ProCon User Manual 0.9.619 - Ruhr
Contents
1. references imported no Clear references Load SLoMo csv config SLoMo csv Browse SLoMo csv imported no Clear SLoModata specity SLoMo 49 0 score threshold n 2 Choose the ProteinScape 1 3 content to convert and export the selected ProteinScape 1 3 content into PRIDE XML Select Separation PROFILE CCC CCC 2701 up gel1D 721 le S OR 7 PMF ms OR r EE Mieka ids Import ProteinScape SearchEvent and export to PRIDE XML Select PRIDE XML output file XML_files ProCon_PRIDEXML xml Medical Proteome Center MPC University of Bochum 2015 16 30 ProCon Proteomics Conversion Tool User Manual Monday December 14 2015 7 Workflow 3 Proteome Discoverer to mzIdentML conversion The output of the Mascot SEQUEST ZCore and MS Amanda 6 search engines of Proteome Discoverer can be converted into the standard mzIdentML1 1 format For the conversion of ProteomeDiscoverer 1 3 and 1 4 results only the msf Mass Spec Format Thermo file is needed For ProteomeDiscoverer 1 1 and 1 2 results conversion in addition the prot xml file must be specified in this case the information spectra data missing in the ProtXML output are combined with the data from the msf file This is done by matching the peptide sequences to the proteins in which they are found Note that version 2 0 of ProteomeDiscoverer is not yet supported The tab for the ProteomeDiscoverer output conversion consists of 2 parts 1 E2. For that the user must define a so called experimental design file of type txt which contains all parameters for the spectral counts conversion After this design file is chosen all other fields of the GUI are set By pressing the Convert button the conversion into mzQuantML is started Currently two designs are currently supported e the comparison of two groups with technical replicates e the comparison of two time series data sets without technical replicates Example design and data files you can find under the SpectCnt folder The spectral counts input file the mzq mzQuantML output file and their paths are already defined in the experimental design files a Conversion parameters for PD gt mzIdentML conversion Protein level spectral counts gt mzQuantML conversion Experimental design file 97 Documents NetBeansProjects ConvertSpectCnts 2MzQuant yesources yeplicate_counts_example_Design txt Files path C Users mayerg97 Documents NetBeansProjects ConvertSpectCnts2MzQuant yesources Experimental Design two groups comparison Number of replicates 3 D time series experiment Organisation data Name Gerhard Mayer Contact address Ruhr Universitaet Bochum Medizinisches Proteom Center MPC Universitaetsstrasse 150 D 48001 Bochum Contact eMail mayerg97 rub de Annotation info I spectral counts input file Protein accession replicate_counts_example txt Protein name Gi mzQuantML output
3. Mac OS X resp so shared object Linux files first to your computer see section 1 Installation and that sqlite3 dll currently only works for 32 Bit Windows The isoelectric point 8 10 is calculated by calculating the zero point of the Henderson Hasselbach equation http isoelectric ovh org files isoelectric point theory html in an iterative way An optimized algorithm is used so that mostly only between 7 and 9 iterations are needed for convergence Because the result depends of the underlying pK values one can choose from the combo box which pK value set for the calculation should be used by default a consensus of the results of all pK value sets with exception of the Patrickios 9 Medical Proteome Center MPC University of Bochum 2015 18 30 ProCon Proteomics Conversion Tool User Manual Monday December 14 2015 value set is used The Patrickios value set is left out from the consensus calculation because it uses no pK values for the residues Cys His and Tyr and therefore the results of the Patrickios value set calculation often differ significantly from the results got by using the other value sets which use pK values for all charged residues i e the terminal NH2 COOH Cys Asp Glu His Lys Arg and Tyr The list box peak list format allows one to specify the peak list file format since this is information is not stored in the msf file We recommend to use mgf as peak list format
4. the connection is working Otherwise contact the ProCon developers specified on http www medizinisches proteom center de ProCon Medical Proteome Center MPC University of Bochum 2015 13 30 ProCon Proteomics Conversion Tool User Manual Monday December 14 2015 6 5 Converting a Search Event e Specify a SearchEventID on the ProteinScape Source tab and click the Import ProteinScape SearchEvent button ProCon imports the proteins marked green their peptides with modifications and the spectra in which those have been identified During the import ProCon asks you to specify any missing information see section Missing Information below Please be patient the import may take some time scroll down the Outputs text area for latest progress messages Further ProteinScape data sets can be imported or the current imports can be cleared e Then on the PRIDE XML tab click the Assemble PRIDE XML button and a PRIDE data set is assembled internally subsequent imports can be added to this assembly or the current assembly can be cleared e Finally click Export to PRIDE XML file and the current data sets currently in the PRIDE assembly are exported to the PRIDE XML file specified in the text field of this tab 6 6 Converting Gel Data e On the ProteinScapeSource tab there is a ComboBox containing all separations of your server entries are structured lt project gt lt sample gt lt gel gt lt Ge
5. which can be easily exported from ProteomeDiscoverer Conversion parameters for PD gt mzIdentML conversion z Parameters for the Proteome Discoverer msf prot xml gt mzIdentML1 1 conversion Proteome Discoverer msf file s NetBeansProjects ConvertProt2Mzident1 1 resources jnput WWeisheit GKO2 04 msf Proteome Discoverer prot xml file e Name of mzIdentML 1 1 file to generate NetBeansProjects ConvertProt2MzIdent1 1yesources nput WWeisheit GK02 04 mzid Browse Organization data Name Medizinisches Proteom Center MPC Contact address Universitaetsstrasse 150 D 44801 Bochum Contact email mayerg97 rub de 7 Use MPC data Sample data Sample name TEST SAMPLE NAME Conversion parameters V Calculate theoretical m z values for the peptide sequences V Export the ProteinDetectionList V Report ProCon J Calculate isoelectric point for the peptide sequences pK value set for pI calculation Consensus X V Use JDBC peak list format MGF X peptide filter criteria All X After export of the mzid file you can check it together with the peak list files by using the PRIDE Inspector 11 and the mzIdentML validator 12 software Medical Proteome Center MPC University of Bochum 2015 19 30 ProCon Proteomics Conversion Tool User Manual Monday December 14 2015 8 Workflow 4 ProteinScape 2 1 to mzIdentML conversion The SearchEvent results of ProteinScape 2 1 can be converted into the standa
6. December 14 2015 The Peptide filter criteria can be set to ALL RELAXED or STRICT and filters according the peptide scores and the thresholds set in the ProteomeDiscoverer workflow The following threshold values are used e STRICT for XCorr SEQUEST CutOffStdChargel High e g 1 35 CutOffStdCharge2High e g 2 455 CutOffStdCharge3High e g 2 87 CutOffStdCharge4High e g 2 875 for IonScore Mascot DefaultStrictScoreThreshold e g 2 3 for AmandaScore MS Amanda AmandaScoreHighConfidenceThreshold e g 120 0 e RELAXED for XCorr SEQUEST CutOffStdChargel Middle e g 1 35 CutOffStdCharge2Middle e g 2 25 CutOffStdCharge3 Middle e g 2 87 CutOffStdCharge4Middle e g 2 875 for IonScore Mascot DefaultRelaxedScoreThreshold e g 1 5 for AmandaScore MS Amanda AmandaScoreMiddleConfidenceThreshold e g 90 0 e ALL Here all score thresholds are set to 0 0 so that no filtering using peptide scores takes place The specification of User defined score thresholds as they can be afterwards set in the ProteomeDiscoverer ResultFilter tab is in preparation prep If you choose the checkbox Use JDBC which is strongly recommended then the access to the SQLite database msf file is done via the general JDBC interface Otherwise the native sqlite4java binding is used Note that if you decide not to use JDBC then you have to install the respective dll Dynamic Link Library Windows dylib
7. Thanks to all people who contributed test files and reported errors especially Oscar Gallardo Laboratori de ProteOmica CSIC UAB Barcelona Spain and Gorka Prieto Agujeta University of the Basque Country UPV EHU Bilbao Spain Medical Proteome Center MPC University of Bochum 2015 29 30 ProCon Proteomics Conversion Tool User Manual Monday December 14 2015 17 References 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 Deutsch EW Albar JP Binz PA et al Development of data representation standards by the human proteome organization proteomics standards initiative J Am Med Inform Assn 22 3 495 506 2015 Jones AR Eisenacher M Mayer G et al The _mzlIdentML data standard for _mass_spectrometry based proteomics results Mol Cell Proteomics 11 7 M111 014381 2012 Walzer M Qi D Mayer G et al The mzQuantML data standard for mass spectrometry based_ quantitative studies in proteomics Mol Cell Proteomics 12 8 2332 2340 2013 Mayer G Jones AR Binz PA et al Controlled vocabularies and ontologies in proteomics overview principles and practice Biochimica et biophysica acta 1844 1 Pt A 98 107 2014 Mayer G Montecchi Palazzi L Ovelleiro D et al The HUPO proteomics standards _initiative mass spectrometry controlled vocabulary Database Oxford 2013 Dorfer V Pichler P Stranzl T et al MS Amanda a universal identification algo
8. bracket Whenever an unknown modification is encountered during import ProCon aborts and displays an info message to correct the obo file File ProteinScape properties The property ENDIAN_TYPE allows specification of base64 encoding of mzdata binary arrays little or big Precision is fixed to 64 double Only necessary if Mascot was used in the analyses that are to be exported SATParameterType should be the ParameterType in the SearchAlgorithmTranslations table for instrument mappings default 8 You can check whether 8 is okay for you if the SQL query select distinct AlgorithmName from SearchAlgorithmTranslations where ParameterType 8 on the ProteinScape database results in some Mascot instruments like BSI FTICR ES I QUAD TOF ESI TRAP ESI TRAP ETD TRAP ESI TRAP MALDI OTOF MALDI TOF TOF Medical Proteome Center MPC University of Bochum 2015 12 30 ProCon Proteomics Conversion Tool User Manual Monday December 14 2015 6 3 ProteinScape Data Generation In order to obtain concise and complete result files you should follow some guidelines in ProteinScape data generation Fill in all fields for to describe project sample separation and spot band nearly all fields are exported if not as CVParam 4 5 then as userParam o AVOID empty fields or default or not specified fields o wrong descriptions go non validated i
9. mzIdentML output contains a globally unique Sequest server URI to specify the location of some files e g the search database file This URI is not necessarily a browsable web address In the Sequest properties file specify the URL part and the name of your Sequest server Example URISequestServerURL www medizinisches proteom center d URISequestServerName sequestmaster This will lead to the following URI for the search database in the mzIdentML file file www medizinisches proteom center de sequestmaster work Datenbank StdCry_nr fasta 4 1 5 File config mzidAuditCollection_1 1 xml For export of mzIdentML a Provider contact role e g researcher and the Provider s organization e g institute within a university should be specified The mzidAuditCollection_1 1 xml config file contains this information using a certain structure similar to FuGE Please overwrite with your details You should not change the sequence of comment and content lines If you accidently destroy the file copy over with mzidAuditCollectionTemplate_1 1 xml If you use the Sequest out to mzIdentML_1 0 export deprecated use the mzidAuditCollection_1 0 xml file analogously Medical Proteome Center MPC University of Bochum 2015 9 30 ProCon Proteomics Conversion Tool User Manual Monday December 14 2015 Sequest out gt mzidentML1x ES Folder with SEQUEST Comet out files SE
10. text should not be too long lt 10 characters Protocol Name You can specify an overall name for the protocol you performed and described in ProteinScape ProteinScape has no possibility for that but PRIDE has Instrument Software Name Version Comments In three dialogs you should specify the details of the instrument software not search engine which was used for spectrum generation Medical Proteome Center MPC University of Bochum 2015 15 30 ProCon Proteomics Conversion Tool User Manual Monday December 14 2015 amp Conversion of 1 Conversion ProteinScape 1 3 gt PRIDE XML Logging messages Initializing DB connection Server ZAPPS X Connect gt 5 Some project names User sa Dd Disconnect demo_2D Gel di MALD Password eeeccee Cose dialog _ lemo_LC I demo_Quantification Login string jdbc jtds sqlserver 134 147 84 137 1433 ProteinScape 1_0 user sa password dcchbpp DB connection successfully initialized Import ProteinScape Separation 1 load required data Loaded instrument and bibliographic reference information overwrites all corresponding sections in exported PRIDE XML files Load mzDatalnstrument XML file instruments MPC_HCTultra xml _ Browse ravens ro Load References config references properties Browse
11. 15 2015 Jul 13 pii 1874 3919 15 30053 1 doi 10 1016 j jprot 2015 06 015 Vizcaino JA Deutsch EW Wang R et al ProteomeXchange provides globally coordinated proteomics data submission and dissemination Nature biotechnology 32 3 223 226 2014 Vizcaino JA Csordas A Del Toro N et al 2016 update of the PRIDE database and its related tools Nucleic acids research 2015 Aiche S Sachsenberg T Kenar E et al Workflows for automated downstream data analysis and visualization in large scale computational mass spectrometry Proteomics 15 8 1443 1447 2015 Medical Proteome Center MPC University of Bochum 2015 30 30
12. 5 for your gel then store it and run all SearchEvents for a gel you want to export with the same stored SearchMethod Please be patient the import may take some time scroll down the Outputs text area for latest progress messages Then click the Assemble PRIDE XML button and a PRIDE data set is assembled internally containing 1 or 2 experiments in PRIDE assembly depending on PMF and or PFF identifications in the gel Finally click Export to File and the current PRIDE data set is exported to the file specified in the text field of this tab Subsequently imported ProteinScape imports are added to the internally assembled PRIDE data set and can be flushed out together using Export to File 6 7 Instrument information and References On the General Source tab instrument details and references can be imported During PRIDE XML export the respective sections mzData instrument and lt Reference gt elements are overwritten filled with the imported information in all data sets of the assembly 6 8 Missing Information Depending on the information or type of results you want to export ProteinScape asks you to specify missing information Dig_before_Sep Specify whether the digestion step was done before the separation step default in LC protocols or whether separation was done before digestion normal in gel protocols Database version Specify the version of the sequence database e g 3 41 for IPI database this
13. A_HOME JAVA_OPTS jar ProCon jar conv SC df SpectCnt replicate_counts_example_Design txt h 12 Versioning Information and Release Notes e 0 9 627 14 December 2015 Corrected error with PeptideEvidence references e 0 9 625 03 December 2015 Build in the filtering of peptides ALL RELAXED STRICT added the flag peptf for peptide filtering to the cmd line options e 0 9 624 30 November 2015 Withdraw the reporting of unique peptides e 0 9 623 18 November 2015 Made some preparations for planned source code switch to Java 8 e 0 9 620 16 November 2015 Location of lt SpectraData gt element works now for lower case and upper case peak list files e 0 9 619 13 November 2015 Added flag rpc for reporting of ProCon as AnalysisSoftware in the mzid file e 0 9 618 10 November 2015 Handling of Fasta lines without accession ie containing only protein name e 0 9 617 Qo September 2015 Some small errors corrected in PD converter e 0 9 616 10 September 2015 Integrated the spectral counts converter corrected error in Sequest Comet conversion e 0 9 610 26 August 2015 Solved now the spectrumID problem also for merged msf files see http www ebi ac uk mzidentml documentation developers Medical Proteome Center MPC University of Bochum 2015 27 30 ProCon Proteomics Conversion Tool User Manual Monday December 14 2015 13 How to cite If you want to cite or acknowledge ProCon you can cite
14. Asp Glu His Lys Arg and Tyr If you have connection problems to your SQLServer you can use the test program TestSQLServerAccess from the tools menu which allows you to check your connection parameters Maybe you must create a new user which not have to go through windows authentication One must give that user read privileges for all ProteinScape 2 databases proteinscape gum Icc processingkernel Conversion of ProteinScape2 1 gt mzidentMLL1 p Conversion ProteinScape 2 1 gt mzIdentML 1 1 Connection data Project ID Project name Creatio Note Server ps bochum m Connect 2814749767 demo_2D Gel 2008 03 05 2D Gel of a cell lysate of Coryneb 2814749767 demo_LC MALDI 2008 03 05 i 2814749767 demo_2D LC 2008 03 05 User sa v DBOwner dbo 2814749767 demo_Import 2008 07 10 Test 2814749767 ZAP CD 2008 07 31 poo suaebew DB structure log 2814749767 Methodenoptimierung MSMS 2008 07 31 2814749767 ZAP CD 2008 08 04 Organization data s ID Sample name Researcher Name Gerhard Mayer 28147497671 Corynebacterium Organization Name Medizinisches Proteom Center MPC Contact address Universitaetsstrasse 150 D 44801 Bochum Contact email mayerg97 rub de V Use MPC data Conversion parameters 5 SearchE SearchEvent name Proc Algorithm
15. EE EEEE E EEES EES EEE ES KSEE NES 28 15 Planned future TMC IONE I Yiacacccate 2tcxsuaacceayecesecsenpaneceessaacnage tearasoreaaraumnensaueretinacacemeeneeis 29 16 Ackp wledg ments srsiiscsniissiriiciiti eniin ieii E Eae Esaa ESY 29 7 Referentes Jesiis imensei nina A e E E E E EAEE E T EE 30 1 Introduction With ProCon you can convert proteomics identification and quantification results into HUPO standard formats 1 which can be used to upload your results into public repositories 2 Installation Install Java SE JRE ProCon was tested with JRE 8 Update 66 64 Bit but should work with all former JRE 7 and newer JRE 8 versions e g from the actual download version here http www oracle com technetwork java javase downloads index html Installation of a new ProCon release If you have already used ProCon and install a new release be sure to save any changes made to config files e g added modifications institute address or server information Then unzip ProCon_dist lt version gt zip into an arbitrary directory e g C ProCon This is the so called working directory from which you start ProCon later see below Verify and potentially change the configuration files see next section and configuration subsections in Sequest out Import and ProteinScape 1 3 Import sections Medical Proteome Center MPC University of Bochum 2015 2 30 ProCon Proteomics Conversion Tool User
16. In the panel Organization data one can enter the name and contact details If one clicks the checkbox Use MPC data then these contact fields are filled in with the data of the MPC Medical Proteome Center in Bochum In the panel Conversion parameters one can choose if the theoretical m z values and isoelectric points for the peptide sequences should be calculated The isoelectric point 8 10 is calculated by calculating the zero point of the Henderson Hasselbach equation http isoelectric ovh org files isoelectric point theory html in an iterative way An optimized algorithm is used so that mostly only between 7 and 9 iterations are needed for convergence Because the result depends of the underlying pK values one can choose from the combo box which pK value set for the calculation should be used by Medical Proteome Center MPC University of Bochum 2015 20 30 ProCon Proteomics Conversion Tool User Manual Monday December 14 2015 default a consensus of the results of all pK value sets with exception of the Patrickios 9 value set is used The Patrickios value set is left out from the consensus calculation because it uses no pK values for the residues Cys His and Tyr and therefore the results of the Patrickios value set calculation often differ significantly from the results got by using the other value sets which use pK values for all charged residues i e the terminal NH2 COOH Cys
17. Manual Monday December 14 2015 The ProteomeDiscoverer version now supports both an access to the SQLite database msf file via JDBC and via a native interface sqlite4java written in C It s recommended to use the JDBC version which uses the driver from https bitbucket org xerial sqlite jdbc If one wants to use the native interface instead one first must install the operating system specific files for sqlite4java from the website http code google com p sqlite4java For Windows operating systems copy the DLL s sqlite4java win32 x64 dll resp sqlite4java win32 x86 dll into the folder C Windows SysWOW64 resp C Windows System32 Also sqlite3 dll available from http www sqlite org should be copied into the proper system directory C Windows System32 Note that at moment only a sqlite3 dll for 32 Bit is available Then in the batch file start_ProCon bat set the JAVA_HOME variable to point to your Java Runtime Environment JRE For Mac OS X resp Linux operating systems one should install the files dylib resp so from the sqlite4java distribution into the respective system directories For starting ProCon you should first set the path to your Java runtime installation in the batch file start_ProCon_from_GUI bat and then right click on this batch file and run it echo on set JAVA_HOME C Program Files Java jre1 8 0_66 bin java exe JAV A_HOME jar ProCon jar pause Medical Proteome Cen
18. ProCon Proteomics Conversion Tool User Manual Monday December 14 2015 ProCon Proteomics Conversion Tool ProCon Proteomics Conversion Tool sssccccesssseceeeessceecessssceeccessaceeeesssaeeeseessaeeeseeaaes 1 T Introductioni ic us 2s eid eke eid le ed Ae a eee 2 Z T stallation hierren ne e E eee EA S E AR Ea 2 ATOMIC A COTE AOI coset a eu a a aa RR Al ee he A R E AER 4 File config ProCon properties esse tecasseactesdieiveesevganeedee iteeneateeed vi vsteaaeesdees teenacteges eat 4 File config log4j PrOp rtieS 5 sgiad canted Uo ssdasdadacnansad vie rinners vanandacaaaaawaecanaudsendeaed vacandungetaes 4 4 Start POGO niee s anase daaa aiaa aaar a a a eTa sa INi 5 5 Workflow 1 Sequest out comet out Import and mzIdentML expott ee eeeeeteeeeeeeees 6 32 Seguest specinic C nfis ration e sni ae Gaston eo Aaa RS A ae 6 The SEQUEST converter converts the out files from an arbitrary folder into the mzIdentML format Besides the out and dta files the folder must contain the following 2 for comet out resp 4 for SEQUEST out files eee eeescecccceeeeseeeenneeeeeeeeeeeeeeenaaeees 6 Header txt only for SEQUEST out not required for comet out conversions 6 sequest log only for SEQUEST out not required for comet out conversions 6 sequest params resp COMeEt paraMS 5 lt sasocadasqaseaaiaqsgeedugiagsasdeasessdaseegseoasedasedastaeseratelaras 6 lt folder na
19. QUEST example_folder Browse maldentM output fe IXM _fles ProCon_sequest_mzIdentM mzid Bronse sequest params resp comet params file sequest params Browse E export version 1 0 0 compliant Comet Export Parse SEQUEST out folder and export to mzIdentML file Ready Medical Proteome Center MPC University of Bochum 2015 10 30 ProCon Proteomics Conversion Tool User Manual Monday December 14 2015 6 Workflow 2 ProteinScape 1 3 Import and PRIDE XML export 6 1 Prerequisites Connection to your local ProteinScape database ProCon connects to the SQL database of your PS 1 3 installation The SQL database must be configured to allow connections via TCP IP default port 1433 A connection string is implemented like jdbc jtds sqlserver lt IP_address_of_server gt 1433 ProteinScapel_0 user lt username gt passwo rd lt password gt Therefore you must know the IP address of the ProteinScape server where the SQL database is normally installed too the port of the SQL database default 1433 for Microsoft SQL Server no firewall should prevent the communication between the computer where ProCon runs and the database server the database name default ProteinScapel_0 the SQL user name we can use sa because ProCon does not CHANGE anything but you may create another user having only read permissions the SQL password for this database user Dat
20. VA_OPTS are set properly in your batch file e g for the Windows environment set JAVA_HOME C Program Files Java jre1 8 0_66 bin java exe set JAVA_OPTS d64 server XX AggressiveOpts Xmn1g Xms2g Xmx4g XX UseParNewGC XX UseConcMarkSweepGC XX ParallelGCThreads 20 The following two options are common to all five converters Option Description Mandatory Default Optional value h Print help screen for command line arguments optional false Cony name of the gt mzid converter program PD 1x mandatory PS13 PS21 SEQO Example JAVA_HOME JAVA_OPTS jar ProCon jar conv h a For the ProteomeDiscoverer 1 x x 1 4 converter the following options are defined Option Description Mandatory Default Optional value pks pK value set for isoelectric Point IP calculation optional Consensus Consensus recommended mz Calculate theoretical mass charge values for the optional true Medical Proteome Center MPC University of Bochum 2015 23 30 ProCon Proteomics Conversion Tool User Manual Monday December 14 2015 peptide sequences recommended ip Calculate isoelectric points for the peptide sequences optional true recommended jdbc Use JDBC driver recommended optional true pdl Export of ProteinDetectionList recommended optional true rpc Report ProCon as An
21. a for First Test ProCon was tested for 2D gels and 1D LC both PMF MS or PFF MS MS either protein assembly by search engine or by ProteinExtractor It was tested with Mascot Sequest and Phenyx runs A best because simplest first test would be a LC MS MS run performed using one search engine Connection to Ontology Lookup Service During import of ProteinScape experiments the taxonomy ID is queried online using the Ontology Lookup Service at the European Bioinformatics Institute http www ebi ac uk ontology lookup services OntologyQuery That works correctly only Medical Proteome Center MPC University of Bochum 2015 11 30 ProCon Proteomics Conversion Tool User Manual Monday December 14 2015 if ProCon as Java application can establish an online connection at runtime You should configure firewall rules appropriately or answer firewall questions with Yes 6 2 ProteinScape specific Configuration File config PAG PS obo In this file the mapping from ProteinScape modifications to PSI MOD is configured As it is name based there may exist differences in your ProteinScape installation This is most probable for modifications you added yourself e g Cy3 differs from Cy3 C You should check your commonly used modifications names and at least one cross reference to PSI MOD before using ProCon the first time ProCon looks for names so you must be quite exact considering each space and
22. alysisSoftware in mzid file optional true affname Contact information affiliation name mandatory affaddr Contact information affiliation address mandatory umail Contact information user email mandatory msf ProteomeDiscoverer 1 x x 2 4 msf input file mandatory prot ProteomeDiscoverer 1 1 1 2 prot xml input file mandatory only for PD1 x sampname Sample name mandatory plff Peak list file format e g MGF PKL mzML optional MGF peptf Peptide filtering ALL RELAXED or STRICT optional All mzid mzIdentML mzid output file mandatory Example JAVA_HOME JAVA_OPTS _ jar ProCon jar conv PD1x pks Consensus mz ip jdbc pdl rpc affname Medizinisches Proteom Center MPC affaddr UniversitatsstraBe 150 D 44801 Bochum msf D ProteomeDiscoverer Oscar Test2 2012_310 MCH_Banda2_03 msf mzid D ProteomeDiscoverer Oscar Test2 2012_310 MCH_Banda2_03 mzid sampname Test Sample plff MGF peptf ALL h b For the ProteinScape 1 3 converter the following options are defined umail mayerg97 rub de Option Description Mandatory Default Optional value sname Connection data server name or IP adress mandatory uname Connection data user name mandatory pw Connection data password mandatory instrf mzData instruments file optional none brf bibliographic references file optional none smf SLoMo S
23. ance peptide_mass_units fragment_ion_tolerance enzyme_info e g diff_search_options 15 9949 M 57 0 C 0 000 X 0 000 X 0 000 X 0 000 X term_diff_search_options 0 0000 0 0000 database_name D Database StdCry fasta first_database_name D Database StdCry fasta second_database_name mass_type_parent O _ 0 average masses 1 monoisotopic masses mass_type_fragment 1 0 average masses 1 monoisotopic masses max_num_internal_cleavage_sites 5 maximum value is 5 peptide_mass_tolerance 1 5000 peptide_mass_units 0 0 amu 1 mmu 2 ppm fragment_ion_tolerance 1 5000 width in amu of bins for fragment ions enzyme_info Trypsin 1 1 KR c comet params in case of comet out conversion e g search_enzyme_number 1 choose from list at end of this params file Medical Proteome Center MPC University of Bochum 2015 7 30 ProCon Proteomics Conversion Tool User Manual Monday December 14 2015 num_enzyme_termini 2 valid values are 1 semi digested 2 fully digested default 8 N term 9 C term fragment_bin_tol 1 0005 binning to use on fragment ions output_outfiles 1 O no l yes write out files d lt folder name gt log Sequest queued xxxxxXXXXXXXXXXXXXXXXXXXX XXXXXXXXXXXXXXXXXXXXXXXXX activity date in the format EEE MMM dd kk mm ss yyyy e g Sequest queued Tue Jun 24 11 32 27 2008 StdCry_nr fasta Trypsin 15 99491 M 57 0000 C 0 0000 X 0 0000 X 0 0000 X 0 0000 X
24. c ccccccccsessssssescscsesecsesesesscscsesssscscsssscsesssscsssvseseceeaes 13 6 4 Testing Initializing the Database Connection ceeeeeeenneeeeeeeeeeeeeennnaeeeeeeeeeeeeees 13 Medical Proteome Center MPC University of Bochum 2015 1 30 ProCon Proteomics Conversion Tool User Manual Monday December 14 2015 6 5 Converting a Search ok lt 1 1 Ree Renee nena ee mene ees eee ene ern eee ene rte ene ener erers ee 14 6 6 Converting Gel Data sisecesctteuse ci ateectandd sce rias aesa EEEE E aa EE 14 6 7 Instrument information and References cseeseceeceeeeeeeeeeenneeeeeeeeeeseeennaeeeeeeeeeeeees 15 6 8 Missing TIOPIMALION ss c snscascsanisatersensannronacadennsasanensomnateranabaunracuyalanentiaenimensatenessnnaatanveast 15 7 Workflow 3 Proteome Discoverer to mzIdentML comversion c ccscsessssesssseesssesseseeseses 17 8 Workflow 4 ProteinScape 2 1 to mzIdentML conversion c ccssssessssessssessssessssesessesseees 20 9 Workflow 5 Spectral Counts to mzQuantML Conversion ccccececeeeeeeeetnteeeeeeeeeeeeeenaaees 22 WO TG IS MEN cosa aa accra e oases eee enaiadeia E E 23 11 Command Line Arguments for batch mode escscceeeescecereesseneeesensceeeneenseneeneencnes 23 12 Versioning Information and Release Notes sseeeeeseseeeeessersssrrreessrerssssreressrrerrssrreeessrree 27 TI HOW tO Ceserani A E E a T A A EI 28 14 Known Bu es gis escsci ede eed aw civddi css Sesdeedsauddtade sdacde E
25. file i replicate_counts_example mzq Molecular weight kDa jd a files mandatory F pl isoelectric point first series aa Condition_E1 raw joe sni Condition_E2 raw T Sequence coverage Condition _E3 raw second series Condition_Fi raw Condition_F2 raw Condition_F3 raw 6 identification files optional H first series first series Medical Proteome Center MPC University of Bochum 2015 22 30 ProCon Proteomics Conversion Tool User Manual Monday December 14 2015 10 Tools menu The tools menu contains the following two small tools 1 PeptidePropertyCalculator this tool allows you to enter a peptide sequence and to calculate the pI value and the molecular weight for this peptide 2 Test MS SQLServer access This tool allows you to test the access to your ProteinScape MS SQLServer backend database If you cannot get access to the database you must check your network and firewall configuration 11 Command Line Arguments for batch mode ProCon can also be started from the command line by specifying all the arguments which are normally specified via the GUI Graphical User Interface One must specify all mandatory arguments If an argument of an option contains blank characters one must use quotation marks If an optional argument is not specified then the given default is used for flag options false means not set Make sure that the variables JAVA_HOME and JA
26. ite LOcalization of MOdifications 13 file optional none Medical Proteome Center MPC University of Bochum 2015 24 30 ProCon Proteomics Conversion Tool User Manual Monday December 14 2015 smthr SLoMo Site LOcalization of MOdifications threshold optional 0 0 pride PRIDE XML output file mandatory sep separation name one of them seid SearchEvent ID is mandatory pmf PMF peptide mass fingerprint flag at least one of pff PFF peptide fragment fingerprint flag them is mandatory inp_sm search method mandatory inp_dbv search database version mandatory inp_prot protocol name mandatory inp_swn instrument software name mandatory inp_swv_ instrument software version mandatory inp_swc instrument software comments mandatory inp_si instrument optional inp_ord String indicating the order of digestion and separation Dig_before either Dig_before_Sep or Sep_before_Dig ee one of them Dig dig_first flag indicating first digestion then separation 18 mandatory sep_first flag indicating first separation then digestion Example JAVA_HOME JAVA_OPTS jar ProCon jar conv PS13 sname ZAPPS uname sa pw dcchbpp pride XML_files ProCon_PRIDEXML xml sep Profile CCC CCC 2701 up gell D 721 pmf inp_sm Search machine inp_dbv 3 84 inp_p
27. lID gt long names are truncated GelID is unique Specify a separation and click the Import ProteinScape Separation button ProCon then considers all spots spectra and searches of this separation and exports the proteins marked green their peptides with modifications and the spectra in which those have been identified Dependent on the selection status of the PMF PFF check boxes PMF and or PFF identifications are exported leading to 1 or 2 ProteinScape imports During the import ProCon asks you to specify any missing information see section Missing Information below e PRIDE can only describe one protocol per data set i e per lt Experiment gt element If the SearchEvents of the specified gel have been run with different SearchMethods ProCon asks you to select one Only SearchEvents done with this SearchMethod are then imported ATTENTION In ProteinScape if you modify a SearchMethod and run a SearchEvent without saving the method changes it is not stored but the SearchEvent is named origSearchMethod modified per default If you anyhow store and then select such a SearchMethod with the modified postfix ProCon will export only last SearchEvent although there may be more SearchEvents using the same default name RECOMMENDATION You should optimize a SearchMethod Medical Proteome Center MPC University of Bochum 2015 14 30 ProCon Proteomics Conversion Tool User Manual Monday December 14 201
28. me gt log e g if your folder is named test_folder then the file should be amed test TOIISE IOS teirru ensenen n oss E eE EEE E SEE ETES 6 4 1 1 File config SEQUEST_massvyalues txt x a iceecesc se Bis Ge iss Se Sanaa a Sones 8 4 1 2 File config SEQUESTMOD obo0 suhiaidesindketiotianakanunatetielinwea nates es 8 4 1 3 File config unimod obo eg 55 cSdecss dade vecadaensdas pein eaceesehaaadde de pichdasdadad es vache sot dadeccgiaak 9 4 1 4 File config Sequest properties cccceeeeesssnncccccceeeeeeeeenneeeeeceeeeeseeenaneeeeeeeeeeeeeee 9 4 1 5 File config mzidAuditCollection_1 1 xml o 0 1c24 opts SSerptalecoretesstenecestgeaetenstvncteitas 9 6 Workflow 2 ProteinScape 1 3 Import and PRIDE XML export c ccccssessssessesesssseeseeee 11 0 1 Prereg isites aeinn cassie thers ect aetna ranide Aida a Ge eatduten ieee eed a 11 Connection to your local ProteinScape database c ccccscessssessssessssessssessssessssesssseeseees 11 Datador First Testine ien ote diated Gn eaapee AG sce Acorn eee 11 Connection to Ontology Lookup Service ces ou esas cen csses on ateeceas goaded sgh ageeesee ey atvoans 11 6 2 ProteinScape specific Configuration c ccccscscsssscsessesesesscsssesscscsvsssscsesessesesvssseseees 12 Pile Conn e PAG PS ODO 95 cscscatiages de saeteaitiaies en puddle E E or e OE EAER eT 12 File ProtemmS cape properties si escien iii iesenii estrissar i deenaa 12 6 3 ProteinScape Data Generation c
29. mods 0 0000 0 0000 cj 4 1 1 File config SEQUEST_massvalues txt This config file contains the mass values Sequest uses Be sure to use the mass value file of your Sequest installation Server path e g C Inetpub etc config 4 1 2 File config SEQUESTMOD obo Sequest uses only masses for modifications In the Sequest obo file a mapping between these masses added to an amino acid have to be mapped to UNIMOD modifications used in mzIdentML If you used a modification mass amino acid not specified an error occurs during export The edit the obo file and add this new combination in the following form Example Oxidation here with mass 15 9949 of Methionine Term id SEQMOD 00002 name M 15 9949 def Oxidation of Methionine UNIMOD UNIMOD 35 Medical Proteome Center MPC University of Bochum 2015 8 30 ProCon Proteomics Conversion Tool User Manual Monday December 14 2015 is_a SEQMOD 00001 Modification Be aware that in Sequest fixed and variable modifications are specified separately and can therefore have different masses e g different number of decimals 4 1 3 File config unimod obo This is just the unimod obo file from http www unimod org obo unimod obo The unimod obo file coming with ProCon should be sufficient for most cases Overwrite with the latest version date stamp inside the file to be up to date 4 1 4 File config Sequest properties The
30. name Analyte Spekt 7 Calculate theoretical m z values for the peptide sequences 28147497 Lift_Bacteria Nov 72005 4 07PM 2005 Unknown Coryneba 28147 a aes A 28147497 Lift_ Bacteria Nov 72005 4 07PM_ 2005 Unknown Coryneba 28147 B Y Calculate isoelectric point for the peptide sequences 28147497 Lift_Bacteria Nov 7 2005 4 07PM 2005 Unknown iCoryneba 28147 Pic kaki set fara code 28147497 Lift_Bacteria Nov 72005 4 07PM 2005 Unknown Coryneba 28147 28147497 Lift_Bacteria Nov 72005 4 07PM 2005 Unknown Coryneba 28147 28147497 Lift_Bacteria Nov 72005 4 07PM 2005 Unknown Coryneba 28147 Convert Gels 28147497 Lift_Bacteria Nov 72005 4 07PM 2005 Unknown Coryneba 28147 28147497 Lift Bacteria Nov 7 2005 4 07PM_ 2005 Unknown Coryneba 28147 T Gel ID Gel Name Creation date Note Sample name Project name 2814749767 Gel_II 2 2005 09 26 Corynebacte demo_2D Gel FileName mzid rynebacterium__Corynebacterium__281474976710674__Gel_II 2 Browse Convert No of SearchEvents found 27 Close dialog Q a m Medical Proteome Center MPC University of Bochum 2015 21 30 ProCon Proteomics Conversion Tool User Manual Monday December 14 2015 9 Workflow 5 Spectral Counts to mzQuantML conversion ProCon supports also the conversion from spectral count result files into mzQuantML
31. ndatory seid SearchEvent ID mandatory Example JAVA_HOME JAVA_OPTS jar ProCon jar conv PS21 sname maldiraumserver uname sa pw bruker2008 resname Gerhard Mayer orgname Medizinisches Proteom Center MPC affaddr Universitaetsstrasse 150 D 44801 Bochum umail mayerg97 rub de mzid C Users Gerhard 101217_sAPP_first_562949953421517_562949953425925_562949 953431912 mzid pks Consensus projID 562949953421517 sampID 562949953425925 seid 562949953431912 d For the SEQUEST out converter the following options are defined Option Description Mandatory Default Optional value seqout SEQUEST out comet out input file folder mandatory mzid mzIdentML mzid output file mandatory vers10 Convert to mzIdentML version 1 0 not recommended optional false off as default comet Conversion of comet out folder optional false Example JAVA_HOME JAVA_OPTS jar ProCon jar conv SEQO seqout SEQUEST example_folder mzid XML_files ProCon_mzIdentML mzid vers10 mod h Medical Proteome Center MPC University of Bochum 2015 26 30 ProCon Proteomics Conversion Tool User Manual Monday December 14 2015 e For the spectral counts converter the following options are defined Option Description Mandatory Default Optional value df spectral counts design file input file mandatory Example JAV
32. ntering the parameters for the conversion process 2 Starting the conversion process into the mzIdentML1 1 standard format In the dialog box for entering the conversion parameters Figure 1 one can choose the input files the msf and for ProteomeDiscoverer 1 1 and 1 2 also the prot xml output files of the ProteomeDiscoverer output After choosing one of them the name of the other one and a name for the mzid output file are proposed but one can also change the proposed file names if needed In the panel Organization data one can enter the name and contact details If one clicks the checkbox Use MPC data then these contact fields are filled in with the data of the MPC Medical Proteome Center in Bochum In the panel Conversion parameters one can choose if the theoretical m z values and isoelectric points for the peptide sequences should be calculated If the checkbox Export the ProteinDetectionList is deselected no protein inference information is exported This can be used if one intends to use one s one protein inference algorithm as e g the Protein Inference Algorithms PIA 7 http www ruhr uni bochum de mpc software PIA index html en The checkbox Report ProCon determines if the converter ProCon is listed as AnalysisSoftware in the generated mzid file Medical Proteome Center MPC University of Bochum 2015 17 30 ProCon Proteomics Conversion Tool User Manual Monday
33. nto the exported XML Use one instrument type for each imported spectrum or each spectrum package called combined spectrum otherwise the results cannot be exported into the same lt Experiment gt element but have to go into separate data sets Use one SearchMethod for all identification runs of a gel not only the same name but really the same method having the same SearchMethodID otherwise the results cannot be exported into the same lt Experiment gt element but have to go into separate data sets 6 4 Testing Initializing the Database Connection A default database connection string is given on the ProteinScape Source tab which can be anytime restored by clicking the Reset DB string button Provide the correct information for your server as described in section 1 see above Example jdbc jtds sqlserver 134 147 123 124 1433 ProteinScapel_0 user iu ser password iuser Before you can import ProteinScape data you have to click the Initialize DB Connection button Please be patient this can take some time ProCon tries to connect to the ProteinScape server and database with the specified account information If an error occurs the error exception text is printed out Check the connection string and try Initialize DB Connection again If no error occurs you will find three project names of your ProteinScape server in the text area next to the button Only if you see these project names
34. onverts the out files from an arbitrary folder into the mzIdentML format Besides the out and dta files the folder must contain the following 2 for comet out resp 4 for SEQUEST out files Header txt only for SEQUEST out not required for comet out conversions sequest log only for SEQUEST out not required for comet out conversions sequest params resp comet params lt folder name gt log e g if your folder is named test_folder then the file should be named test_folder log If you don t find this information in your SEQUEST folder containing the out files then you have to create the content of these files by your own using any text editor according to the following description a Header txt only for SEQUEST out not required for comet out conversions Sample LastName e g LastName Joppich Sample PMXPWE080620_38 b sequest log only for SEQUEST out not required for comet out conversions TurboSEQUEST XXXXXXXXXXXXXXX II XXXXXXXXXXXXXXX SEQUEST version Medical Proteome Center MPC University of Bochum 2015 6 30 ProCon Proteomics Conversion Tool User Manual Monday December 14 2015 e g TurboSEQUEST PVM Master v 27 rev 12 c 1998 2007 c sequest params in case of SEQUEST out conversion diff_search_options term_diff_search_options database_name first_database_name second_database_name mass_type_parent mass_type_fragment max_num_internal_cleavage_sites peptide_mass_toler
35. rd mzIdentML1 1 format In the panel Connection data Figure 2 one must first select the server to use and must specify the user name and the password Also the database owner should be changed if it s not dbo If you don t know your database owner you can check it with the Microsoft SQLServer 2012 Management Studio http www microsoft com en us download details aspx id 29062 There are empty entries selectable from the comboboxes which are editable and allow you to specify your own server After pressing the Connect button one can choose in the tables the desired project sample and single SearchEvent for which the results should be converted into mzIdentML 1 1 Then in the text field an output file name is automatically proposed but it can be changed by pressing the Browse button After pressing the Convert button the conversion process is started and a progress bar shows the status of the conversion Alternatively one can click on the radio button Convert Gels Then all the gels for a given project sample combination are shown If you select a gel then all search events for the whole gel are shown automatically in the table for search events and you can again start the conversion process by pressing the Convert button After finishing the conversion a message box informs the user and the connection to the ProteinScape 2 1 database is automatically closed
36. rithm optimized for high accuracy tandem mass spectra J Proteome Res 13 8 3679 3684 2014 Uszkoreit J Maerkens A Perez Riverol Y et al PIA An Intuitive Protein Inference Engine with a Web Based User Interface J Proteome Res 14 7 2988 2997 2015 G R Grimsley J M Scholtz C N Pace A summary of the measured pK values of the ionizable groups in folded proteins Protein Sci 18 2009 247 251 C S Patrickios E N Yamasaki Polypeptide amino acid composition and _ isoelectric point II Comparison between experiment and theory Analytical biochemistry 231 1995 82 91 A Sillero J M Ribeiro Isoelectric points of proteins theoretical determination Anal Biochem 179 1989 319 325 Perez Riverol Y Xu QW Wang R et al PRIDE Inspector Toolsuite moving towards a universal visualization tool for proteomics data standard formats and quality assessment of ProteomeXchange datasets Mol Cell Proteomics 2015 Ghali F Krishna R Lukasse P et al Tools Viewer Library and Validator that Facilitate Use of the Peptide and Protein Identification Standard Format Termed mzIdentML Mol Cell Proteomics 12 11 3026 3035 2013 C M Bailey S M Sweet D L Cunningham M Zeller J K Heath HJ Cooper SLoMo automated site localization of modifications from ETD ECD mass spectra J Proteome Res 8 2009 1965 1971 G Mayer C Stephan H E Meyer M Kohl K Marcus M Eisenacher ProCon PROteomics CONversion tool J Proteomics 20
37. rmed allowed In case ProCon does not start check the contents of the log file in the log folder log ProCon txt More detailed information about errors can be found in the log files in the log folder ProCon log for ProCon ProteinScape and Sequest classes and pride log for pride classes There are four workflows you can follow in the current version 1 Import of Sequest out files and export to mzIdentML 2 2 ProteinScape 1 3 import and PRIDE XML export 3 Proteome Discoverer 1 1 1 2 and 1 3 to mzIdentML 1 1 conversion 4 ProteinScape 2 1 to mzIdentML 1 1 conversion 5 Spectral counts to mzQuantML 3 conversion Medical Proteome Center MPC University of Bochum 2015 5 30 ProCon Proteomics Conversion Tool User Manual Monday December 14 2015 5 Workflow 1 Sequest out comet out Import and mzIdentML export Functionality has been added for import of a Sequest out folder one search engine run and export of this Sequest data set to mzIdentML Use the tab Sequest out comet out to mzIdentML for export Sequest import was tested with Bioworks Sequest version 3 2 Comet import was tested with Comet version 2015 01 rev 1 Because this implementation is important to establish the mzIdentML standard please report all errors and suggestions to the ProCon developers specified on http www medizinisches proteom center de software 5 1 Sequest specific Configuration The SEQUEST converter c
38. rot Protocol name inp_swn SW name inp_swv SW version inp_swc SW comments dig_first h c For the ProteinScape 2 1 converter the following options are defined Option Description Mandatory Default Optional value pks pK value set for isoelectric Point IP calculation optional Consensus Consensus recommended mz Calculate theoretical mass charge values for the optional true peptide sequences recommended ip Calculate isoelectric points for the peptide sequences optional true recommended Medical Proteome Center MPC University of Bochum 2015 25 30 ProCon Proteomics Conversion Tool User Manual Monday December 14 2015 dblog Switch on DataBase structure logging not optional false recommended off as default sname Connection data server name or IP address mandatory maldiraumserver as default uname Connection data user name sa as default mandatory sa pw Connection data password mandatory dbo Connection data database owner dbo as default optional dbo resname Contact information researcher name mandatory orgname Contact information organization name mandatory affaddr Contact information affiliation address mandatory umail Contact information user email mandatory mzid mzIdentML mzid output file mandatory projID Project ID mandatory sampID Sample ID ma
39. ter MPC University of Bochum 2015 3 30 ProCon Proteomics Conversion Tool User Manual Monday December 14 2015 3 General Configuration File config ProCon properties Specify the details of the person s responsible for the mass spectrometry of the sample measured and the data set probably you ie MassSpecContactName MassSpecInstitution MassSpecEMailPhoneFax DataSetContactName DataSetInstitution DataSetEMailPhoneFax fill in directly after the These details are for example used in the ProteinScape 1 3 to PRIDE XML conversion File config log4j properties Lines log4j appender ProCon_file File and log4j appender pride_core_file File should contain as path separator for Windows and for Unix based operating systems Medical Proteome Center MPC University of Bochum 2015 4 30 ProCon Proteomics Conversion Tool User Manual Monday December 14 2015 4 Start ProCon Start the ProCon jar by double clicking it or by giving the command java jar ProCon jar ensure that it starts in the working directory where you unzipped it more exactly the directory with subfolders config instruments XML_files ProCon now runs with both the Java 7 and Java 8 runtime The example batch file start_ProCon bat shows how one can set Java Runtime options Any firewall message or any question of a protection tool about an application start should be confi
40. the following paper 14 ProCon PROteomics CONversion tool Mayer G Stephan C Meyer HE Kohl M Marcus K Eisenacher M J Proteomics 2015 Jul 13 1874 3919 15 30053 1 doi 10 1016 j jprot 2015 06 015 PMID 26182917 14 Known Bugs PD conversions of msf files which reference mzML peak list files produce output which is not validated by the ProteomeXchange 15 PRIDE 16 validation procedure Search Engine MSFit http prospector ucsf edu prospector cgi bin msform cgi form msfitstandard not implemented Exception raised If more than one separation and digestion protocol is used for one gel regarding tables MaldiPreparationProtocol EnzymeLot CleavageEnzyme IEF_Protocol StainProtocol PAA Protocol DigestionProtocol SpotTools than a more than one rows in result set exception is thrown PRIDE http www ebi ac uk pride allows only one protocol Future implementation could be to let the user select the SepAndDig protocol for which he wants to convert results If you find further bugs please sent an email with the following log files e For ProteomeDiscoverer conversions o ConvertProt2MzlIdent1 1 txt o Memory_Properties_Log txt o ProCon txt e For ProteinScape 2 1 conversions o ConvertPS2Mzldent1 1 txt o SQLServerDBLogFile txt o ProCon txt e For ProteinScape 1 3 conversions o pride txt from the log resp logs directories to mayerg97 rub de or martin eisenacher r
41. ub de Medical Proteome Center MPC University of Bochum 2015 28 30 ProCon Proteomics Conversion Tool User Manual Monday December 14 2015 Please specify also e your exact operating system Windows or Linux 32 or 64 bit e the versions of your Java runtime type java version on your command interpreter cmd exe e the version of ProCon see Help About menu from ProCon e incase of ProteomeDiscoverer conversions the msf file or at least the msf file size in kBytes 15 Planned future functionality e Support of filtering afterwards Tab ResultFilter in ProteomeDiscoverer e Generating mzIdentML 1 2 output e Integration into the KNIME 17 workflow system 16 Acknowledgements The ProCon development was funded by the following projects The ProDaC http www fp6 prodac eu Coordination Action 6 EU framework programme project number LSHG CT 2006 036814 the ProteomeXchange http www proteomexchange org consortium EU FP7 grant ProteomeXchange grant number 260558 and de NBI http www denbi de project funded by the German Federal Ministry of Education and 414 Research BMBF grant number FKZ 031 A 534A the Deutsche Gesetzliche 411 Unfallversicherung DGUV http www dguv de de Forschung Aktuelle laufende Forschungsprojekte index jsp project DGUV Lunge 617 0 FP 339A and P U R E 412 http www pure rub de a project of Nordrhein Westfalen a federal state of Germany
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