive electrospray ionization from Agilent QTOF 6530 mass spectrometers were used.

Techniques: Mass Spectrometry

Journal: Journal of the American Society for Mass Spectrometry

Article Title: Monitoring Copopulated Conformational States During Protein Folding Events Using Electrospray Ionization-Ion Mobility Spectrometry-Mass Spectrometry

doi: 10.1016/j.jasms.2007.09.017

Figure Lengend Snippet: ( a )–( c ): ESI-IMS-MS Driftscope plots showing drift time (x axis) versus m/z (y axis) for β 2 m and variants at pH 6.8. ( a ) wild-type β 2 m, ( b ) single mutant I7A, and ( c ) double mutant I7A/P32G. Insets at the right hand side: the summed, full scan m/z spectra of each protein showing the charge state ions detected.

Article Snippet: ESI-IMS-MS Analyses Samples were infused into the ESI source of a Synapt HDMS, a hybrid quadrupole-IMS-orthogonal acceleration time-of-flight mass spectrometer (oa-TOF) [ ] (Waters UK Ltd, Manchester, UK) using a Harvard syringe pump (model 22; Harvard Apparatus, Holliston, MA) with a flow rate of 10 μL min−1 .

Techniques: Mass Spectrometry, Mutagenesis

Journal: Journal of the American Society for Mass Spectrometry

Article Title: Monitoring Copopulated Conformational States During Protein Folding Events Using Electrospray Ionization-Ion Mobility Spectrometry-Mass Spectrometry

doi: 10.1016/j.jasms.2007.09.017

Figure Lengend Snippet: ESI-IMS-MS Driftscope plots showing drift time (x axis) versus m/z (y axis) for wild-type β 2 m analyzed at ( a ) pH 6.23, ( b ) pH 4.28, ( c ) pH 3.54, and ( d ) pH 2.60. The number of conformeric species observed for each individual charge state can be seen. Insets at the right hand side of each plot: the summed, full scan m/z spectra of wild-type β 2 m for each data acquisition showing the charge state ions detected.

Article Snippet: ESI-IMS-MS Analyses Samples were infused into the ESI source of a Synapt HDMS, a hybrid quadrupole-IMS-orthogonal acceleration time-of-flight mass spectrometer (oa-TOF) [ ] (Waters UK Ltd, Manchester, UK) using a Harvard syringe pump (model 22; Harvard Apparatus, Holliston, MA) with a flow rate of 10 μL min−1 .

Techniques: Mass Spectrometry

Journal: Journal of the American Society for Mass Spectrometry

Article Title: Monitoring Copopulated Conformational States During Protein Folding Events Using Electrospray Ionization-Ion Mobility Spectrometry-Mass Spectrometry

doi: 10.1016/j.jasms.2007.09.017

Figure Lengend Snippet: ( a ) The summed m/z spectrum from an ESI-IMS-MS data acquisition of cytochrome c analyzed in 50 mM aqueous ammonium acetate solution acidified to pH 3 showing a charge state distribution from +6 to +20 ions consistent with monomeric protein (12,359.4 Da). ( b ) ESI-IMS-MS Driftscope plot showing drift time (x axis) versus m/z (y axis) for the analysis of cytochrome c in 50 mM aqueous ammonium acetate solution acidified to pH 3. ( c ) ESI-IMS-MS drift time versus intensity graphs for the m/z 1237.0 (+10 ions; upper), m/z 1374.4 (+9 ions; middle), and m/z 1546.0 (+8 ions; lower) signals detected during the analysis of cytochrome c in 50 mM aqueous ammonium acetate solution acidified to pH 3.

Article Snippet: ESI-IMS-MS Analyses Samples were infused into the ESI source of a Synapt HDMS, a hybrid quadrupole-IMS-orthogonal acceleration time-of-flight mass spectrometer (oa-TOF) [ ] (Waters UK Ltd, Manchester, UK) using a Harvard syringe pump (model 22; Harvard Apparatus, Holliston, MA) with a flow rate of 10 μL min−1 .

Techniques: Mass Spectrometry

Journal: Journal of Clinical Microbiology

Article Title: Broad-Range PCR Coupled with Electrospray Ionization Time of Flight Mass Spectrometry for Detection of Bacteremia and Fungemia in Patients with Neutropenic Fever

doi: 10.1128/JCM.01066-16

Figure Lengend Snippet: Assessment of factors influencing performance of PCR/ESI-MS.

Article Snippet: Episodes with polymicrobial infection, where PCR/ESI-MS detected only the definite pathogen and not the potential contaminant(s), were categorized as true positive for PCR/ESI-MS compared to BC. summarizes all microorganisms detected by both methods, PCR/ESI-MS only, and BC only.

Techniques: Polymerase Chain Reaction, Mass Spectrometry

Journal: Journal of Clinical Microbiology

Article Title: Broad-Range PCR Coupled with Electrospray Ionization Time of Flight Mass Spectrometry for Detection of Bacteremia and Fungemia in Patients with Neutropenic Fever

doi: 10.1128/JCM.01066-16

Figure Lengend Snippet: PCR/ESI-MS and blood culture results by specimen.

Article Snippet: Episodes with polymicrobial infection, where PCR/ESI-MS detected only the definite pathogen and not the potential contaminant(s), were categorized as true positive for PCR/ESI-MS compared to BC. summarizes all microorganisms detected by both methods, PCR/ESI-MS only, and BC only.

Techniques: Polymerase Chain Reaction, Mass Spectrometry

Journal: Journal of Clinical Microbiology

Article Title: Broad-Range PCR Coupled with Electrospray Ionization Time of Flight Mass Spectrometry for Detection of Bacteremia and Fungemia in Patients with Neutropenic Fever

doi: 10.1128/JCM.01066-16

Figure Lengend Snippet: Results of blood cultures (BC) and PCR/ESI-MS in the 105 cases of neutropenic fever. Bloodstream infection (BSI) included both definite and probable BSI based on BC and/or PCR/ESI-MS. MO, microorganism; +, positive result; −, negative result;

Article Snippet: Episodes with polymicrobial infection, where PCR/ESI-MS detected only the definite pathogen and not the potential contaminant(s), were categorized as true positive for PCR/ESI-MS compared to BC. summarizes all microorganisms detected by both methods, PCR/ESI-MS only, and BC only.

Techniques: Polymerase Chain Reaction, Mass Spectrometry, Infection

Journal: Frontiers in Immunology

Article Title: Alterations of Gut Microbiome and Metabolite Profiling in Mice Infected by Schistosoma japonicum

doi: 10.3389/fimmu.2020.569727

Figure Lengend Snippet: Three-dimensional score plots of partial least squares-discriminatory analysis from healthy mice and infected mice at different time points. Each point represents an individual. (A) Serum samples in positive electrospray ionization (ESI+) mode. (B) Urine samples in ESI+ mode. (C) Liver aqueous extracts in negative electrospray ionization (ESI-) mode. (D) Serum samples in ESI- mode. (E) Urine samples in ESI- mode. (F) Colon aqueous extracts in ESI- mode.

Article Snippet: Quadrupole-Time-of-Flight Mass Spectrometry Conditions Mass spectrometry data were collected by a SYNAPT G2-Si High-Definition Mass Spectrometer with an electrospray ionization (ESI) source (Waters Ltd., Milford, MA, USA) in both positive and negative ion modes for the serum and the urine samples, whereas only negative ion mode was used for the liver and colon aqueous extracts due to the limited valuable compounds detected in the positive ion mode.

Techniques: Mouse Assay, Infection

Journal: Frontiers in Immunology

Article Title: Alterations of Gut Microbiome and Metabolite Profiling in Mice Infected by Schistosoma japonicum

doi: 10.3389/fimmu.2020.569727

Figure Lengend Snippet: Three-dimensional score plots of principal component analysis from healthy mice and infected mice at different time points. Each point represents an individual. (A) Serum samples in positive electrospray ionization (ESI+) mode. (B) Urine samples in ESI+ mode. (C) Liver aqueous extracts in negative electrospray ionization (ESI-) mode. (D) Serum samples in ESI- mode. (E) Urine samples in ESI- mode. (F) Colon aqueous extracts in ESI- mode.

Article Snippet: Quadrupole-Time-of-Flight Mass Spectrometry Conditions Mass spectrometry data were collected by a SYNAPT G2-Si High-Definition Mass Spectrometer with an electrospray ionization (ESI) source (Waters Ltd., Milford, MA, USA) in both positive and negative ion modes for the serum and the urine samples, whereas only negative ion mode was used for the liver and colon aqueous extracts due to the limited valuable compounds detected in the positive ion mode.

Techniques: Mouse Assay, Infection

Journal: Toxins

Article Title: Anti-Breast Cancer Activity of Latroeggtoxin-V Mined from the Transcriptome of Spider Latrodectus tredecimguttatus Eggs

doi: 10.3390/toxins10110451

Figure Lengend Snippet: Purification and identification of rLatroeggtoxin-V. ( A ) Chromatogram of RP-HPLC purification of rLatroeggtoxin-V. ( B ) Molecular weight determination of rLatroeggtoxin-V by electrospray ionization mass spectrometry. The m / z value and the number of charges for each rLatroeggtoxin-V ion peak were labeled.

Article Snippet: The molecular weight of the components in each elution peak was determined by electrospray ionization mass spectrometry (Waters ACQUITY UPLC/Xevo G2 QTOF, Waters, Milford, MA, USA) and thus the peak containing recombinant Latroeggtoxin-V (rLatroeggtoxin-V) was selected and lyophilized.

Techniques: Purification, High Performance Liquid Chromatography, Molecular Weight, Mass Spectrometry, Labeling

Journal: Journal of biological inorganic chemistry : JBIC : a publication of the Society of Biological Inorganic Chemistry

Article Title: Amino acid variability in the peptide composition of a suite of amphiphilic peptide siderophores from an open ocean Vibrio species

doi: 10.1007/s00775-013-0995-3

Figure Lengend Snippet: Electrospray ionization-tandem mass spectrum of moanachelin gly-D (C14:0).

Article Snippet: The masses of the siderophores and the siderophore fragments were determined by electrospray ionization mass spectrometry (ESI-MS) and tandem mass spectrometry on a Micromass Q-TOF2 (Waters Corp.).

Techniques:

Journal: Journal of biological inorganic chemistry : JBIC : a publication of the Society of Biological Inorganic Chemistry

Article Title: Amino acid variability in the peptide composition of a suite of amphiphilic peptide siderophores from an open ocean Vibrio species

doi: 10.1007/s00775-013-0995-3

Figure Lengend Snippet: Electrospray ionization-tandem mass spectrum of moanachelin ala-D (C14:0).

Article Snippet: The masses of the siderophores and the siderophore fragments were determined by electrospray ionization mass spectrometry (ESI-MS) and tandem mass spectrometry on a Micromass Q-TOF2 (Waters Corp.).

Techniques:

Journal: Scientific Reports

Article Title: Efficient biosynthesis of a Cecropin A-melittin mutant in Bacillus subtilis WB700

doi: 10.1038/srep40587

Figure Lengend Snippet: Identification of CAM-W produced by recombinant B. subtilis WB 700. ( A ) Analysis of tricine-SDS-PAGE (a) cropped from Supplementary Figure 1 and western blots (b and c) cropped from Supplementary Figures 2 and 3 of the total extracellular proteins from B. subtilis WB700 harboring pDM031 induced without maltose (lane 1) or with maltose (lane 2). These gels were run under the same experimental conditions. The EDDIE and CAM-W bands are indicated by (←) and (← ← ). The bands present in (a) lane 2 were confirmed by western blotting, as shown in (b) and (c). The marker lane contained a broad range protein marker (#P7702, New England Biolabs, USA). ( B ) RP-HPLC analysis of purified CAM-W. ( C ) Electrospray ionization mass spectrometry analysis of purified recombinant CAM-W.

Article Snippet: The molecular weight of the purified CAM-W was measured using electrospray ionization mass spectrometry (Agilent, USA).

Techniques: Chick Chorioallantoic Membrane Assay, Produced, Recombinant, Western Blot, SDS Page, Marker, High Performance Liquid Chromatography, Purification, Mass Spectrometry