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

Slides:



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

Sequence alignment of C-terminal phosphorylated plant aquaporins
Distribution of phosphorylation sites identified in the cytosolic phosphoproteome.A, numbers of approved phosphopeptides, previously phosphorylated peptides,
NSAF and GeneChip datasets have a similar variance-versus-mean dependence.A–C, the rowMean and the rowS.D. of the abundance values for each transcript.
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 ).
Percentage of proteins identified in envelope membrane extracts according to the purification method and the number of transmembrane domains. Percentage.
Plasma CEP markers stratified by demographic and health factors.
Plasma CEP adducts and autoantibodies by donor age.
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,
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.
Relative quantitation of phosphopeptides from conditioned media from subtype specific breast cancer cell lines. Relative quantitation of phosphopeptides.
Top-down protein identification.
Schematic of MS1 filtering.
Frequency distribution of the effect size measure (ESM) of sperm protein spots of type-1 diabetic (A), type-2 diabetic (B) and non-diabetic obese (C) patients.
Relative abundance of proteins identified in MALDI IMS
Comparison of ROC plots for the PMF quality metrics using test dataset 2 (44 C. difficile proteins).a, ROC curves for coverage (open squares), MC (solid.
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.
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.
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.
A, myelinated nerve fibers in the control and biopsied mouse striatum were stained with anti-MBP antibody. A, myelinated nerve fibers in the control and.
Colonopshere-enriched proteins display functional interactions.
Correlation between the amounts of PCPs and PSPs generated from LLO291–317 by 20S s- and i-proteasomes. Correlation between the amounts of PCPs and PSPs.
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.
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.
Cleavage and splicing in a representative specific substrate sequence by yeast active site β subunits. Cleavage and splicing in a representative specific.
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.
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
The PPAR-α agonist GW7647 reduces experimentally induced myopia.
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,
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.
Differential expression of apoA-I and Vimentin on 2D gels
Comparison of mapped epitopes and peptides identified in immuno-SILAC screening of polyclonal antibodies against trypsin-digested PrESTs. Comparison of.
Immuno-MS results from antibodies toward 20 different target proteins in HeLa cell lysates. Immuno-MS results from antibodies toward 20 different target.
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.
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.
A and B, ROC curves of the proteomics panel diagnosis.
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.
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.
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.
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.
The Coming Age of Complete, Accurate, and Ubiquitous Proteomes
Relationship between protein concentration and several parameters
Influence of MS measurement conditions on the deviation factors between the estimated and measured concentrations of 46 proteins in neuro2a cells.A, QSTAR.
Label-free pyQms quantification of metabolites and peptides.
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.
Statistical evaluation of CD56+ NK cell subset data.
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.
Presentation transcript:

Stability and variation of metrics over a range of sample injection amounts. Stability and variation of metrics over a range of sample injection amounts. Serial dilutions of a tryptic digest of the CPTAC yeast reference proteome were analyzed in triplicate by LC-MS/MS on an LTQ instrument. Median values for each series were plotted according to the categories in Fig. 1. Error bars represent ±median error. Some values have been scaled as indicated in the panel legends. pep, peptide; IDs, identifications; med., median; ID'd, identified; fract., fraction; num, number; FWHM, full width at half-maximum; inject., injection. Paul A. Rudnick et al. Mol Cell Proteomics 2010;9:225-241 © 2010 by The American Society for Biochemistry and Molecular Biology, Inc.