Schematic of MS1 filtering.

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Proteomics Informatics – Overview of Mass spectrometry (Week 2)

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Correlation of log-transformed signal intensity from two Affymetrix microarray hybridizations using platelet RNA. Plotted are those probesets with an average.

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.

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,

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

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,

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.

Top-down protein identification.

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

Visual validation of the computational outputs.

Schematic representation of proteogenomic annotation strategy.

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.

Skyline MS1 filtering graphical user interface.

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.

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

BIRC6 is expressed in the tumorigenic Aldefluorhigh fraction of colonosphere cells. BIRC6 is expressed in the tumorigenic Aldefluorhigh fraction of colonosphere.

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

Putative targets of miRNAs directly induced by p53 with down-regulated mRNA- and de novo protein synthesis or reduced de novo protein synthesis only. Putative.

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.

Standard concentration curves for stable isotope-labeled and acetyllysine containing peptides. Standard concentration curves for stable isotope-labeled.

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

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.

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.

Transcriptionally regulated genes in Δsaci_ptp and Δsaci_pp2a as compared with the strain MW001. Transcriptionally regulated genes in Δsaci_ptp and Δsaci_pp2a.

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.

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.

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.

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.

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

Separation of colonospheres from differentiated tumor cells by cluster analysis. Separation of colonospheres from differentiated tumor cells by cluster.

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.

Label-free pyQms quantification of metabolites and peptides.

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.

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.

GeneGoTM-based signaling pathway annotations of proteins identified in CD56+ NK cell subsets. GeneGoTM-based signaling pathway annotations of proteins.

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.

Monitoring the acetylation profile of mitochondrial proteins in SIRT3 KO mice. Monitoring the acetylation profile of mitochondrial proteins in SIRT3 KO.

RNA expression data. RNA expression data. Heat maps comparing the normalized log2 of the ratios of Fur−, F90, and F1 signals on the cl20 control signal.

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:

Schematic of MS1 filtering. Schematic of MS1 filtering.A, heat map of MS1 signal across the chromatographic gradient for the entire m/z range as acquired on a high resolution mass spectrometer. B, “zoom-in” display of an isotopic envelope for the molecular ion of a typical peptide with peaks at M, M + 1, and M + 2 selected showing changes in MS1 intensity over time. C, high resolution data allow specific filtering of molecular ions and separation of individual peaks within the isotope distribution. Skyline sums intensities within a single resolution to either side of the predicted mass to charge ratio allowing for a filter window of twice the theoretical resolution, predicted full width at half-maximum (2×FWHM). The resolution setting can be selected by the user depending on MS instrument type and preferred isotope m/z acquisition range. Birgit Schilling et al. Mol Cell Proteomics 2012;11:202-214 © 2012 by The American Society for Biochemistry and Molecular Biology, Inc.