La Cristalera, Miraflores de la Sierra, 10-11 December 2012 HPPHPP Use of SEQUEST search results with ProteoRed.org MIAPE Extractor.

Slides:

Advertisements

Similar presentations

The Proteomics Core at Wayne State University

Advertisements

Proteomics Informatics – Protein characterization I: post-translational modifications (Week 10)

UC Mass Spectrometry Facility & Protein Characterization for Proteomics Core Proteomics Capabilities: Examples of Protein ID and Analysis of Modified Proteins.

In-depth Analysis of Protein Amino Acid Sequence and PTMs with High-resolution Mass Spectrometry Lian Yang 2 ; Baozhen Shan 1 ; Bin Ma 2 1 Bioinformatics.

CHR 16 - Human Proteome Project Data dependent and inclusion list results on LTQ – (Orbitrap) Velos 27-28th August 2012 La Cristalera - Madrid PCB – Eliandre.

EBI is an Outstation of the European Molecular Biology Laboratory. PRIDE associated tools: Practical exercise 1 PRIDE team, Proteomics Services Group PANDA.

MIAPE Extractor Tutorial SHPP meeting, 28 Aug 2012 La Cristalera, Miraflores de la Sierra, Madrid Salvador Martínez de Bartolomé Izquierdo CNB-CSIC / ProteoRed.

1336 SW Bertha Blvd, Portland OR 97219

Knowledge Enabled Information and Services Science What can SW do for HCLS today? Panel at HCSL Workshop, WWW2007 Amit Sheth Kno.e.sis Center Wright State.

De Novo Sequencing v.s. Database Search Bin Ma School of Computer Science University of Waterloo Ontario, Canada.

Peptide Identification by Tandem Mass Spectrometry Behshad Behzadi April 2005.

Proteomics: A Challenge for Technology and Information Science CBCB Seminar, November 21, 2005 Tim Griffin Dept. Biochemistry, Molecular Biology and Biophysics.

Beta-Galactosidase Digest from 500 fmole Loaded on a 1-D Gel A. B. C. Bovine Serum Albumin Digest from 250 fmole Loaded on a 1-D Gel Automation of In-Gel.

ProReP - Protein Results Parser v3.0©

Lawrence Hunter, Ph.D. Director, Computational Bioscience Program University of Colorado School of Medicine

Proteomics Informatics – Protein identification II: search engines and protein sequence databases (Week 5)

FIGURE 5. Plot of peptide charge state ratios. Quality Control Concept Figure 6 shows a concept for the implementation of quality control as system suitability.

Scaffold Download free viewer:

Proteomics Informatics (BMSC-GA 4437) Course Director David Fenyö Contact information

Facts and Fallacies about de Novo Sequencing & Database Search.

Proteomics Informatics (BMSC-GA 4437) Course Director David Fenyö Contact information

Evaluated Reference MS/MS Spectra Libraries Current and Future NIST Programs.

Protein sequencing and Mass Spectrometry. Sample Preparation Enzymatic Digestion (Trypsin) + Fractionation.

Conclusion  Comprehensive workflow identified approximately 70% more high confident peptide as compare to general search strategy.  The comprehensive.

Tryptic digestion Proteomics Workflow for Gel-based and LC-coupled Mass Spectrometry Protein or peptide pre-fractionation is a prerequisite for the reduction.

Data standards from the Proteomics Standards Initiative Andy Jones University of Liverpool.

Introduction The GPM project (The Global Proteome Machine Organization) Salvador Martínez de Bartolomé Bioinformatics support –

HPP Preliminary Results La Cristalera, August 2012 Montserrat Carrascal, Joan Villanueva, Joaquín Abián LP-CSIC/UAB.

How to assure MIAPE compliance of the data using the ProteoRed MIAPE Extractor tool HUPO-PSI meeting - Liverpool (15th April 2013) Salvador Martínez-Bartolomé.

INF380 - Proteomics-91 INF380 – Proteomics Chapter 9 – Identification and characterization by MS/MS The MS/MS identification problem can be formulated.

Common parameters At the beginning one need to set up the parameters.

Data Standards Submission 1 st CHr-16 Workshop. Miraflores de la Sierra August, 28 th -29 th 2012 Alberto Medina.

Analysis of Complex Proteomic Datasets Using Scaffold Free Scaffold Viewer can be downloaded at:

Laxman Yetukuri T : Modeling of Proteomics Data

PeptideProphet Explained Brian C. Searle Proteome Software Inc SW Bertha Blvd, Portland OR (503) An explanation.

Poster produced by Faculty & Curriculum Support (FACS), Georgetown University Medical Center Application of meta-search, grid-computing, and machine-learning.

自動化蛋白質定量系統 Automatic Protein Quantitation System 生物資訊實驗室計畫主持人許聞廉特聘研究員宋定懿研究員 Relative quantitative proteomics Labeling Label-free MS MS/MS 14 N / 15.

In-Gel Digestion Why In-Gel Digest?

Standards for proteomics: The HUPO Proteomics Standards Initiative (HUPO PSI) Public Repository for Mass spectrometry spectral.

Proteomics What is it? How is it done? Are there different kinds? Why would you want to do it (what can it tell you)?

Johannes Griss PSI Meeting Heidelberg, April 2011 EBI is an Outstation of the European Molecular Biology Laboratory. mzTab Proposal for.

CSE182 CSE182-L11 Protein sequencing and Mass Spectrometry.

Peptide Identification via Tandem Mass Spectrometry Sorin Istrail.

Eat Raw & Fresh: Introducing isotopic Mass-to-charge Ratio and Envelope Fingerprinting (iMEF) and ProteinGoggle for Protein Database Search Zhixin(Michael)

Overview of Mass Spectrometry

EBI is an Outstation of the European Molecular Biology Laboratory. In silico analysis of accurate proteomics, complemented by selective isolation of peptides.

FIRST APPROACH TO THE SHOTGUN UNKNOWN PROTEINS sHPP CHROMOSOME 16 MEETING August, 28, 2012 La Cristalera, Miraflores de la Sierra.

Proteomics Informatics (BMSC-GA 4437) Instructor David Fenyö Contact information

ProteoRed WG1-WG2 Meeting Salamanca, March,16th 2010 PME5: Quantitative LC-MS differential analysis F. Canals.

Poster produced by Faculty & Curriculum Support (FACS), Georgetown University Medical Center Application of meta-search, grid-computing, and machine-learning.

Peptide-assisted annotation of the Mlp genome Philippe Tanguay Nicolas Feau David Joly Richard Hamelin.

C HROMOSOME 16 Marta Mendes Ignacio Casal Centro de Investigaciones Biológicas August 2012.

Protein identification. Peptide Mass Fingerprinting In situ digestion Peptide extraction MALDI-MS Putative Candidates Score 1. Larval serum protein 2.

Proteome Discoverer Workshop I Orbi 4, Overview Why Proteome Discoverer? Support and additional information BRIMS portal, Planet Orbitrap, Sparkplug.

Proteomics Informatics (BMSC-GA 4437) Course Directors David Fenyö Kelly Ruggles Beatrix Ueberheide Contact information

What is proteomics? Richard Mbasu and Ben Richards.

Using Scaffold OHRI Proteomics Core Facility. This presentation is intended for Core Facility internal training purposes only.

SRM working plan. La Cristalera, 5-6 November 2013.

김지형. Introduction precursor peptides are dynamically selected for fragmentation with exclusion to prevent repetitive acquisition of MS/MS spectra.

Finding the unexpected in SWATH™ Data Sets – Implications for Protein Quantification Ron Bonner; Stephen Tate; Adam Lau AB SCIEX, 71 Four Valley Drive,

Agenda Welcome from the Skyline team!

Protein identification by mass spectrometry The shotgun proteomics strategy, based on digesting proteins into peptides and sequencing them using tandem.

Protein identification by mass spectrometry The shotgun proteomics strategy, based on digesting proteins into peptides and sequencing them using tandem.

Post translational modification n- acetylation Peptide Mass Fingerprinting (PMF) is an analytical technique for identifying unknown protein. Proteins to.

Algorithms and Computation: Bottom-Up Data Analysis Workflows

Open source tools for data analysis

Proteomics Informatics David Fenyő

Proteomics Informatics –

Sim and PIC scoring results for standard peptides and the test shotgun proteomics dataset. Sim and PIC scoring results for standard peptides and the test.

Proteomics Informatics David Fenyő

Presentation transcript:

La Cristalera, Miraflores de la Sierra, December 2012 HPPHPP Use of SEQUEST search results with ProteoRed.org MIAPE Extractor

1.A working Workflow to extract MIAPE information from Proteome Discoverer 1.3 search results using ProteoRed MIAPE Toolkit 1.A working Workflow to extract MIAPE information from Proteome Discoverer 1.3 search results using ProteoRed MIAPE Toolkit Óscar Gallardo, Joan Villanueva, Montserrat Carrascal, Joaquín Abián 2.Data dependent acquisition using inclusion list (IL) 2.Data dependent acquisition using inclusion list (IL) Joan Villanueva, Óscar Gallardo, Joaquín Abián, Montserrat Carrascal I NDEX

Ó. Gallardo M ASCOT W ORKFLOW MIAPE Generation MIAPE Extractor Mass Spectra Identification Mascot Output file mzIdentML MIAPE MSMIAPE MSI MIAPE Generator Tool RAW MGF

MIAPE Extractor Ó. Gallardo Mass Spectra Identification Output file P ROTEOME D ISCOVERER W ORKFLOW RAWMSFMGFmzIdentML

Ó. Gallardo P ROTEOME D ISCOVERER W ORKFLOW RAWMGF (GPL) (GPL) LP-CSIC/UAB

Ó. Gallardo P ROTEOME D ISCOVERER W ORKFLOW RAWMGF

MIAPE Extractor Ó. Gallardo Mass Spectra Identification Output file P ROTEOME D ISCOVERER W ORKFLOW RAWMSFMGFmzIdentML

Ó. Gallardo A. Medina August 2012 P ROTEOME D ISCOVERER W ORKFLOW MSFmzIdentML

Ó. Gallardo P ROTEOME D ISCOVERER W ORKFLOW MSF.Prot.XML mzIdentML % finished TaxID for organismName unknown: Leptospira interrogans serogroup Icterohaemorrhagiae serovar Lai.TaxID for organismName unknown: Sphaerochaeta globosa...TaxID for organismName unknown: Leptospira borgpetersenii serovar..... MyProgressBar for getSpectrumIdentificationListAndProteinDetectionListAndPeptideEvidences for SEQ finished SequenceCollection written CV term for unknown modification Deamidated / Da (N, Q) not found. CV term for unknown modification Acetyl / Da (Any NTerminus) not found. Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException at de.mpc.Prot2MzIdent.AParamHandler.createThresholdParameterList(AParamHandler.java:526) at de.mpc.Prot2MzIdent.PD12ToMzIdentML.getProteinDetectionProtocol(PD12ToMzIdentML.java:851) % finished TaxID for organismName unknown: Leptospira interrogans serogroup Icterohaemorrhagiae serovar Lai.TaxID for organismName unknown: Sphaerochaeta globosa...TaxID for organismName unknown: Leptospira borgpetersenii serovar..... MyProgressBar for getSpectrumIdentificationListAndProteinDetectionListAndPeptideEvidences for SEQ finished SequenceCollection written CV term for unknown modification Deamidated / Da (N, Q) not found. CV term for unknown modification Acetyl / Da (Any NTerminus) not found. Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException at de.mpc.Prot2MzIdent.AParamHandler.createThresholdParameterList(AParamHandler.java:526) at de.mpc.Prot2MzIdent.PD12ToMzIdentML.getProteinDetectionProtocol(PD12ToMzIdentML.java:851) 1.ProCon ProCon was unable to interpret correctly the Controlled Vocabulary used by Proteome Discoverer to identify Post Translational Modifications (PTMs) % finished TaxID for organismName unknown: Leptospira interrogans serogroup Icterohaemorrhagiae serovar Lai.TaxID for organismName unknown: Sphaerochaeta globosa...TaxID for organismName unknown: Leptospira borgpetersenii serovar..... MyProgressBar for getSpectrumIdentificationListAndProteinDetectionListAndPeptideEvidences for SEQ finished SequenceCollection written CV term for unknown modification Deamidated / Da (N, Q) not found. CV term for unknown modification Acetyl / Da (Any NTerminus) not found % finished TaxID for organismName unknown: Leptospira interrogans serogroup Icterohaemorrhagiae serovar Lai.TaxID for organismName unknown: Sphaerochaeta globosa...TaxID for organismName unknown: Leptospira borgpetersenii serovar..... MyProgressBar for getSpectrumIdentificationListAndProteinDetectionListAndPeptideEvidences for SEQ finished SequenceCollection written CV term for unknown modification Deamidated / Da (N, Q) not found. CV term for unknown modification Acetyl / Da (Any NTerminus) not found. 2.ProCon ProCon also had problems with it’s internal array references

MIAPE Extractor Mass Spectra Identification Output file OMSSA W ORKFLOW RAWMGF Ó. Gallardo OMX (GPL) (GPL) LP-CSIC/UAB

MGF MIAPE Extractor Mass Spectra Identification Output file OMSSA W ORKFLOW RAW Ó. Gallardo mzIdentMLOMX

mzIdentMLOMX A. Medina August 2012 OMSSA W ORKFLOW Ó. Gallardo % finished TaxID for organismName unknown: Leptospira interrogans serogroup Icterohaemorrhagiae serovar Lai.TaxID for organismName unknown: Sphaerochaeta globosa...TaxID for organismName unknown: Leptospira borgpetersenii serovar..... MyProgressBar for getSpectrumIdentificationListAndProteinDetectionListAndPeptideEvidences for SEQ finished SequenceCollection written CV term for unknown modification Deamidated / Da (N, Q) not found. CV term for unknown modification Acetyl / Da (Any NTerminus) not found. Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException at de.mpc.Prot2MzIdent.AParamHandler.createThresholdParameterList(AParamHandler.java:526) % finished TaxID for organismName unknown: Leptospira interrogans serogroup Icterohaemorrhagiae serovar Lai.TaxID for organismName unknown: Sphaerochaeta globosa...TaxID for organismName unknown: Leptospira borgpetersenii serovar..... MyProgressBar for getSpectrumIdentificationListAndProteinDetectionListAndPeptideEvidences for SEQ finished SequenceCollection written CV term for unknown modification Deamidated / Da (N, Q) not found. CV term for unknown modification Acetyl / Da (Any NTerminus) not found. Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException at de.mpc.Prot2MzIdent.AParamHandler.createThresholdParameterList(AParamHandler.java:526) mzIdentML Parsers mzIdentML Parsers were unable to process big OMX files because of internal memory management problems BIG, real-world, file

Ó. Gallardo P ROTEOME D ISCOVERER W ORKFLOW MSF.Prot.XML mzIdentML % finished TaxID for organismName unknown: Leptospira interrogans serogroup Icterohaemorrhagiae serovar Lai.TaxID for organismName unknown: Sphaerochaeta globosa...TaxID for organismName unknown: Leptospira borgpetersenii serovar..... MyProgressBar for getSpectrumIdentificationListAndProteinDetectionListAndPeptideEvidences for SEQ finished SequenceCollection written CV term for unknown modification Deamidated / Da (N, Q) not found. CV term for unknown modification Acetyl / Da (Any NTerminus) not found. Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException at de.mpc.Prot2MzIdent.AParamHandler.createThresholdParameterList(AParamHandler.java:526) at de.mpc.Prot2MzIdent.PD12ToMzIdentML.getProteinDetectionProtocol(PD12ToMzIdentML.java:851) % finished TaxID for organismName unknown: Leptospira interrogans serogroup Icterohaemorrhagiae serovar Lai.TaxID for organismName unknown: Sphaerochaeta globosa...TaxID for organismName unknown: Leptospira borgpetersenii serovar..... MyProgressBar for getSpectrumIdentificationListAndProteinDetectionListAndPeptideEvidences for SEQ finished SequenceCollection written CV term for unknown modification Deamidated / Da (N, Q) not found. CV term for unknown modification Acetyl / Da (Any NTerminus) not found. Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException at de.mpc.Prot2MzIdent.AParamHandler.createThresholdParameterList(AParamHandler.java:526) at de.mpc.Prot2MzIdent.PD12ToMzIdentML.getProteinDetectionProtocol(PD12ToMzIdentML.java:851) 1.ProCon ProCon was unable to identify correctly Post Translational Modifications (PTMs), marking all of them as “unknown modification” in the resulting mzIdentML file % finished TaxID for organismName unknown: Leptospira interrogans serogroup Icterohaemorrhagiae serovar Lai.TaxID for organismName unknown: Sphaerochaeta globosa...TaxID for organismName unknown: Leptospira borgpetersenii serovar..... MyProgressBar for getSpectrumIdentificationListAndProteinDetectionListAndPeptideEvidences for SEQ finished SequenceCollection written CV term for unknown modification Deamidated / Da (N, Q) not found. CV term for unknown modification Acetyl / Da (Any NTerminus) not found % finished TaxID for organismName unknown: Leptospira interrogans serogroup Icterohaemorrhagiae serovar Lai.TaxID for organismName unknown: Sphaerochaeta globosa...TaxID for organismName unknown: Leptospira borgpetersenii serovar..... MyProgressBar for getSpectrumIdentificationListAndProteinDetectionListAndPeptideEvidences for SEQ finished SequenceCollection written CV term for unknown modification Deamidated / Da (N, Q) not found. CV term for unknown modification Acetyl / Da (Any NTerminus) not found. 2.ProCon ProCon had still problems with it’s internal array references

Ó. Gallardo P ROTEOME D ISCOVERER W ORKFLOW MSF.Prot.XML mzIdentML

MIAPE Generation MIAPE Generator Tool MIAPE Extractor Ó. Gallardo Mass Spectra Identification Output file P ROTEOME D ISCOVERER W ORKFLOW RAWMSFMGF.Prot.XML mzIdentML

MIAPE Generation MIAPE Extractor Ó. Gallardo Mass Spectra Identification Output file P ROTEOME D ISCOVERER W ORKFLOW RAWMSFMGF.Prot.XML mzIdentML % finished TaxID for organismName unknown: Leptospira interrogans serogroup Icterohaemorrhagiae serovar Lai.TaxID for organismName unknown: Sphaerochaeta globosa...TaxID for organismName unknown: Leptospira borgpetersenii serovar..... MyProgressBar for getSpectrumIdentificationListAndProteinDetectionListAndPeptideEvidences for SEQ finished SequenceCollection written CV term for unknown modification Deamidated / Da (N, Q) not found. CV term for unknown modification Acetyl / Da (Any NTerminus) not found % finished TaxID for organismName unknown: Leptospira interrogans serogroup Icterohaemorrhagiae serovar Lai.TaxID for organismName unknown: Sphaerochaeta globosa...TaxID for organismName unknown: Leptospira borgpetersenii serovar..... MyProgressBar for getSpectrumIdentificationListAndProteinDetectionListAndPeptideEvidences for SEQ finished SequenceCollection written CV term for unknown modification Deamidated / Da (N, Q) not found. CV term for unknown modification Acetyl / Da (Any NTerminus) not found. Spectra IDs didn’t match between MGF file and mzIdentML file ID mgf ID mzid ID ID ID ID PepMSChargeRT

MIAPE Generation MIAPE Generator Tool MIAPE Extractor Ó. Gallardo Mass Spectra Identification Output file P ROTEOME D ISCOVERER W ORKFLOW RAWMSFMGF.Prot.XML mzIdentML MIAPE MSMIAPE MSI ID ID PepMSChargeRT ID

Ó. Gallardo P ROTEOME D ISCOVERER W ORKFLOW MIAPE Generation MIAPE Generator Tool MIAPE Extractor Mass Spectra Identification Output file RAWMSF MGF.Prot.XML mzIdentML MIAPE MSMIAPE MSI

1. 1.Uploading of MSF + mzIdentML files through MIAPE Extractor is not yet automatized 2. 2.Although we can generate MIAPE data from Sequest search results, MIAPE Toolkit doesn’t work very well with this data for the analysis stage: we can not retrieve the identified proteins, there are problems with the Sequest Score fields, … 1. 1.We are working in an automation script, to automatize MIAPE Extractor data extraction: MIAPE Extractor Automator v Development of MIAPE Extractor and MIAPE Generator tool continues improvement in each version 1. 1.Exportation of Prot.XML files from the MSF ones, and utter conversion of MSF + Prot.XML files to mzIdentML files is not automatized 2. 2.ProCon has still some errors, is very slow with large files, and is memory hungry ProCon developers are working in a new version that doesn’t need Prot.XML files, making the conversion process much faster and easier. W ORK IN P ROGRESS Ó. Gallardo

1.A working Workflow to extract MIAPE information from Proteome Discoverer 1.3 search results using ProteoRed MIAPE Toolkit 1.A working Workflow to extract MIAPE information from Proteome Discoverer 1.3 search results using ProteoRed MIAPE Toolkit Óscar Gallardo, Joan Villanueva, Montserrat Carrascal, Joaquín Abián 2.Data dependent acquisition using inclusion list (IL) 2.Data dependent acquisition using inclusion list (IL) Joan Villanueva, Óscar Gallardo, Joaquín Abián, Montserrat Carrascal I NDEX

RATIONAL OF USING DDP WITH INCLUSION LIST (IL): a.- Most target proteins assigned to the groups of the shotgun project were not detected using shotgun approaches. b.- The few detected peptides were not optimum for MRM analysis (not proteotypic, with Met/Cys, with missed cleavage). c.- Preliminary tests at LP-CSIC/UAB using targeted approaches require a limited list of peptides (need to restrict the list of target m/z values to 20-30) and failed to detect the target proteins. DDP with Inclusion list increases the probability to positively detect low abundant proteins/peptides without the constraints of targeted approaches. 16 PROTEINS SELECTED FOR INCLUSION LIST - 6 proteins assigned to the LPCSICUAB laboratory - 10 proteins assigned to MRM labs and not detected by shotgun LaboratoryUniprotName CanalsP69905 HBA_HUMAN FBQ6GPI1 CTRB2_HUMAN CGP24855 DNAS1_HUMAN MPVQ6A1A2 PDPK2_HUMAN FCP16444 DPEP1_HUMAN CGQ9BSW7 SYT17_HUMAN CGP11597 CETP_HUMAN MPVP15391 CD19_HUMAN CGQ53FZ2 ACSM3_HUMAN FVQ8N4N3 KLH36_HUMAN AbianQ9BUU2 METTL22_HUMAN AbianP33076 CIITA_HUMAN AbianQ9Y661 HS3ST4_HUMAN AbianQ14703 MBTPS1_HUMAN AbianB7ZMK8 PRSS36_HUMAN AbianA4GXA9 EME2_HUMAN Data dependent acquisition with inclusion list J. Villanueva

To obtain the inclusion list: 1.- All tryptic peptides 7-25AA. 2.- m/z values assuming z=2 and z=3 for all peptides. 3.- Filter duplicate m/z values (software requirement) Number of m/z values in the inclusion list: 556 (num peptides 282) Signal IDm/z P33076_GCTLLLTARPR P11597_VFHSLAK P16444_YPDLIAELLR Q53FZ2_EGWGNLK P24855_YDIALVQEVR Q8N4N3_VASMNQR Q8N4N3_VKPAVCSLLPK Q14703_APCPGCSHLTLK Q9Y661_AISDYTQTLSK Q9BSW7_TAVEQWHSLR P69905_VDPVNFK P16444_TLEQMDVVHR A4GXA9_MGLLAVGPDLSR Samples CCD18 and MCF7 Aliquot 250 µg protein OffGel (12 fractions) FASP digestion LC-MS/MS (DDP, IL, Targeted) Protein Discoverer Procedure: Data Dependent with IL J. Villanueva

DATA DEPENDENT WITH INCLUSION LIST: LTQ-ORBITRAP Offgel Fr6 Offgel Fr7 Sample VH: MCF-7 MS traces J. Villanueva

RESULT: Data dependent with IL: 282 Listed peptides undetected (same that targeted experiments) Low amount of target proteins Proteins not expressed in these cells RESULTS: Inclusion list and targeted DATA PROCESSING FOR IL DATA: 1.- MGF generation with PDv Database search: Proteome Discoverer and Mascot 3.- FDR 5% J. Villanueva

DATA PROCESSING: 1.- MGF generation with PDv Database search: Proteome Discoverer (and Mascot) 3.- Search results and Filtering (1 %FDR): MIAPE Extractor (Data Inspector Module) and Proteome Discoverer. Work in progress: MIAPE EXTRACTOR: The data could be uploaded and the FDR process could be achieved. Data Inspector Module: Detected errors to be solved: unable to extract protein information from SEQUEST data. Chromosome 16 protein description: Data Dependent Analysis J. Villanueva

Sample Acquisition method search method MIAPE EXTRACTORPROTEOME DISCOVERER Num peptidesNum proteinsNum peptidesNum proteins MCF7DDPMASCOT SEQUEST CCD18DDPMASCOT SEQUEST Work in progress... Number of proteins that passed the 1%FDR filter: 1.- Significant differences between searching algorithms Need an in-depth data revision. J. Villanueva

La Cristalera, Miraflores de la Sierra, December 2012 HPPHPP Use of SEQUEST search results with ProteoRed.org MIAPE Extractor