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

Slides:

Advertisements

Similar presentations

From Genome to Proteome Juang RH (2004) BCbasics Systems Biology, Integrated Biology.

Advertisements

Mass spectrometry in organic chemistry

S 3.1 Positive ionization low energy CID fragmentation spectrum of the singly phosphorylated peptide pSLKPDTENQESSVK of Rec 10 MS 3 spectrum of the doubly.

20-30% of a trypsinised proteome are constituted of peptides with Mw≥3000 (TReP) Identification of large peptides by shotgun MS is not efficient Isolation.

Previous Lecture: Regression and Correlation

Introduction to 2D LC- MS/MS (Yuanming Luo) Institute of Microbiology Chinese Academy of Sciences.

Methods for LTQ Orbitrap A Guided Tour with Examples

STRUCTURAL DETERMINATION MASS SPECTRUM (MS) LAB 12.

B Monoisotopic mass of neutral peptide M r (calc): Fixed modifications: Carbamidomethyl Ions score: 45 † Expect: ‡ Matches (red): 18/50.

Multi-Analyte LC-MS/MS Methods – Best Practice.

Mass Spectrometry makes it possible to measure protein/peptide masses (actually mass/charge ratio) with great accuracy Major uses Protein and peptide identification.

Proteomics Informatics – Overview of Mass spectrometry (Week 2)

From: Phosphorylation and Glycosylation of Bovine Lens MP20

Accelerating Research in Life Sciences

LC-MS/MS Identification of Impurities Present in Synthetic Peptide Drugs Dr Anna Meljon*, Dr Alan Thompson, Dr Osama Chahrour, and Dr John Malone Almac.

S2 Fig. Ion suppression for aniline, 4-aminopyridine and 4-aminobenzontrile Left: ESI-MS response in presence of 1 mM different, pH-modifying electrolytes.

Purple discoloration of the colon found during autopsy: Identification of betanin, its aglycone and metabolites by liquid chromatography–high-resolution.

Accelerating Research in Life Sciences

Agenda Welcome from the Skyline team!

From: Methoxycarbonyl-etomidate:A Novel Rapidly Metabolized and Ultra–short-acting Etomidate Analogue that Does Not Produce Prolonged Adrenocortical Suppression.

GlycoAnalytics Complex Carbohydrate Research Center,

Pinpointing phosphorylation sites using Selected Reaction Monitoring and Skyline Christina Ludwig group of Ruedi Aebersold, ETH Zürich.

Candidate phosphopeptides Verified by mutagenesis

Figure 1. LC-MS/MS for monitoring the formation of N 3-CMdT and O4 -CMdT in calf thymus DNA upon treatment with diazoacetate. Shown are the.

Protein/Peptide Quantification

PKA phosphorylates catalytic α‐ and regulatory β‐subunits of AMPK at multiple sites. PKA phosphorylates catalytic α‐ and regulatory β‐subunits of AMPK.

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

(A) (E) (B) (C) (F) (D) Control HLM MLM Chemical synthesis M6

Phosphopeptide sequencing by MALDI-TOF/TOF of the C-terminal tail of AtPIP2;4.A, MS/MS spectrum of singly phosphorylated 277ALGSFGSFGSFRSFA291 (m/z ).

(A) (E) (B) (C) (F) (D) Control HLM MLM Chemical synthesis M2 M2'

Volume 15, Issue 19, Pages (October 2005)

Proteomics Informatics David Fenyő

Phosphopeptide sequencing by MALDI-TOF/TOF of the C-terminal tail of AtPIP2;7.A, MS/MS spectrum of singly phosphorylated 270ALGSFRSNATN280 (m/z ).

Proteomic Approaches to Cancer Biomarkers

Interpretation of Mass Spectra I

(A) (E) (B) (C) (F) (D) Control HLM MLM Chemical synthesis M4 M4'

(E) (A) (B) (C) (F) (D) Control HLM MLM Chemical synthesis M3'' M3'''

Volume 8, Issue 4, Pages (April 2015)

Proteomics Informatics –

A Photoreactive Small-Molecule Probe for 2-Oxoglutarate Oxygenases

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.

Discovery and development of the N-terminal procollagen type II (NPII) biomarker: a tool for measuring collagen type II synthesis O.V. Nemirovskiy, Ph.D.,

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.

Volume 17, Issue 8, Pages (August 2010)

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.

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.

Relative quantification of cis and trans PSP gp10040–42/47–52 variants

Volume 21, Issue 5, Pages (March 2006)

Shotgun Proteomics in Neuroscience

Comparisons of MS/MS ion fragmentation spectra derived from GNPS network annotations (see Table S4 posted at ftp://massive.ucsd.edu/MSV /updates/ _aedlund_ /other/)

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.

Tandem Mass Spectrometry-Based Approaches

Transglutaminase-3 Enzyme: A Putative Actor in Human Hair Shaft Scaffolding? Sébastien Thibaut, Nükhet Cavusoglu, Emmanuelle de Becker, Franck Zerbib,

Compound is first vaporized and converted into ions, which are then separated and detected. Electron Impact (EI) Mass Spectrometry 1.

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.

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.

Daniël Blom, Dave Speijer, Gabor E. Linthorst, Wilma G

Proteomics Informatics David Fenyő

Identification of Post Translational Modifications

Interpretation of Mass Spectra

MS3 for peptide identification and mapping phosphorylation sites

ASPP2 hydroxylation is detectable in vivo and the amount of hydroxylation depends on FIH-1 abundance. ASPP2 hydroxylation is detectable in vivo and the.

Volume 2, Issue 1, Pages (January 2014)

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

Presentation transcript:

B. Neutral loss triggered MS3 scan of 983.1, 2+ A. MS/MS of 1032.17, 2+ Probe4 # 3759 RT: 35.77 NL: 3.98E4 F: ITMS + c NSI d Full ms2 1032.17@30.00 [ 270.00-2000.00] 100 983.1 95 90 85 80 75 FQSpEEQQQTEDELQDK Xcorr: 5.20 70 65 60 55 Relative Abundance 50 45 40 35 y13+2 810.5 b13+2 836.9 30 b10+1 1316.5 b7+1 957.3 b8+1 1086.5 25 b6+1 829.2 b13+1 1673.4 20 b5+1 701.2 y6+1 748.3 b14+1 1801.4 15 y5+1 633.3 y7+1 877.4 y9+1 1106.4 y10+1 1234.5 y11+1 1362.5 y12+1 1491.6 10 y14+1 1787.6 y4+1 504.3 y13+1 1620.6 5 400 600 800 1000 1200 1400 1600 1800 2000 m/z B. Neutral loss triggered MS3 scan of 983.1, 2+ Probe4 # 3760 RT: 35.78 NL: 8.81E2 F: ITMS + c NSI d Full ms3 1032.17@30.00 983.10@35.00 [ 260.00-2000.00] y14+2 845.3 100 95 90 FQ(Dha)EEQQQTEDELQDK Xcorr: 5.44 85 80 75 70 65 60 y13+1 1620.6 55 b12+2 731.4 b10+1 1218.4 Relative Abundance 50 y13+2 810.9 b5+1 603.1 45 y11+2 681.9 y7+1 877.4 y14+1 1689.6 40 b9+1 1089.5 b11+1 1333.4 b4+1 474.4 35 b3+1 345.2 y12+1 1491.8 y5+1 632.6 y6+1 748.3 y10+1 1234.5 30 y9+1 1106.5 y11+1 1362.5 b13+1 1575.5 y3+1 390.1 b14+1 1703.3 25 20 y4+1 504.3 15 b15+1 1818.9 10 5 400 600 800 1000 1200 1400 1600 1800 2000 m/z FIG. S1. Identification of the monophosphopeptide from beta-casein by nano LC-ESI-MS2 and by neutral loss triggered MS3. (A) Identification of the phosphopeptide FQSpEEQQQTEDELQDK by the MS2 fragmentation pattern of the peptide ion 1032.17 from the full MS scan indicates the phosphorylation site on Ser. (B) Identification of the peptide FQ(Dha)EEQQQTEDELQDK by the MS3 fragmentation pattern of the detected neutral loss fragment 983.1. Dha (Dehydroalanine) indicates the site of the neutral loss of phosphoric acid from the phospoSer. Only prominent y- and b-fragment ions have been labeled.

Neutral loss triggered MS3 scan of 976.45, 3+ RELEELNVPGEIVESpLSp(Dha)(Dha)EESITR Xcorr: 5.60 y4+1 476.4 y8+1 872.5 b7+1 884.4 y7+1 804.5 b13+2 740.3 y5+1 605.5 y12+2 725.2 y14+2 830.8 y15+2 895.7 y9+1 1039.3 y10+1 1153.4 y11+1 1319.6 b13+1 1479.7 b10+1 1138.4 y14+1 1661.4 y16+1 1847.8 Probe4 # 4343 RT: 41.46 NL: 5.53E3 F: ITMS + c NSI d Full ms3 1009.25@30.00 976.45@35.00 [ 255.00-2000.00] 400 600 800 1000 1200 1400 1600 1800 2000 m/z 5 10 15 20 25 30 35 40 45 50 55 60 65 70 75 80 85 90 95 100 Relative Abundance 943.8 y16+2 923.6 FIG. S2. Identification of the tetraphosphopeptide from beta-casein by neutral loss triggered nano LC-ESI-MS3. The MS2 fragmentation spectrum of the peptide ion revealed no sufficient fragment information for peptide identification. Identification of the peptide RELEELNVPGEIVESpLSp(Dha)(Dha)EESITR) by neutral loss triggered MS3 of peptide ion 976.45. Dha (Dehydroalanine) indicates the sites of the neutral loss of phosphoric acid from phosphoSer. Only prominent y- and b-fragment ions have been labeled.