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.

Slides:

Advertisements

Similar presentations

Sequence alignment of C-terminal phosphorylated plant aquaporins

Advertisements

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 ).

Experimental overview A sequential protein and peptide IMAC enrichment was analyzed by four different LC-MS/MS strategies. Experimental overview A sequential.

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.

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

Phosphorylation reduces peptide solution charge state and alters SCX elution at low pH.A, at pH 2.7, a theoretical tryptic peptide without histidine residues.

Separation of embryonic brain proteins and peptides by sequential preparative SDS-PAGE and SCX chromatography.A, 6 mg of embryonic day 16.5 murine brain.

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

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.

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.

Work flow for the LAXIC strategy to quantify the phosphorylation change in response to osmotic stress. Work flow for the LAXIC strategy to quantify the.

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

Visual validation of the computational outputs.

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.

Experimental setup.A, topology models of the overexpressed membrane protein GFP fusions. Experimental setup.A, topology models of the overexpressed membrane.

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

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.

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.

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

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

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.

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

The principle of the immuno-SILAC method.

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.

Analytical metrics of yeast proteome analysis using the Q-OT-qIT (Fusion) as compared with qIT-OT (Orbitrap Elite) and Q-OT (Q-Exactive) hybrids. Analytical.

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.

Summary of intralaboratory and interlaboratory variation for metrics for three LTQ and three LTQ-Orbitrap instruments in six replicate analyses of a tryptic.

Stability and variation of metrics over a range of sample injection amounts. Stability and variation of metrics over a range of sample injection amounts.

Performance metrics for triplicate analyses of a tryptic digest of the CPTAC yeast reference proteome on four LTQ-Orbitraps at three different sites in.

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.

Protein identification using MS/MS.

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.

Expression of σ in SCCs Expression of σ in SCCs. Shown is a magnified section of a representative 2D PAGE gel run with a lysate from an SCC.

Influence of MS measurement conditions on the deviation factors between the estimated and measured concentrations of 46 proteins in neuro2a cells.A, QSTAR.

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.

SDS-PAGE of IGFBP-5 from 32P-labeled T47D cells and separation of tryptic phosphopeptides separated by HPLC.a, an autoradiograph (lane 1) is shown next.

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.

Schematic of AIMS-to-MRM experiment.

Survey of phosphorylation motifs

MS3 for peptide identification and mapping phosphorylation sites

SCX chromatography at low pH permits strong enrichment of phosphopeptides of distinct solution charge states.A, the number of phosphopeptides (blue triangles)

Presentation transcript:

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 of the analytical workflow used in this study and a representative MS/MS spectrum.a, Overview of the analytical workflow used in this study. Trypsin digestion of the whole cell lysate was followed by enrichment of phosphopeptides using two stages of chromatography (SCX and TiO2). Phosphopeptides were separated on nano-HPLC and mass-measured and fragmented in the high performance LTQ-Orbitrap mass spectrometer. b, MS/MS spectrum of the phosphopeptide HRDLLGApTNPANALAGTLR from the nucleoside diphosphate kinase (ndk). Precursor (peptide) ion mass was measured in the orbitrap mass analyzer with mass deviation of 0.09 ppm. Rich backbone fragmentation in the MS/MS spectrum localized the phosphorylation site to Thr93. Boris Macek et al. Mol Cell Proteomics 2008;7:299-307 © 2008 The American Society for Biochemistry and Molecular Biology