Progenesis LC-MS and Phenyx

Transcription

1 Progenesis LC-MS and Phenyx Une combinaison unique d un logiciel d analyse différentielle en LC-MS et d une plateforme d identification et de caractérisation de protéines et peptides à partir de données MS/MS. Identifiez les vraies différences en Protéomique

2 Nonlinear Dynamics Ltd. Who are we? Nonlinear Dynamics is dedicated to solving your problems in the fields of Proteomics, Genomics and Biomarker Discovery. This is achieved by applying our core strength in developing innovative, high quality data analysis solutions What is Progenesis LC-MS? Progenesis LC-MS is an advanced proteomics research solution for the label-free quantitative analysis of complex samples It uses unique technology to deliver the advantages of speed, objectivity and statistical power It applies simple workflows so you can easily visualise complex analysis data MS-MS protein identifications can be integrated back into the software and linked with the original analysis results

3 Nonlinear Dynamics Ltd. Qui sommes nous? La mission de Nonlinear Dynamics est d essayer de résoudre les problèmes en Protéomique, Génomique et la découverte de Biomarqueurs. Notre force est de pouvoir développer des solutions d analyses innovatrices, de grande qualité et simple d utilisation Progenesis LC-MS? Progenesis LC-MS est un outil de recherche protéomique qui permet l analyse quantitative d échantillons complexes sans mass tags Il utilise une technologie unique alliant vitesse, objectivité et puissance statistique. Vous êtes guidé au travers du logiciel, vous permettant ainsi de visualiser facilement des données complexes. L identification des protéines grâce aux spectres MS-MS peut être liée aux résultats de la quantification à postériori.

4 A workflow for the differential analysis of complex samples 4

5 A workflow for the differential analysis of complex samples Obtain sequence data using targeted LC-MS/MS Generate and export MS-MS search list 5

6 Progenesis LC-MS Workflow : Data Modelling 6

7 Progenesis LC-MS Workflow : Alignment Total Ion Chromatogram LC-MS run Alignment Automatic Uses mass and retention time data Section prior to alignment Section after alignment Example of pre- and post- alignment on LC-MS run 7

8 Progenesis LC-MS Workflow : Feature Detection Intelligent detection of co-eluting peptides 8

9 Overlapping Feature Detection Feature detection in Progenesis LC-MS enables the correction detection and quantitation of overlapping pepties (features) 9

10 Viewing MS2 data for overlapping features In Protein ID you can see that the 2 overlapping features only feature 7959 actually has MS2 spectra available whereas feature 9896 does not. Furthermore according to the Stats in the results view 7959 has a high p value and is therefore unlikely to be of significance (see previous slide) 10

11 Significant feature masked by insignificant feature Examining Feature 9896 in the 1D views shows a that it is clearly differentially expressed across the groups with consistent behaviour within each group 11

12 Focusing on Data that has Protein Id information from Phenyx Following data analysis in the LC-MS Workflow. The detected features with MS2 spectra can be searched using Protein search engines such a Phenyx, Mascot and Sequest. This data can be used with the Multivariate Statistical analysis tools to focus the data exploration by using only identified features. 12

13 Correlation analysis of identified features (up regulation) Experiment looking at changes between two conditions focusing on Identified features with P<0.05 (tagged selection for up regulation) 13

14 Correlation analysis of identified features (up regulation) Experiment looking at changes between two conditions focusing on Identified features with P<0.05 (tagged selection for down regulation) 14

15 Examine Protein ID table showing modifications Protein ID table shows Peptide Ids and highlighted modifications (in red) for tagged group of features from correlation Analysis (Previous slide) 15

16 Export Data from LCMS to Excel Export table and sort out put in Excel to show features related to same protein Peak number m/z Retention time (s) Charge Max fold Protein Ids change Anova Protein Ids MS2 No IDs p<0.05 Increased with ID_p<0.05 Decreased with ID_p0.05 Score Protein Sequence x T_MOUSE AVTEQGAELSNEER x T_MOUSE MEKTELIQKAK x 22.27ACINU_MOUSE SGQKSALVK x 76.89ACTA_MOUSE AGFAGDDAPR x 59.73ACTA_MOUSE DSYVGDEAQSK x 57.13ACTA_MOUSE DSYVGDEAQSKR x x 37.87ACTA_MOUSE EITALAPSTMK x 22.5ACTB_MOUSE HQGVMVGMGQK x x 23.8ACTB_MOUSE QEYDESGPSIVHR x 29.9ACTB_MOUSE QEYDESGPSIVHR x 63.94ACTB_MOUSE SYELPDGQVITIGNER x 29.48ALDOA_MOUSE ADDGRPFPQVIK x 50.36ALDOA_MOUSE ELSDIAHR x 88.42ALDOA_MOUSE GILAADESTGSIAK x x 32.32ALDOA_MOUSE RLQSIGTENTEENRR 5 Same Protein x x 22.23ARI4B_MOUSE ADKIVRPADKNVPKIK x 20.44ARI4B_MOUSE KDTTDKALKPQTKRGK x x 20.61ARI4B_MOUSE KQKRSHKATVVNNKKK x 69.94ASF1A_MOUSE VGYYVNNEYTETELR x 44.54BXDC1_MOUSE GGNANATVTQVLR x x x 85.59BXDC1_MOUSE NISQDTFGTTFGR x 65.27BXDC2_MOUSE FLVQNIHTLAELK x 22.23CBX3_MOUSE SKKKRDAADKPR x x 46.84CBX3_MOUSE WKDSDEADLVLAK x x 58.5CBX3_MOUSE WKDSDEADLVLAK 10 16

17 Export Data from LCMS to Excel Order table on Tags and examine Protein IDs for increased expression Suz + MS Suz - MS Tags Best peptide match Peak number m/z Retention time (s) Charge Increased Decreased Max fold Protein Ids with with change Anova Protein Ids MS2 No IDs p<0.05 ID_p<0.05 ID_p0.05 Score Protein Sequence x x x T_MOUSE AVTEQGAELSNEER x x x 54.35H12_MOUSE GTGASGSFK Infinity 1.25E x x x 30.31H13_MOUSE AASGEAKPK Infinity 5.57E x x x 27.62H13_MOUSE KAASGEAKPK Infinity 4.07E x x x 31.83H13_MOUSE KAASGEAKPK Infinity 1.12E x x x 23.74H13_MOUSE KATGAATPK Infinity 1.96E x x x 26.52H13_MOUSE KATGAATPK Infinity 1.01E x x x 26.91H13_MOUSE KATGAATPK Infinity 1.33E x x x 29.31H13_MOUSE KATGAATPK Infinity 1.17E x x x 30.75H13_MOUSE KATGAATPK Infinity 1.40E x x x 36H13_MOUSE KATGAATPK Infinity 8.86E x x x 40.95H13_MOUSE KATGAATPK Infinity 5.64E x x x 45.75H13_MOUSE KATGAATPK Infinity 2.37E x x x 50.05H13_MOUSE KATGAATPK Infinity 1.37E x x x 20.34H14_MOUSE AAKPKKTAAKKK x x x 84.63H2A1F_MOUSE NDEELNKLLGR Infinity 3.05E x x x 20.07H2A3_MOUSE KGNYSER Infinity 1.09E x x x 20.91H2A3_MOUSE KGNYSER Infinity 2.59E x x x 28.55H2A3_MOUSE KGNYSER Infinity 5.54E x x x 32.89H2A3_MOUSE KGNYSER Infinity 1.87E x x x 33.35H2A3_MOUSE KGNYSER Infinity 1.68E x x x 35.18H2A3_MOUSE KGNYSER Infinity 1.78E x x x 36.26H2A3_MOUSE KGNYSER Infinity 9.48E x x x 37.51H2A3_MOUSE KGNYSER Infinity 8.88E x x x 38.57H2A3_MOUSE KGNYSER Infinity 8.54E x x x 38.74H2A3_MOUSE KGNYSER Infinity 1.13E x x x 39.35H2A3_MOUSE KGNYSER Infinity 2.13E x x x 40.7H2A3_MOUSE KGNYSER Infinity 3.07E x x x 40.77H2A3_MOUSE KGNYSER Infinity 3.40E x x x 40.78H2A3_MOUSE KGNYSER Infinity 3.19E x x x 40.8H2A3_MOUSE KGNYSER Infinity 2.99E x x x 40.8H2A3_MOUSE KGNYSER Infinity 7.39E x x x 40.9H2A3_MOUSE KGNYSER 6 17

18 Progenesis LC-MS Workflow : Multivariate Statistics 18

19 Progenesis LC-MS Workflow : MS-MS Data Integration Integration of Protein IDs 19

20 Phenyx Overview 20

21 Phenyx 2.5 Get more highly Confident Identifications Powerful and flexible scoring system Enriched search parameters (2-rounds, submission profiles, ) Extensive use of annotations in databases (PTMs, variants, AA modifs in Swiss-Prot, TrEMBL...) Enhanced accuracy and reliability thanks to the manual validation functionality and the unique conflict resolution algorithm 21

22 Phenyx 2.5 Plus de confiance dans les identifications Un score très puissant Des paramètres de recherche sophistiqués (2 tours; sauvegarde des paramètres) Usage total des annotations présentes dans les bases de données(ptms, variants, AA modifs in Swiss-Prot, TrEMBL...) Précision et confidence accrue grâce à la fonction de validation manuelle et l algorithme de résolution de conflit 22

23 Phenyx 2.5- Powerful and Interactive Platform for Data Management Full Visualization (interactive Web interface, dynamic views for, proteins overview and details, spectra overview and peptides details ) Comparison/cross-validation of Phenyx, Mascot, Sequest and X!Tandem results via the results comparison tool Expanded Exports/Reports Functionalities (Global Excel report, XML/PDF/text exports, FDR, calibration status of the instrument ) One-click results sharing with 3 levels of rights (read only, resubmission, deletion ) Automated data submission with the Phenyx Daemon Easy integration with your own Proteomics pipeline and third-party applications (Scaffold, TPP ) and bioinformatics pipelines (thanks to Web services, API, battery of Perl scripts, Perl modules, XML result files, command line interface ) 23

24 Phenyx 2.5- Plateforme puissante et interactive Nombreux outils visuels(interface Web interactif, vues dynamiques générales et en détail des protéines, spectres et peptides ) Comparaison et validation croisée des résultats de Phenyx, Mascot, Sequest et X!Tandem via l outil de comparaison Fonctions d export et de rapports étendus (rapport Excel global, exports XML/PDF/text, FDR, rapport de calibration de l instrument) Echange des résultats One-click avec 3 niveaux de droits d accès (read only, resubmission, deletion ) Soumission automatisée grâce à Phenyx Daemon Intégration simple dans votre flux Protéomique, dans les applications connexes (Scaffold, TPP ) et votre bioinformatique (grâce aux services Web, API, batterie de scripts Perl, modules Perl, fichiers de résultats XML, interface ligne de commande ) 24

25 To try Phenyx, a public server is available at: More info on Phenyx at:

26 Progenesis LC-MS and Phenyx A unique LC-MS expression analysis tool combined with a software platform dedicated to the identification and characterization of proteins and peptides from MS/MS data. Identify the real differences in your proteomics data

27 Progenesis LC-MS and Phenyx Une unique combinaison d un logiciel d analyse différentielle en LC-MS et d une plateforme d identification et de caractérisation de protéines et de peptides à partir de données MS/MS. Identifiez les vraies différences en Protéomique

28 Progenesis LC-MS and Phenyx A unique LC-MS expression analysis tool combined with a software platform dedicated to the identification and characterization of proteins and peptides from MS/MS data. Identify the real differences in your proteomics data