MS spectra of intact histones (A) and peptides 1–41 (B) of the second H2A HPLC peak.A, molecular masses of intact histones H2A determined after deconvolution.

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binding sites 58 of the 473 unambiguously assigned phosphorylation sites are predicted by Scansite to be sites for binding. 50 of these correspond.

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Quantification of C-terminal phosphorylation of AtPIP2;1 upon NaCl (A) and H2O2 (B) treatments.A, plants were either untreated (white bars) or treated.

Sequence alignment of C-terminal phosphorylated plant aquaporins

Principle for quantification of phosphorylation of the C-terminal tail of AtPIP2;1. Principle for quantification of phosphorylation of the C-terminal tail.

MALDI-TOF MS spectrum of phosphopeptides from plant PM aquaporins.

Phosphopeptide sequencing by MALDI-TOF/TOF of the C-terminal tail of AtPIP2;1.A, MS/MS spectrum of singly phosphorylated 277SLGSFRSAANV287 (m/z ).

Phosphorylation and sequence disorder in microtubule-associated protein Tau.A, schematic illustration of the domain profile of Tau with all known phosphorylation.

Distribution of phosphorylation sites identified in the cytosolic phosphoproteome.A, numbers of approved phosphopeptides, previously phosphorylated peptides,

Phosphopeptide sequencing by MALDI-TOF/TOF of the C-terminal tail of AtPIP2;4.A, MS/MS spectrum of singly phosphorylated 277ALGSFGSFGSFRSFA291 (m/z ).

Phosphopeptide sequencing by MALDI-TOF/TOF of the C-terminal tail of AtPIP2;7.A, MS/MS spectrum of singly phosphorylated 270ALGSFRSNATN280 (m/z ).

A quantitative proteomics strategy to identify SUMO-conjugated proteins. A quantitative proteomics strategy to identify SUMO-conjugated proteins. HeLa.

Percentage of proteins identified in envelope membrane extracts according to the purification method and the number of transmembrane domains. Percentage.

Novel phosphorylation sites on H+-ATPase proteins

A, high resolution MS/MS spectrum (lower panel) of 1435

Illustration of matched (FL-IFN-γR2/GFP and IFN-γR1/EBFP) and mismatched (IFN-γR1/EBFP and FL-IL-10R2/GFP) pairs of receptors. Illustration of matched.

Frequency distribution of the GRAVY of the theoretical proteins (open bars) and of 110 genes encoding proteins identified on a 2-D electrophoresis gel,

Beam-type (Q-TOF) CID data of m/z (3+).

Relative quantitation of phosphopeptides from conditioned media from subtype specific breast cancer cell lines. Relative quantitation of phosphopeptides.

Time course of phosphorylation changes at Ser-293, Ser-300, and Ser-232 in PDHE1α following kinase inhibition with DCA. A, relative quantitation over three.

Top-down protein identification.

Schematic of MS1 filtering.

Distributions of the ELDP values and Mascot scores for all protein identifications.a, frequency of ELDP value returned by correct (gray bars) and incorrect.

Significantly enriched phosphorylation motifs from up-regulated phosphopeptides by Motif-X analysis. Significantly enriched phosphorylation motifs from.

Visual validation of the computational outputs.

Relative abundance of proteins identified in MALDI IMS

A, Averaged full MS (ions converted to monoisotopic MW by Xcalibur Xtract) of Segment I-3 (see supplemental Fig. A, Averaged full MS (ions converted to.

Representative example of LAXIC performance for complex plant phosphoproteome. Representative example of LAXIC performance for complex plant phosphoproteome.A.

Results from the Morris water task.

A, Base peak chromatogram of apomyoglobin digest generated by 0

The evolutionary conservation of the phosphoproteomes.a, E. coli. b, B. subtilis. The evolutionary conservation of the phosphoproteomes.a, E. coli. b,

Colonopshere-enriched proteins display functional interactions.

Identification of SUMO3peptides from 2D-LC-MS/MS analyses of a tryptic digest of HEK293-SUMO3 cells using DDA and DIA methods. Identification of SUMO3peptides.

A, schematic presentation of fetuin-A domains.

Proteins previously reported in published MALDI IMS studies and their frequency of observation in the present study. Proteins previously reported in published.

Schematic summarizing the various functions and features of MASH Suite Pro. Schematic summarizing the various functions and features of MASH Suite Pro.

MS/MS spectra of INEILSNALKR with a Lys residue modified with SUMO1 or SUMO3 remnant chains. MS/MS spectra of INEILSNALKR with a Lys residue modified with.

Manual assessment of the quality of peptide spectra with scores ranging from 5 to 10 of OFFGEL electrophoresis fractions 3 and 4 that were rejected by.

Testing the effectiveness of the three-step peptide fractionation method.A, μLC mass chromatograms of SCX fractions for an acidic FFE fraction. Testing.

Resolution and mass accuracy of A, a peptide isotope cluster (m/z 558

2D-LC-MS/MS analysis of tryptic digest of HEK293-SUMO3 cells (2 μg inj

Overview of the analytical workflow used in this study and a representative MS/MS spectrum.a, Overview of the analytical workflow used in this study. Overview.

Analysis of E. coli peptides by OFFGEL electrophoresis and HPLC-Chip/MS.a, total number of peptides identified (id.) in each fraction; the dark shaded.

Identification of chaperonin GroEL (Rv0440) with representative MS/MS spectrum. Identification of chaperonin GroEL (Rv0440) with representative MS/MS spectrum.A,

Example of MS/MS spectrum of peptide FPTLTGFNR (hypothetical protein with signal peptide EAK88888; N77) from a protein digestion mixture prepared by labeling.

Plot of the deviation of the predicted pI value of every peptide spectrum from the average pI calculated for each fraction for validated (a) and non-validated.

Relative quantification of cis and trans PSP gp10040–42/47–52 variants

Distribution of the phosphoproteins based on GO analysis, including biological process (Left) and cellular component (Right). Distribution of the phosphoproteins.

A, Absolute ion intensities of m/z 322, 922 and 1522 as function of the transfer time. A, Absolute ion intensities of m/z 322, 922 and 1522 as function.

K-Means clustering of protein and mRNA expression patterns after PPAR agonists treatments. k-Means clustering of protein and mRNA expression patterns after.

Chromatograms, MS and MS/MS spectra obtained by LC-MS/MS (Q-TOF) of peptides from UPIII identified after Western blotting followed by on-membrane digestion.

Processing of fragment ion information in DTA files to remove isotope ions and noise. Processing of fragment ion information in DTA files to remove isotope.

High level view of the MAE algorithm.

Biochemical characterization of the protein phosphatases Saci-PP2A.

Analysis of a tryptic digest of subunit B12 by MALDI-TOF mass spectrometry. Analysis of a tryptic digest of subunit B12 by MALDI-TOF mass spectrometry.

Schematic of the Q-OT-qIT hybrid mass spectrometer (Fusion).

Biochemical characterization of the protein phosphatases Saci-PTP.

Identification and quantification of cathepsin D in chronic pancreatitis.A, identification of two peptides, AIGAVPLIQGEYMIPCEK (A) and LLDIACWIHH (MS/MS.

Illustration of chromatography metric C-2A applied to LC-MS/MS data from three Thermo LTQ systems in analyses of yeast proteome samples in CPTAC Study.

Classification of the 1458 identified proteins into molecular functions. Classification of the 1458 identified proteins into molecular functions. The pie.

Top-down analysis of intact bovine carbonic anhydrase II by LTQ Orbitrap Velos. Top-down analysis of intact bovine carbonic anhydrase II by LTQ Orbitrap.

Tryptic phosphopeptides of AdIGFBP-5, [γ-32P]ATP-labeled in vitro by phosphorylation with CK2, were separated by HPLC and detected and sequenced by mass.

Tryptic phosphopeptides of 32P-labeled IGFBP-5 from T47D cells separated by HPLC and sequenced by tandem MS.a, tandem MS spectrum of the triply charged.

Tryptic glycopeptides of IGFBP-5 from T47D cells separated by HPLC detected by ESI-MS and sequenced by tandem MS.a, ESI-MS spectrum of combined fractions.

Eight serum analytes with greatest differences in levels between clinically infected and non-infected neonates. Eight serum analytes with greatest differences.

Full-length AdIGFBP-5 and T47D cell-derived IGFBP-5 analyzed by mass spectrometry.a, intact AdIGFBP-5 was analyzed by ESI-MS. Full-length AdIGFBP-5 and.

Schematic of AIMS-to-MRM experiment.

Occurrence of fur−-only genes and expected sensitivity to Fur.

Peptide mass spectra of SUMO target proteins.

Survey of phosphorylation motifs

MS3 for peptide identification and mapping phosphorylation sites

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MS spectra of intact histones (A) and peptides 1–41 (B) of the second H2A HPLC peak.A, molecular masses of intact histones H2A determined after deconvolution of the multiply charged ion series. MS spectra of intact histones (A) and peptides 1–41 (B) of the second H2A HPLC peak.A, molecular masses of intact histones H2A determined after deconvolution of the multiply charged ion series. Unmodified, acetylated, and phosphorylated histone H2AC; unmodified and phosphorylated histone H2AE; and histone H2AL, H2AG, H2AA, and Q96KK5 variants were assigned. The dots represent non-attributed molecular masses. B, nano-ESI-MS spectrum of endoproteinase Glu-C peptide 1–41. The ions at m/z 562.37, 567.61, and 572.29 were identified as [M + 8H]8+ of unmodified peptide 1–41 from H2AC, H2AE, and Q96KK5; acetylated peptide 1–41 from H2AC; and phosphorylated peptides 1–41 from H2AC and/or H2AE, respectively. The ions at m/z 560.62 and 564.30 were characterized as [M + 8H]8+ of peptide 1–41 from H2AL and H2AA and/or H2AG, respectively. The asterisks represent peptides with a different charge state, unrelated to peptide 1–41 of histone H2A. Ac, acetylated; P, phosphorylated. Débora Bonenfant et al. Mol Cell Proteomics 2006;5:541-552 © 2006 The American Society for Biochemistry and Molecular Biology