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.

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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
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 ).
Distribution of disorder in the cytosolic phosphoproteome
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 ).
Phosphopeptides identified harboring minimal binding motifs
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.
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.
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.
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.
Representative example of LAXIC performance for complex plant phosphoproteome. Representative example of LAXIC performance for complex plant phosphoproteome.A.
Success rates in validation of antibodies from external providers
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.
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.
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.
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,
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.
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.
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.
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.
Performance metrics for triplicate analyses of a tryptic digest of the CPTAC yeast reference proteome on four LTQ-Orbitraps at three different sites in.
Classification of the 1458 identified proteins into molecular functions. Classification of the 1458 identified proteins into molecular functions. The pie.
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.
Western blotting analysis of purified cytoplasmic membranes.
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.
Metabolic labeling of IGFBP-5 by T47D breast carcinoma cells
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.
The role of CK2 in IGFBP-5 phosphorylation
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.
Occurrence of fur−-only genes and expected sensitivity to Fur.
Phosphopeptides identified harboring minimal binding motifs
Survey of phosphorylation motifs
MS3 for peptide identification and mapping phosphorylation sites
Model of the change in receptor structure on engagement of the ligand IFN-γ. Model of the change in receptor structure on engagement of the ligand IFN-γ.
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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 parent ion at m/z 983.1 from fraction 21. 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 parent ion at m/z 983.1 from fraction 21. The sequence matched IGFBP-5-(92–115) where Ser96 is phosphorylated and Met107 is oxidized (shown underlined). The parent ion has been truncated, and the m/z range from 990 to 2,000 has been multiplied by a factor of 30 to show the fragment ions more clearly. Neutral loss of methane sulfenic acid (CH3SOH, −64 Da) is shown. b, tandem MS spectrum of the triply charged parent ion at m/z 886.4 from fraction 31. The sequence matched IGFBP-5-(231–252) where Ser248 is phosphorylated. The deduced presence of oxidized Met234 is shown underlined. Also the Cys243 alkylated with acrylamide (see “Experimental Procedures”) is shown underlined. The m/z range from 900 to 1,400 has been multiplied by a factor of 10 to show the fragment ions more clearly. Mark E. Graham et al. Mol Cell Proteomics 2007;6:1392-1405 © 2007 The American Society for Biochemistry and Molecular Biology