MS3 for peptide identification and mapping phosphorylation sites

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B. Neutral loss triggered MS3 scan of 983.1, 2+

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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.

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 ).

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

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.

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.

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.

Mass spectrometry identification of spots in 2D blue native gels of cytoplasmic membranes isolated from BL21(DE3)pLysS Spots in 2D BN gels of cytoplasmic.

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.

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.

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

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.

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.

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

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.

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.

Identification and quantification of cathepsin D in chronic pancreatitis.A, identification of two peptides, AIGAVPLIQGEYMIPCEK (A) and LLDIACWIHH (MS/MS.

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.

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

Relationship between protein concentration and several parameters

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.

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.

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.

Peptide mass spectra of SUMO target proteins.

Phosphopeptides identified harboring minimal binding motifs

Survey of phosphorylation motifs

Phosphorylated tyrosine residues in FGFR3, FGFR3(K650E), FGFR3-TACC3, and FGFR3(K650E)-TACC3 identified by mass spectrometry analysis. Phosphorylated tyrosine.

Presentation transcript:

MS3 for peptide identification and mapping phosphorylation sites MS3 for peptide identification and mapping phosphorylation sites.A, MS2 fragmentation (parent ion m/z, 656.56) of phosphopeptide IQELKGpSQER (where pS is phosphoserine) (carboxylesterase 5, gi|Mb18381028) shows a dominant neutral loss peak at m/z 606.93 and few fragment masses providing sequence information. MS3 for peptide identification and mapping phosphorylation sites.A, MS2 fragmentation (parent ion m/z, 656.56) of phosphopeptide IQELKGpSQER (where pS is phosphoserine) (carboxylesterase 5, gi|Mb18381028) shows a dominant neutral loss peak at m/z 606.93 and few fragment masses providing sequence information. B, MS3 spectrum after fragmentation of the neutral loss peak shows a rich fragmentation pattern for peptide identification and phosphorylation site determination. Asterisks indicate water loss peaks. Jaeick Lee et al. Mol Cell Proteomics 2007;6:669-676 © 2007 The American Society for Biochemistry and Molecular Biology