Phosphopeptide sequencing by MALDI-TOF/TOF of the C-terminal tail of AtPIP2;1.A, MS/MS spectrum of singly phosphorylated 277SLGSFRSAANV287 (m/z 1188.53).

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From: Phosphorylation and Glycosylation of Bovine Lens MP20

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

Quantification of intracellular fuzzy staining (A) and of spherical bodies (B) in root cells upon an NaCl treatment. Quantification of intracellular fuzzy.

Role of C-terminal phosphorylation in the subcellular localization of AtPIP2;1 in response to salinity. Role of C-terminal phosphorylation in the subcellular.

binding sites 58 of the 473 unambiguously assigned phosphorylation sites are predicted by Scansite to be sites for binding. 50 of these correspond.

Quantification of C-terminal phosphorylation of AtPIP2;1 upon NaCl (A) and H2O2 (B) treatments.A, plants were either untreated (white bars) or treated.

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.

Distribution of disorder in the cytosolic phosphoproteome

Role of C-terminal phosphorylation in the subcellular localization of AtPIP2;1.A, the figure shows typical laser-scanning confocal micrographs of the fluorescence.

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

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 ).

Interpretation of Mass Spectra I

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.

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.

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.

Bottom-up proteomic characterization of MALDI IMS samples.

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

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.

Proteins previously reported in published MALDI IMS studies and their frequency of observation in the present study. Proteins previously reported in published.

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.

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

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.

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.

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.

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.

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.

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.

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

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.

Schematic of AIMS-to-MRM experiment.

Interpretation of Mass Spectra

Phosphopeptides identified harboring minimal binding motifs

Survey of phosphorylation motifs

MS3 for peptide identification and mapping phosphorylation sites

Presentation transcript:

Phosphopeptide sequencing by MALDI-TOF/TOF of the C-terminal tail of AtPIP2;1.A, MS/MS spectrum of singly phosphorylated 277SLGSFRSAANV287 (m/z 1188.53). y7 and y8 ions allowed identification of Ser280 as the phosphorylated residue. Phosphopeptide sequencing by MALDI-TOF/TOF of the C-terminal tail of AtPIP2;1.A, MS/MS spectrum of singly phosphorylated 277SLGSFRSAANV287 (m/z 1188.53). y7 and y8 ions allowed identification of Ser280 as the phosphorylated residue. B, MS/MS spectrum of the corresponding diphosphorylated peptide (m/z 1268.54). y4, y5, y7, and y9 ions allowed identification of the two phosphorylated residues as Ser280 and Ser283. *, fragment ions arising from loss of phosphoric acid (−98 Da). pS, phosphorylated serine; [MH]+, precursor ion; [MH − P]+, precursor ion with a loss of one metaphosphoric acid (-80 Da); [MH − P − 18]+, precursor ion with a loss of one phosphoric acid (−98 Da); [MH − 2P − 18]+, precursor ion with a loss of one metaphosphoric acid (−80 Da) and one phosphoric acid (−98 Da); [MH − 2P −2 × 18]+, precursor ion with a loss of two phosphoric acids (−196 Da). Sodana Prak et al. Mol Cell Proteomics 2008;7:1019-1030 © 2008 The American Society for Biochemistry and Molecular Biology