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

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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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Sequence alignment of C-terminal phosphorylated plant aquaporins

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 ).

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

Microvesicles released by PC-3 cells.

Analysis of CD151 and CD147 as potential prostate cancer biomarkers.

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 ).

Novel phosphorylation sites on H+-ATPase proteins

MIDAS workflow (MRM-triggered MS/MS) verification of the identity of peptide DLQFVEVTDVK representing fibronectin (normal concentration, ∼300 μg/ml)

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

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

EThcD spectrum of m/z (3+), acquired on a Orbitrap Fusion Lumos Tribrid mass spectrometer (Thermo Fisher Scientific) (at NCE = 15%). EThcD spectrum.

Complementary identification and novel protein discovery

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.

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.

Top-down protein identification.

Schematic of MS1 filtering.

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

Schematic illustration of the assembly and interactions of sperm-bound eppin protein complex (EPC) components. Schematic illustration of the assembly and.

Schematic representation of proteogenomic annotation strategy.

Novel p53 target genes identified by RNA-Seq, pSILAC and ChIP-Seq.

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.

Bottom-up proteomic characterization of MALDI IMS samples.

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

Degree of glycosylation of human milk LF from individual donors across lactation. Degree of glycosylation of human milk LF from individual donors across.

A, Base peak chromatogram of apomyoglobin digest generated by 0

Correction of translational start site by identification of N-terminal peptide. Correction of translational start site by identification of N-terminal.

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.

N-terminal extension of a gene using peptides mapping upstream to an annotated start site. N-terminal extension of a gene using peptides mapping upstream.

Analysis of newly synthesized proteins by combined pulsed SILAC and click chemistry enrichment. Analysis of newly synthesized proteins by combined pulsed.

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

Changes in bacterial adhesion with hmLF addition and the purified glycan from hmLF. Changes in bacterial adhesion with hmLF addition and the purified glycan.

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.

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

Altered pathways in prostate cancer.

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

Interaction networks of the regulated phosphoproteins.

LC-MS/MS analyses of synthetic peptides with SUMO1 and SUMO3 remnant chains using ETD, CID, and HCD activation modes. LC-MS/MS analyses of synthetic peptides.

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.

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.

Comparison of mapped epitopes and peptides identified in immuno-SILAC screening of polyclonal antibodies against trypsin-digested PrESTs. Comparison of.

Bar plot representation of the transcriptomic changes in Δsaci_ptp and Δsaci_pp2a. Bar plot representation of the transcriptomic changes in Δsaci_ptp and.

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.

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.

Biochemical characterization of the protein phosphatases Saci-PTP.

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.

A simplified example of a protein summary list.

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

2-D gel images visualized by Coomassie Brilliant Blue staining representing total proteins extracted from HCT-8 under apoptotic conditions in 2 mm Gln.

Antibody specificity ascertained by 2D-PAGE Western immunoblotting (IEF) of total cellular protein extracts from the RT4 human bladder cancer cell line.

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 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.

Schematic of AIMS-to-MRM experiment.

Changes in protein expression during distinct stages of NK cell differentiation. Changes in protein expression during distinct stages of NK cell differentiation.

The average median S.D. and PEV reduction after applying different normalization methods compared with raw data. The average median S.D. and PEV reduction.

MS3 for peptide identification and mapping phosphorylation sites

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Beam-type (Q-TOF) CID data of m/z 815.73(3+). Beam-type (Q-TOF) CID data of m/z 815.73(3+). From these data one could identify the modified peptide as AVGAQVLESTPPPHVMR ([682–698] of bovine ITIH2 protein (Uniprot ID: F1MNW4)). The glycan composition can be “guessed” from the oxonium ions of HexNAc and Neu5Ac, and from the presence of m/z 895.49(2+) as Neu5AcHexHexNAc. Intensity pattern of the fragments of the HexNAc oxonium ion (m/z 204) ascertain its identity as GalNAc (89). Thus, the sugar structure is most likely Neu5AcGalGalNAc. Its linearity or branching cannot be determined, because larger Y fragments were not detected, nor were m/z 454.16 or 495.18 observed, indicating sialylation of Gal or GalNAc, respectively. The site of modification cannot be assigned. All ions that were gas-phase deglycosylated, and thus, were detected unmodified are printed in blue. Fragment y8 belongs to this series only if Thr-10 is the modification site. Zsuzsanna Darula, and Katalin F. Medzihradszky Mol Cell Proteomics 2018;17:2-17 © 2018 by The American Society for Biochemistry and Molecular Biology, Inc.