ProHits MS Data Management User manual
Contents
1. The Options in the last column allow you to download the data RAW mzXML or mgf onto your computer h and to open the parent folder h o mo E U Minds Help Analyst Logout LTQ_DEMO Fetch Raw File Fetch Raw File Machine Name All Raw File Status Faa Manaa Date From January 2000 TO February lt t 2010 4 Backup Loc Fetch si i Search ID Folder File Name Size KB Bait Date Options Task Sample LTQ_DEMO 2010 01 06 22 8 MEPCE pelletA RAW 167 540 rina 5 fis 2010 01 06 23 9 MEPCE pelletB RAW 180 071 NOOO 5 2010 01 06 at 32 8 MEPCE pelletAmzXML 223 027 K 16 14 66 a 2010 01 06 at 33 8 MEPCE _pelletA maf 387 447 ie 16 52 42 gt To retrieve the searched results you can click the search task number in the Search Task column Data management module 2 9 10 page 17 Basic Troubleshooting of the Data Management module ProHits Data Management requires a connection between all of your acquisition computers the search engine computers s and the storage computer Storage Auto Search Broken link amp ee fonction link LTQ1 Raw Data Storage ili i 1 LTQMT The storage of Prohits is designed to automatically perform data collection agd management for mass To facilitate the detection of broken links spectrometry All MS raw data files will be saved to the Prohits computer 192 197 250 146 export between these computers ProHits has LTQACG home02. B B yapa AA T iee Help Analyst Logout LTQ Search Task Task ID 4 Task Name Demo_human Folder ID Folder Name Project 21 Demo_Human_GelFree_P3 Demo Human Gel Free Sort Folder Status Stopped by Prohits Administrator Start Time 2010 01 06 16 07 37 total 10 LTQ Search Task Automatically add files Process ID 16927 auto search is running in the background Mascot eS a Edit The GPM v human gt Edit Task ID 5 J Task Name Demo_human Folder ID Folder Name Project 21 Demo_Human_GelFree_P3 Demo Human Gel Free 21 10_EIF4A2_pelletC RAW TPP Name demo_human1 21 11_EIF4A2_pelletD RAW TPP Parameter set unlabeled Edit 21 12_WASL_pelletA RAW Status Running canoe a 13_WASL_pelletB RAW Start Time 2010 01 06 16 13 49 21 14_RAF1_pelletA RAW ini 21 15_RAF1_pelletB RAW Set By Prohits Administrator 21 16_FLAG_alone_pelletC RAW 21 17_FLAG_alone_pelletD RAW X Pan 4 a 21 8_MEPCE_pelletA RAW total 10 B300 T5000 110 S1 G1 M0 1 Edit 15 7 8 EE DAE AAW Mascot Database Human_RefseqV33 Taxonomy All entries Automatically add files from the Folder Fixed Mod No Start Now Variable Mod Deamidated Lod NQ Oxidation M Q Start Every 12 Hours pends Cleavages 1 21 10_EIF4A2_pelletC RAW Peptide tol 3 Da 21 11_EIF4A2_pelletD RAW 21 12_WASL_pelletA RAW MS MS tol 0 6 Da Sie
3. The Auto Search section allows you to perform and schedule database search tasks on specified files using user defined search engines and parameters to explore the results and to link search results to the experimental information in the Analyst module Data management module 2 9 10 page 3 Storage gt Select the Storage tab ProHits manages the backup and storage of data files in an instrument dependent manner The left of this screen provides links to all available instruments in the mass spectrometry facility also shown as pictures Here you can also view the Backup log This page also specifies the location of the database and data storage The central part of the page details the status of each of the connections A green arrow indicates a functional connection while a broken red arrow denotes a broken connection Note that this example is for the Samuel Lunenfeld Research Institute facility the demo version lists a single instrument LTQ_ demo For the purpose of this user manual we will toggle between the demo version and the live site at the Samuel Lunenfeld Research Institute A P ro H its MS Data Management gt Protein High throughput Solution Home Storage Auto Search Help Analyst Logout 4000QTRAP Raw Data Storage LcQ The storage of Prohits is designed to automatically perform data collection and management for mass spectrometry All MS raw data files will be saved to the Prohits computer
4. 10074 end of QOSTARELITE 2009 05 21 23 06 51 lama Create or modify Mascot search parameter set 10073 copy 0 mnt QSTARELITE Tempo Method Maker Project Information eventl http 192 197 250 115 mascot 10072 copy 1 mnt QSTARELITE Tempo Method Maker Project Information eventli 10071 copy 1 mnt QSTARELITE Tempo Method Maker BioAnalyst 10070 copied 10 mnt QSTARELITE 1_AJ 2009_05 20 Grb2_iTRAQ op Data The GPM Parameters 10069 copied 2 mnt QSTARELITE 1 AJ 2009_ 05 20 Grb2_iTRAQ op Batch D Create or modify the GPM search parameter set 10068 process QSTARELITE 2009 05 21 23 05 15 httpu thegpm mshri on ca tandem thegpm_tandem html 10067 end of LTQXL 2009 05 21 23 05 15 10066 copied 1 mnt LTQXL Yasmina_P36 10065 process LTQXL 2009 05 21 23 05 05 The TPP Parameters 10064 end of ORBITRAP 2009 05 21 23 05 05 PP Create or modify the TPP parameter set 10063 copied 10 mnt ORBITRAP FallO8dev v4 0 JETSTREAM rev 2 Build 200808111800 linux 10062 copied 1 mnt ORBITRAP Ek Install Data 10061 process ORBITRAP 2009 05 21 23 04 27 10060 end of LTQACG 2009 05 21 23 04 27 10059 copied 3 mnt LTQACG MM_IP_LCMS 10058 process LTQACG 2009 05 21 23 04 01 10057 end of LTQMT 2009 05 21 23 04 01 10056 process LTOMT 2009 05 21 23 04 01 The same visual display and log details are also found in the AutoSearch module
5. 192 197 250 146 LCQtrap lexport home0 and a MYSQL database 192 197 250 119 prohits_manager will store the data information This page will check all connections between Prohits and mass spectrometry computers If LTQ1 there are any broken connections m gi Please notify Prohits administrator This links to individual instruments backed up on Prohits in your ili Sto Database facility fieron Location of storage IP address ei mE storage Database Name this is set up by your prohits_manager administrator Select to monitor file transfer A from your acquisition i computer to Prohits and view OSTARELITE the log for the RAW file converters and the RAW file August merge functions 2008 v Go Today Status notification Successful links are shown by green arrows Dili Storage Computer Gibi IP address ZI August 2008 gt When Prohits is unable to backup data from one ARAMETE 3m 5 6 7 8 9 10 1412 13 14 15 16 mass spectrometer an 17 18 19 20 21 22 23 Nanospray Storage Folder QstarOMaldi orange broken arrow will 24 25 26 27 28 29 30 No backup setup export home0 No backup setup Hk ss appear You will also see a note appearing at the bottom of the page detailing the problem LCQtrap No backup setup Prohits lost connection with 4000QTRAP data folder i No backup setup The source directory is empty 04 Aug
6. 2008 Data management module 2 9 10 page 4 Selecting instruments and folders The files backup organization mirrors the set up on each acquisition computer the computer linked to the MS instrument Subfolders are allowed on the acquisition computer Selecting the instrument will open a new page allowing you to browse files and projects In this demo version only one instrument LTQ_demo is available gt Select an instrument LTQ_demo by clicking on a link on the left of the page P P FO FLIES iss v unon Protein High throughput Solution eww E Xone Help Analyst Logout LTQ DEMO raw data Fetch Raw File Raw File Status Backup File Now File Now Upload Raw Files Raw Files Backup Log _ _ _ _ _ ___ Total 3 1 agait 1 Browse Project All O lt Go Jamy t De oe om os 2010 2 N 2010 01 06 21 3 Demo_Human_GelFree_P3 00 00 00 5 2008 07 15 KI February 2010 J 3 2 YST_GelFree_P2 dir 46 27 44 6 aw 2008 07 15 1 4 20030205_YDP00155_A1_P1 dir aow ilelslalsle 16 18 53 7 7 8 9 10 11 112 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 E At the bottom of the page the folders associated to this instrument are listed along a unique identifier assigned by ProHits Folders are associated to individual Analyst projects defined in the Admin Office Note that adding as a suffix to t
7. and a MYSQL databas 192 197 250 119 prohits_manager wjf store the data information g i This page will check all connectioNs between Prohits and mass spectrom try computers If there are implemented an easy visual guide both In ORBITRAP any broken connections mss ai EASE notify Prohits administrator the storage and auto search modules ony QSTARELITE gt From the Data Management entry anaes page select the Storage tab aiai As before all of the instruments in the Hes facility are listed The green arrows Loi jaer indicate that the connection between each QstarOMaldi Soe heck ORBITRAP instrument and the storage areas is LCQtrap n E prohits_manager a functional If an automated backup has Te oe oe been selected this also indicates that the 4000QTRAP2 QSTARELITE backup was performed on schedule Note i that there is a broken connection between Fetch Raw File i l one of the instruments and the storage ee lt t E computer easily identified by a broken re 4000QTRAP ri orange arrow in this case the computer was Offline for maintenance Notify the ProHits administrator when you detect Such arrows zI May 2009 192 197 250 146 gt gt Click on the Backup log left side Storage Folder of the screen toward bottom to SS lexportihome0 q 7 monitor the transfer of data from the M erd a acquisition computers to the storage computers and read any error messages Log File raw_back log Di
8. ee en indicated by green arrows and broken links by a broken orange arrow SMATRIX Mascot Parameters SCIE NC E fi Create or modify Mascot search parameter set http 192 197 250 115 mascot The GPM Parameters Create or modify the GPM search parameter set http Ahegpm mshri on ca tandem thegpm_tandem htm The TPP Parameters PP Create or modify the TPP parameter set v4 0 JETSTREAM rev 2 Build 200901301833 linux You can modify the general search parameters from this page you will also be able to modify search parameters when initiating searches ProHits simply employs the standard interfaces provided by the search engines and allows you to create Taoka cid Mosii several standard search parameters sets LTQ_DEMO i Setup new task a View tasks Browse search results by folder e Parse search results to Prohits Analyst The bottom part of the page allows you to access individual instruments for search purposes by simply clicking on the links or on the instruments gt Select an instrument for searching for this tutorial we will select LTQ_Demo N Sop gen A P ro H its MS Data Management gt gt The entry page lists all of the search tasks Protein High throughput Solution k f that were performed for files collected on a Auto Search 4 aw T Help Analyst Logout given instrument A given task may be applied to several files not necessarily located within the same subf
9. manually created intact green chain indicates that a link has been created automatically also called Autolink Upload Raw Files Back 2010 01 06 00 00 00 2010 01 06 00 00 00 2010 01 06 00 00 00 u 2010 01 06 Link Raw file to Prohits Sample Machine Name LTQ Raw File Demo_Human_GelFree_P3 16 FLAG alone _pelletC RAW Folder Project Demo Human Gel Free Link to Experiment Sample OGel Gel Free 3 Demo Human Gel Free 4 Project Name Bait 10 FLAG_alone new Experiment 12 FLAG_alone_pelletC bad new Gel Gel Free Sample 16 FLAG_alone_pelletC T9 new Submit 3 Close In the next section we will navigate through the searching and parsing functions Data management module 2 9 10 page 7 Using AutoSearch for database searching Select the AutoSearch tab at the top of the page A p ro i its MS Data Management 3 a a 3 oe E i x Protein High throughput Solution This view displays all the search engines and Auto Search other tools which have been linked to your Logout ProHits database in the top portion of the Parameter Setup page AS with the link to different mass ProHits monitors connections to the search engines Broken connections are indicated by a broken red arrow Spectrometers in the Storage area wren sae alee ie Storage Folder e 5 RawConverter successful links to search engines are aeei i n
10. Data management module 2 9 10 page 1 2 ProHits MS Data Management User manual demo A pP ro H its MS Data Management Protein High throughput Solution Version demo 1 prepared on Feb 09 2010 by Anne Claude Gingras earlier versions prepared with the help of Frank Liu JP Zhang Brian Raught Brett Larsen Karen Colwill Zhen Lin and Lisa D Ambrosio Contents Using the MS Data Management module sasasnsnsnsnnnsnsnnnrnsnrnsnrnsasnnnsnnnsnnnsnnnnnnnnnnnnnnnnrnnnnn 2 OIO eee ee eT er Te eT ee re eee eee ee eee re ere 3 SClECtING INSEFUMIENLS and TOMSYS cissscanscsssesanvaesesasessnssepsawecensaeresussaeaweeser E 4 Daca TIVE CONN GlS Ol an trees essieeneaas ince sneee ancuanaaee rece aendaie is A 5 Linking files to the Analyst module i csiccsscasddeaseissdassanqeasddsasetsseneniacenedasasaseeneeiaaeaniseateiunaneen 6 Using Auto Search for database searching s ssssssssssnnsnsssnrnnrrrrerenrrnrnenenrnnrnrnenrurrnrrerenrrnrn 7 Manually mitate SCOVGNC S aeriana AE O EE EESE 9 Automatically initiate Searches cscecesccdivectavdinecteiestacedtetacdctaeeaesdedadestantintetekss esaetataedceaceneras 10 SOA TASK VICW oeann EEE EE OEE AE EEA E i 10 VIEW Search RESUL ices cceetenesacaeorccesnesccitn a a E E A AE 11 Analyze results using the TransProteomic Pipeline ssssosssnnnnnrnrnnnnnrrrnsrrnnrrnrrenrnrrenrrnrnrnnn 11 Linking files to Analys serrssrisrireerisoiniwansnnn iinn naia enn AA E EE AA TNA AAE 12 Parsi
11. Q raw data E Ik it The chain link icons in each table of the Data Management module indicate the linking status Anahat Logout a broken white chain link indicates that the file is not linked to any sample in the Analyst module Raw File Stats Backup Log download 1 auto link K manual link no tink Folder Storage ID 21 Prohits Analyst Plate ID Edit Project Name Demo Human Gel Free Created on 2010 01 06 00 00 00 Total files 10 Convert Selected file to o mzXxML Convert Demo_Human_GelFree_P3 o me 2010 01 06 31 16 FLAG_alone_pelletC RAW 102 264 30 17_FLAG_alone_pelletD RAW 143 728 Ey 29 15_RAF1_pelletB RAW 152 160 Ey y gt To create manual links click in the project Bait sample column This opens up a new dialog box allowing you to select the desired Project Bait and Sample AA closing the box the yellow chain link icon will appear Creating automatic links requires interfacing with the Analyst module and using a Standardized naming scheme This will be described in a separate section Creation of New Baits and Samples will be described in the instructions for the Analyst module module This completes the overview of the Storage part of the Data Management module of ProHits Plate Folder Name Demo _ Human _ GelFree P3 intact yellow chain indicates that a link to a sample in the Analyst module has been
12. TPP You can Sr CD 0 simply click on the boxes in the TPP column of the results tables When desired files are selected press Run TPP To Merges together search result files Select Files Cancel Cancel Run TPP Reset create a completely new TPP task e g if the TPP parameters have changed click New select desired parameter set and desired files and press Run TPP Data management module 2 9 10 page 12 There are cases where you may want to merge files prior to running the TPP examples include fractionated samples gel based or otherwise This is a simple process in ProHits The two requirements are that the searches be performed using the same search engine Mascot and X Tandem files cannot be combined and that the results are located within the same Search Task folder Select the Merge option and the files to be combined Selecting the Merge option will create a new entry at the bottom of the page The TPP can be run on this entry in the same fashion as on individual files by selecting the desired parameters and pressing Run TPP At this point we have performed database searching and have obtained results directly from the search engines as well as results from the TPP pipeline We are now ready to transfer these search results into the Analyst module The transfer involves two steps 1 linking the initial file to an entry created in the Analyst module and 2 pa
13. a management module 2 9 10 page 15 Other options You have now completed the basic tour of the Data Management module The following few pages will explore a few other options within the Data Management module 1 Creating activity reports 2 Searching fetching files 3 Basic troubleshooting of the Data Management module The first few options are accessed from the Storage page e Storage a o be Help Analyst Logout Raw Data Storage This section allows you to monitor the transfer of data from each of the acquisition computers to the ProHits backup system It also allows you to search browse and download files convert raw files to other formats and manually upload raw data All MS raw data will be saved to the ProHits computer 192 197 251 36 mnt storage1 and a MySQL database 192 197 251 36 Prohits_manager will store the data information ProHits monitors all connections with acquisition computers Broken connections are indicated by a broken red arrow Creating activity reports for the RAW files gt From the storage tab select the Raw File Status option This opens up a new window here we are simply showing one of the SLRI instruments as an example gt Select the instrument you want the report on the dates of the report and time units as well as the contents and style of the display You could also choose to get the report for all instruments linked to ProHits Raw Fil
14. ase you also have TPP results Both types of results can be parsed Select the Detail link in the parsing area arse Hits to Prohits Analyst database Detail Parse Hits Status not saved Parsed By Pre defined Filter Set default Save As Parse Results from GPM Mascot TPP Both GPM Mascotand TPP lons score cut off lt 35 Require bold red peptide Vv Save Protein Score gt save all hits Max number of hits 500 Significance threshold p lt 0 lons expect log e cut off gt 1 Save Protein expect log e lt 1 TPP_PARSE_MIN_PROBABILITY 0 05 Run Reset Reload A 22 21 8_MEPCE_pelletA RAW 167 540 Z v ory VS pepXML Ma wo AA 23 21 9_MEPCE_pelletB RAW 180 071 GPM V roXMLE g You can transfer parse results from the search engines GPM Mascot from the TPP or both You can select the parameters for the parsing cut off for Mascot and X Tandem GPM search engines For the TPP all hits with a probability greater than the cut off selected by the administrator in the Prohits configuration file we are using P gt 0 05 are automatically parsed Check the select all box at the top of the appropriate column or manually select files to be transferred to the Analyst module Press Run to initiate parsing The processing status notification will appear Data management module 2 9 10 page 14 When parsing is successfully c
15. e or merge several files Selecting either of these formats for conversion expands the dialog box selecting merge files allows you to manually select the individual files to be merged in the final file and to give a new name to the merged file This option is especially useful to combine files from fractionation of the same sample e g gel bands from the same lane Convert Selected file to DTA V Merge files Convert B Xcalibur Parameters 8300 T5000 M1 51 Type merged file name pload Raw Files i Back Convert Cancel __ O Demo_Human_GelFree_P3 ome 2010 0 Note that at the present time the publically released version of ProHits can only convert data from Thermo instruments Please refer to http tools proteomecenter org wiki index php title Formats mzXML http psidev info index php q node 257 or http proteowizard sourceforge net for converters for additional instruments proprietary formats Data management module Linking files to the Analyst module 2 9 10 page 6 As mentioned in the general introduction RAW files located in the Data Management module can be linked to Baits gt Experiments gt Samples defined in the Analyst module and the Search Results can be transferred parsed from the Data Management module to the Analyst module P LOFTS iis v mnnm Protein High throughput Solution 2 Home Storage Fetch Raw File S s iy J LT
16. e Statistics Machine Name tTaacc File Type _ All types H Date From May IA 2008 H TO May b 2009 E Time Unit Month D Year Display Contents M Number of Files M File si fe lt o bet e ov r _ m a gt Press show to visualize selected display Show Raw Files Statistics Raw Files Statistics Files size GB Files size GB 2008 05 2008 06 2008 07 2008 08 2008 09 2008 10 2008 11 2008 12 2009 01 2009 02 2009 03 2009 04 2009 05 ORBITRAP total size 405 36 GB LTQACG 617 7 65 968 11 38 48 10 23 755 677 124 1921 2148 23 38 10 33 LTQACG total size 151 03 GB 2008 05 I 6 17 GB 2008 06 D 7 65 GB 9 68 GB 11 38 GB 4 8 GB 10 23 GB 7 55 GB 6 77 GB 12 4 GB 19 21 GB 21 48 GB 10 33 GB Number of Files Number of Files 2008 05 2008 06 2008 07 2008 08 2008 09 2008 10 2008 11 2008 12 2009 01 2009 02 2009 03 2009 04 2009 05 ORBITRAP total files 2442 LTQACG 52 71 74 85 53 96 58 58 90 123 153 183 66 LT ACG total files 1162 2008 05 M 2005 05 M 2005 07 M 2005 05 M 2005 09 M 2005 10 2003 11 M 2005 12 M Data management module 2 9 10 page 16 Searching files and retrieving RAW data Select Fetch Raw File This will open a new window Select the desired instrument or all instruments dates if applicable as well as keywords that are part of the file name note that you can perform logical operations Press Fetch to retrieve results
17. emo Human Gel Free Save Reset Close 06 Jan 2010 Data management module 2 9 10 page 9 Manually initiate searches To manually initiate a search select the Start Now option and click the Add Files button located on the bottom right This will open the folders for the specified instrument Select LTQ Raw files allowing you to select as many files as desired for searching Total Folder 3 1 Page 1 Each user can only have one running task per machine SP 119 additional tasks unlimited number will be placed in a 2 21 Demo Human GelFree P3 queue The search will automatically initiate in the order they were queued once the initial searches are completed V 16_FLAG_alone_pelletC RAW 4102 264 KB 2010 01 06 V 17_FLAG _alone_pelletD RAW 143 728 KB 2010 01 06 Vi 15 RAF1_pelletB RAW 152 160 KB 2010 01 06 V 14_RAF1_pelletA RAW 166 849 KB 2010 01 06 Vi 13_WASL_pelletB RAW 141 198 KB 2010 01 06 Vi 12_WASL_pelletA RAW 134 509 KB 2010 01 06 V 11_ElF4A2_pelletD RAW 132 643 KB 2010 01 06 v 10_EIF4A2_pelletC RAW 183 275 KB 2010 01 06 M9 MEPCE_pelletB RAW 180 074 KB 2010 01 06 M8 MEPCE_pelletA RAW 167 540 KB 2010 01 06 3 YST_GelFree_P2 1 20030205 YDP00155 A1 P1 Once all parameters are selected ant the files transferred click the Run Task button at the bottom of the screen a ProHits v ug s c Protein High throughput Solution Auto Search D Bi B B B B B i
18. es on every new file added to the folder s that are initially selected for the search Before you can select to automatically add files and search them you have to point to at least one file in a folder manually as indicated above By selecting the Start every X hours left hand side and Automatically Add Files right side options every file of the selected format subsequently acquired within the same folder s or subfolder s will be automatically searched using the same parameters Search Task view Select the LTQ_DEMO Search Tasks option on the left side This opens the page listing the searches performed on this instrument Searches still running will be highlighted in green List Search Results by Folder Other important status information can also be obtained Total 513 11 Pages 1234567821011 jm Search Tasks view While green indicates a file being Analyst Task Resul TaskiD biareip Project Tash Name Status petail Detail aCtively searched a blue colour indicates that a sample is currently in the queue Yellow highlights an error with the search No other searches can be initiated until this problem is resolved either through successful running of se test es A i 577 2 EE mia T the problematic search or by stopping the task 576 32 duas Stopped by py IMPORTANT If an error is encountered while tasks are Frank Liu 575 32 large fle mam seh LU in the queue one of these tasks must be manually
19. he Demo_Human_GelFree folder name _P3 enables the creation of Autolinks as will be discussed later The Search Task column allows you to navigate to the search results page s associated with files in this folder In the Options column clicking will open the folder while selecting will download the files associated to this folder on your local computer ProHits automatically backs up any new files from the acquisition computer at a time specified by the administrator The user may also initiate manual back up and by clicking Backup File Now towards the top of the page Please note that to prevent file corruption ProHits has a timed delay for file transfer delay specified by administrator we use 2 5 hours after last modifications To upload raw files from an instrument not connected to the ProHits backup system select Upload Raw Files and navigate through options This function can also be used to upload converted files to be searched in ProHits Data management module 2 9 10 page 5 gt Select a folder Demo_Human_GelFree_P3 to open In addition to the files located on the acquisition computer the selected folder will also contain any files that you have converted from original raw file to other formats and any file types stored on the acquisition computer e g doc xls etc This folder will also contain any file manually uploaded on the previous page Here we show the raw file 9 MEPCE_pelletB RAW acqu
20. ired on a Thermo LTQ instrument already converted to mzXML for searches using X Tandem and mgf for Mascot searches i ie IP ro im its MS Data Management E Protein High throughput Solution os Le F p T Er 4 Help Analyst Logout 2 LTQ DEMO F LTQ_DEMO raw data Fetch Raw File Raw File Status download H auto link KA manual link no link Plate Folder Name Demo_Human_GelFree_P3 Folder Storage ID 21 Prohits Analyst Plate ID Edit Project Name Demo Human Gel Free Created on 2010 01 06 00 00 00 Backup Log Total files 30 Convert Selected file to mzxML Convert Upload Raw Files 4 Back O Demo_Human_GelFree_P3 ome 2010 01 06 Project Search ID File Name Size Bait Date ae Download Convert sample 2010 01 06 23 9 MEPCE pelletB RAW 180 071 epeka 5 g 34 9 MEPCE _pelletB mzXML 239 997 oe E 15 43 30 2010 01 07 Pact 35 9 MEPCE _pelletB mgf 435 683 g 16 16 23 3 Data file conversion ProHits can automatically convert Thermo RAW files to the database search engine preferred file types as part of the AutoSearch pipeline Alternatively RAW files can easily be converted here To convert a RAW file to mgf mZXML or dta format choose the desired files by clicking the boxes in the Convert column select the desired format and conversion parameters if available and hit Convert If you select conversion to either mgf or dta files you can combin
21. itiate database searches using the commercial Mascot search engine licence from Matrix Science is necessary and or the free Open Source search engine X Tandem Search results can y be further analyzed using the TransProteomic y4 Pipeline TPP an Open Source software 20 vid suite and viewed directly within the MS Data be b47 Management module Alternatively search dosl AI yb engine and or TPP results can be transferred o 250 500 750 1000 1250 1500 1750 parsed into a bait centric relational database mt the Analyst module Relative Imensity ota 8 b10 bi The Storage section allows you to monitor the transfer of data from each of the acquisition computers to the ProHits backup system It also allows you to search browse and download files convert RAW files to other formats and manually upload RAW data The Auto Search section allows you to perform database searching on specified files using user defined search engines and parameters to explore the results and to transfer search results to the Analyst module It also allows for database searches to be pre scheduled for data files that will be acquired at a later time The Storage section allows you to monitor the transfer of the data from each of the acquisition computers to the ProHits backup system It also allows you to search and browse and download backed up files convert RAW files to other formats and manually upload RAW data
22. lows you to combine several files into a single TPP analysis P PrOH It sonon Protein High throughput Solution Home Storage Auto Search gt a l ik Help Analyst Logout LTQ Search Task Task Name Folder ID Folder Name Project total 0 Automatically add files _ Mascot MW demo_human 3 The GPM C human g TPP Name TPP Parameter set sd B300 T5000 110 S1 G1 M0 1 Start Now Start Every 12 Hou MATRIX Mascot Parameters SCIENCE Create or modify Mascot search parameter set Your name frank liu Email gliu mshri on ca Search title demo human Database Human_RefseqV33 re 06 Jan 2010 Taxonomy Allenties ssi Allow up to 1 missed cleavages Enzyme Trypsin Fixed Acetyl K Variable Cation Na C term modifications Acetyl N term i modifications Cation Na DE Acetyl Protein N term Deamidated NQ Amidated C term Dehydrated N term C Amidated Protein C term Dehydro C Quantitation None 4 Peptide tol 3 Da clfo MS MStol 0 6 Da 2 Ne Nee a Peptide charge 2 and 3 Monoisotopic Average O Data format Mascot generic Precursor m z Instrument ESI TRAP Errortolerant Decoy O Report top 200 hits Parameter Set New Set O Modify Set Set by Prohits Administrator Set date 2010 01 06 Set name demo_human for Project D
23. ng files to the Analyst module sssssssnsnssssnssnsrsrrsrernnrnenrnnnnrnrnenrnnrnrrenenrrnrnenenrnnrnrn 13 HEr ODUN eter eer re ete E E EE ere rer Tr re 15 Creating activity reports for the RAW fil S ccc cc cccce cece eee eeee eee eens essen eee eeeeeeeaaeeeneeenaaes 15 Searching files and retrieving RAW Cata ccccccccc cece eee cee eee e ee eee eee eee eens essen eee eeeseeaeeeeeeeenaaes 16 Basic Troubleshooting of the Data Management module ccc cccecce cece ee eeeeee seen eeeeeeeneeeneees 17 Data management module 2 9 10 page 2 Using the MS Data Management module Once you have selected the MS Data Management module from the ProHits access page and have logged in the following screen will appear At the top of the page left you will find the tabs Home Storage and Auto Search that allow you to navigate between the storage and the search areas of the MS Data Management Module On the left is a link to the Analyst module that can be accessed from every page of the MS Data Management module P FOPIIES vs os tanagsmen Protein High throughput Solution Home Help Analyst Logout Overview Welcome to ProHits A PE I RL LP Pe lt ProHits is an open source software tool on y7 designed to help scientists manage search bjs and analyze mass spectrometry data MS Data Management allows you to store raw mass spectrometry data from multiple instruments and to in
24. older or in the LTQ DEMO Search Tasks P Project Name ID same format We will return to this list later Demo Yeast Gel 1 Demo Yeast Gel Free 2 after we have created a New Task Demo Human Gel Free 3 List Search Results by Folder Total 4 1 Page 1 The table lists the current Tasks To view the search parameters and a list of the Taskin APAS Project Task Name Status e Result A re 7 1 1 Gel_based demo search Finished A searched files press To view the search i a r ae ES y 5 3 Demo_human Finished LQ results press Results details R naa a The left menu bar allows you to add or manage Tasks as well as to view the logs Data management module 2 9 10 page 8 gt Select LTQ_Demo New Task This opens up a new page Enter a Task Name of your choice select the search engine s and parameter set s to be utilized these can be edited If needed an automatic conversion of RAW files to the mof format used by Mascot or the mzXML format used by X Tandem can be applied The search can be initiated manually and immediately Start Now or automatically as files are added every X hours see below You have an option of automatically running the TPP statistical software tools on the search results If you choose to do so select the Run TPP box Note that you can also run the TPP tools after you get the search results Running TPP manually post acquisition is a more flexible option because it al
25. ompleted a green check mark will appear arse Hits to Prohits Analyst database Detail not saved Pre defined Filter Set default Save As Parse Results from GPM Mascot TPP Both GPM Mascot and TPP lons score cut off lt 35 Require bold red peptide v Save Protein Score gt save all hits Max number of hits 500 Significance threshold p lt lons expect log e cut off gt Save Protein expect log e lt TPP_PARSE_MIN_PROBABILITY 0 05 Reload Kj 22 21 8_ MEPCE_pelletA RAW 167 540 e GPM eX z 7 pepXML J 23 21 9_ MEPCE_pelletB RAW 180 071 Pm XML v XML 24 21 10_EIF4A2 pelletc RAW 183 275 cpm PEA ao protxXML v In the event that you decide to link or parse different file s to the same Analyst entry you can remove the parsed files or the link Alongside the tick box the icon x can be selected if you want to remove the hits LA EA from the Analyst module Note that you can also unlink a sample by clicking on the 7 or K and selecting remove link ssssssssssssessssssssesssssses Parse Hits to Prohits Analyst database Parse Hits Status Completed 2010 01 13 11 01 36 Parsed By Prohits Administrator Detail pepXML EH 22 21 8 MEPCE_pelletA RAW 167 540 GPM W v K XML E wv Bd Z pepXML E 23 21 9_ MEPCE_pelletB RAW 180 071 GPM W v X XML E wf Be 24 21 10 EIF4A2_pelletC RAW 183 275 A GPM v pepXML protXML v K Dat
26. re 574 32 cluster test Finished R started the other Tasks will then be searched in queue gt Clicking on the Task Detail re amp aen icon in the column will open up the A ProHits MS Data Management J gt JF same status page as above Protein High throughput Solution n a i mi Auto Search Mem TRS Help Analyst Logout gt To obtain the results click on the Result Detail icon at the extreme right of the table LTQ DEMO Search Tasks Project Name ID Demo Yeast Gel 1 Demo Yeast Gel Free 2 Demo Human Gel Free 3 List Search Results by Folder Total 4 1 Page 1 Task ID eae Project Task Name Status Rael pair 7 1 1 Gel_based demo search Finished A 6 0 2 yeast_demo_search Finished A 5 3 Demo_human Finished A 1 1 1 demo seach Finished A Data management module View Search Results 2 9 10 page 11 Select the Result Detail for one search task This opens up a new page The search results are displayed at the bottom of the page The blue link will connect to the search engine page Note that if using the Demo sites from external computers you will not be able to view the results from the search engines firewall protection This page also provides you with 1 list of the other Task IDs associated with this folder 2 the option of analyzing your search results using the TPP either for single files of for merged files 3 the possibility to link files to the Analys
27. rsing the search results Linking files to Analyst link the file You may have already linked the native file not searched to the Analyst modules through the Storage area If so the link icon by the file size will be coloured gr s u Home Storage Auto Search 2e Try Help Analyst Logout LTQACG Search Results Task ID 107 Task Name test_TPP Folder ID Folder Name Project 317 O aeg_Nov07_network 374 mB Gingras_Lab_Public Status Finished Start Time 2008 05 23 15 25 19 Set By Frank Liu for demo Mascot flag_RefSeq ow Finished 7 test TPP Mascot flag_RefSeq GPM GPM_RefSeq1 Now Finished sike Mascot acg_IPI Now Finished Set Search Results to Run TPP New TPP ID TPP Name Parameter Set Status Set By 1 log test Gingras_MML Finished Ka Anne Claude Gingras Parse Hits to Prohits Analyst database Detail Parse Hits Status not saved Parsed By Reload 320 317 F_LPPP2CAwt17_a_20071112 RAW 136 475 l F GPM pepXML 4 protXML 320 317 F_PPP2CAwt17_a_20071112 RAW 136 475 Mascot a A white link indicates that no link has been established at this point as in the example above See page 6 for details about manual and automatic link creation Data management module 2 9 10 page 13 Parsing files to the Analyst module You are now ready for parsing transferring results to the Analyst module as you have a linked file SAA i oe and search results In this c
28. splay last 100 lines submit Refresh Click to view log details No backup setup No backup setup F n QstarOMaldi No backup setup 10089 end of QSTARELITE 2009 05 22 8 04 27 f Home Auto Search sr 4 Va 10088 copied 6 mnt QSTARELITE 1_AJ 2009 05 20 Grb2_iTRAQ op Data we 10087 process QSTARELITE 2009 05 22 8 03 36 Help _ Analyst Logout 10086 Backup QSTARELITE start at 2009 05 22 8 03 36 10085 PSID 3771 QSTARELITE Parameter Setup 10084 end of 4000QTRAP2 2009 05 21 23 07 01 This page will check connections between Prohits and search engines If there are any broken connections 10083 copied 2 mnt 4000QTRAP2 Andrew_J 2009_05_20 Data please notify Prohits administrator 10082 copied 1 mnt 4000QTRAP2 Andrew_J 2009 05 20 Batch o gt 10081 rocess 4000QTRAP2 2009 05 21 23 07 00 p j 10080 end of 4000QTRAP 2009 05 21 23 07 00 Storage Compuler Xcalibur Parameters 10079 copy 6 mnt 4000QTRAP CJ_Yong 2009_05_07_0430ShcA Data 0430ShcA_R_21 192 197 250 146 RawConverter 10078 copied 20 mnt 4000QTRAP CJ_Yong 2009 05 _07_0430ShcA Data 0430ShcA_r1 Storage Folder AL Convert Finnigan Xcalibur RAW file into peak lists 10077 copied 1 mnt 4000QTRAP CJ_Yong 2009_05_07_0430ShcA Batch lexport home0 http 10 197 104 18 RawConverter 10076 copied 1 mnt 4000 TRAP CJ_Yong 2009_05_07_0430ShcA Acquisition Meth 10075 process 4000QTRAP 2009 05 21 23 06 51 MATRIX Mascot Parameters
29. t module 4 the file parsing tool that allow you to transfer your search results to the Analyst module LTQ DEMO Search Results Task ID 5 Task Name Demo_human Folder ID Folder Name Project 21 O Demo_Human_GelFree_P3 ome Demo Human Gel Free Status Finished Start Time 2010 01 07 19 50 19 Set By Prohits Administrator Mascot demo_human Finished GPM human inishe 5 Demo_human 4 Set Search Results to Run TPP TPP ID Stopped by Prohits Demo human Mascot Yeast GPM YST Ji Administrator Now Of New Set By Prohits Administrator TPP Name demo1 Status Finished he Parameter Set 3 log unlabeled Parse Hits to Prohits Analyst database Detail Parse Hits Status Parsed By not saved Reload pepXML 22 21 8_MEPCE_pelletA RAW GP rotXML SI pepXML protXML pepXML protXML pepXML w protXML 167 540 X 23 21 9 MEPCE_pelletB RAW 180 071 z 24 21 10_EIF4A2_pelletC RAW 183 275 G e aa Q X 25 21 11_EIF4A2_pelletD RAW 132 643 Running the TPP after completion of searches and merging samples prior to TPP analysis To add new results files to be analyzed with the TPP to an existing TPP task click Set Search Results to Run TPP New 7 TPP Name Parameter Set Status Set By icon in the Status column of the box demo unlabeled Finished Maa Prohits Administrator Set Search Results to Run
30. ta Remove File Ada Files MASS Monoisotopic fot 14 RAFI pellet Rae Peptide charge 2 and 3 7 15_RAF ns Aap Gunta Cancel Enzyme Trypsin 21 16_FLAG_alone_pelletC RAW Aun Task tance GPM dh Eukaryotes ae uman_RefseqV33_20090226 fasta 21 9_MEPCE_pelletB RAW Taxon Prokaryotes Measurement errors 0 4 Daltons i i Complete modifications The task will now be running and the search nice aide aiead parameters will be locked Tip instead of creating a Refinement specification R1 15 994915 W 0 984016 N new search task for each file you analyze using the Refinement specification R2 uN n 31 98983 M 31 98983 W Same search parameters use the Modify Task option Proin eave CIPS centre at the bottom of the page this will group all your searches within the same search task folder making it Se easier to retrieve and will also ensure that the same TPP Parameter Set unlabeled search parameters are used for each file Clicking per re Modify Task allows you to add files to be searched with the same parameters but not to change the search parameters To research the same raw files B300 T5000 110 S1 G1 M0 1 with different search parameters a New Task must be created mee ae SS WS SS Saar Ww Previous Task Modify Task Stop Task Data management module 2 9 10 page 10 Automatically initiate searches For some high throughput projects users may want to automatically initiate search
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