Agilent G6825AA MassHunter Pathways to PCDL Software Quick Start Guide

Transcription

1 Agilent G6825AA MssHunter Pthwys to PCDL Softwre Quick Strt Guide Wht is Agilent Pthwys to PCDL? Fetures of Pthwys to PCDL Agilent MssHunter Pthwys to PCDL converter is stnd-lone softwre designed to fcilitte the cretion of custom Agilent PCDLs from metolites present in pthwy content culled from populr dtses such s BioCyc, KEGG, nd WikiPthwys. You cn crete personl compound dtse (PCD) or personl compound dtse nd lirry (PCDL) from one or more compounds (metolites/lipids) tht prticipte, or re ssocited with metolic rections, in selected pthwy(s). The PCD/PCDL is creted y finding compound nmes nd their ssocited formuls in reference METLIN dtse, tht is sed on selected pthwy(s). You cn filter nd select pthwys sed on dtse, orgnism, nd/or custom text entries. The pthwy metolites cn e filtered sed on their reltionship with the pthwy (memer of the pthwy or rection prtner) or through custom text entries. The Pthwys to PCDL converter currently supports pthwy content from BioCyc, KEGG (with the required license), nd WikiPthwys. The dtses creted with Pthwys to PCDL cn e used to query cquired dt in trgeted dt mining workflow, the results of which cn e mpped onto iologicl pthwy mps. Crete custom MssHunter METLIN compound PCD/PCDL from pthwy informtion contined in BioCyc, KEGG, nd WikiPthwys. The pthwys my e selected sed on: one or mny orgnisms custom serch text entries Agilent Technologies

2 comintions of orgnism nd text entries The list of trget compounds tht you cn extrct cn e filtered sed on the compound eing present: in the selected pthwy(s) s rection prtner to compounds involved in the selected pthwy(s) The pthwy PCD/PCDL tht you crete my e used for identifiction of metolites s source dtse in other MssHunter softwre (for exmple, MssHunter Qulittive Anlysis nd ID Browser). Terminology Where to Find More Informtion PCD: An ccurte mss compound dtse. The dtse my or my not contin retention time dt. PCDL: An ccurte mss compound dtse tht lso contins n MS/MS ccurte mss spectrl dtse (spectrl lirry). Compound Nme: Mny compounds re commonly known y their slts. The mss spectrometer, however, detects the nion or ction portion of the slt, rther thn the neutrl slt. PCD/PCDL entries my contin the fmilir compound nmes, ut the empiricl formule reflect the detectle ction or nion portion of the molecule rther thn the formul of the neutrl compound slt. For exmple, the full nme Vecuronium romide my e used for identifiction in the PCD/PCDL, even though the mss/formul only includes the Vecuronium ction. METLIN dtse: The MssHunter METLIN PCD/PCDL (METLIN dtse) is one of the est-known nd most-comprehensive metolite nd lipid dtses in the world tody. The METLIN dtse contins endogenous nd exogenous metolites, s well s lipids, drug metolites, nd di- nd tripeptides. Ech entry my include mss, chemicl formul, nd structure informtion, s well s ID numers tht link to more informtion out the compound, such s the CAS nd ChemSpider IDs. Go to for the most current informtion on Agilent products. 2 Pthwys to PCDL Quick Strt Guide

3 Getting Strted How do I get strted? This Quick Strt Guide helps you lunch Pthwys to PCDL, ecome fmilir with typicl workflow, nd use the softwre to crete custom PCD/PCDL metolite dtse from reference METLIN Metolite PCD/PCDL dtse. Strt Pthwys to PCDL 1 Doule-click the Pthwys to PCDL icon locted on your desktop, or click Strt > All Progrms > Agilent > MssHunter Worksttion > Pthwys to PCDL > Pthwys to PCDL. 2 The first time you run Pthwys to PCDL you re prompted to set reference METLIN dtse pth nd filenme. Click Select in the Select Reference METLIN PCD/PCDL dilog ox (see Figure 1). Figure 1 Select Reference METLIN PCD/PCDL dilog ox Select your METLIN dtse in the Plese specify reference METLIN *.cd file dilog ox (see Figure 2 on pge 4). Pthwys to PCDL Quick Strt Guide 3

4 Figure 2 Plese specify reference METLIN *.cd file dilog ox Pthwys to PCDL Workflow 3 Study the Pthwys to PCDL Workflow shown in Figure 3. 4 Review the rest of this Quick Strt Guide nd follow the steps using your METLIN dtse. Figure 3 Typicl Pthwys to PCDL Workflow 4 Pthwys to PCDL Quick Strt Guide

5 User Interfce The min functionl res of Pthwys to PCDL softwre re shown in Figure 4. The Pthwys to PCDL window consists of two prts: the Menu Br nd the Disply Pne. The Disply Pne is divided into the Pthwy List nd the Compound List to help you visulize your progress s you select pthwy(s) nd compound(s) to crete your PCDL sed on pthwy metolites. The numer of pthwys nd compounds tht meet your criteri re shown ove ech tle. Figure 4 Screen res of Pthwys to PCDL converter You cn updte the pthwy dtses from Tools locted on the Menu Br (see Figure 5). This Quick Strt Guide nd the softwre version re ville from Help locted on the Menu Br (see Figure 5). Figure 5 Tools nd Help options on the Menu Br Pthwys to PCDL Quick Strt Guide 5

6 Creting Custom PCDL Creting custom PCD/PCDL from metolites present in pthwy content follows simple workflow s shown in Figure 3 on pge 4. Steps Detiled Instructions Comments 1 Strt Pthwys to PCDL. Click the Pthwys to PCDL icon on your desktop. You cn lso click Strt > All Progrms > Agilent > MssHunter Worksttion > Pthwys to PCDL > Pthwys to PCDL. 2 Select Source under Pthwy Dt. Select BioCyc/MetCyc for the Source under Pthwy Dt. If you select KEGG, go to step c on pge 7. Review the updted list of pthwys in the Pthwy List, nd then go to step 3. The Pthwys to PCDL converter supports pthwy content from BioCyc, KEGG, nd WikiPthwys. KEGG pthwy dtse license: c d e Click OK in the Options dilog ox. Enter your license informtion if you select the KEGG pthwy dtse. Click OK. When you select the KEGG pthwy dtse, you re required to enter your license User nme nd Pssword in the KEGG Login dilog ox. > If the User nme or Pssword is incorrect dilog ox notifies you. 6 Pthwys to PCDL Quick Strt Guide

7 Steps Detiled Instructions Comments 3 Select the orgnism(s) you wnt to include within the pthwy dt source. c d Click Add/Remove under Pthwy Dt. Click on the heding of the column to sort the orgnisms. For exmple click the Nme column heding. Mrk Homo spiens. Mrk the check ox(es) in the Choose column nd in the row of the orgnism(s) tht you wnt to include in your Orgnism/ Dtse selection list. Click OK. In the Choose Orgnisms to Show dilog ox, the Pwy Count column is the numer of pthwys ssocited with ech orgnism. Ech of the orgnisms tht you select in the Choose Orgnisms to Show dilog ox re ville in the Orgniztion/Dtse selection list. The selection is persistent the next time you run Pthwys to PCDL. > e f Select Homo spiens from the Orgnism/Dtse list. Review the updted list of pthwys in the Pthwy List. Orgnisms my e removed from the Orgnism/Dtse selection list. Click Add/Remove nd cler the orgnism check oxes. Pthwys to PCDL Quick Strt Guide 7

8 Steps Detiled Instructions Comments 4 Option: Select compounds when Fellow Pthwy Memers is the Selection Mode. c d Click Fellow Pthwy Memers. Review the updted list of compounds in the Pthwy List. Select the first eleven (11) compounds in the Pthwy List. Click Select Highlighted. Three options re ville s the Selection Mode: Pthwy Nme: Select compounds tht mtch the pthwy nme(s) you select from the Pthwy List view (see the lst figure on the prior pge). Fellow Pthwy Memers: Select compounds from pthwys relted to the initil compound list tht is displyed in the Pthwy List view. After you click Select Highlighted or Select All, the Fellow Pthwys re selected from the Select Interesting Pthwys dilog ox (see the figures on this pge). e f Select one or more pthwys, with or without filtering the pthwy list using custom serch text. Select the first fifteen (15) pthwys. Click Select Highlighted. Rection Prtners: Select compounds tht re relted to the selected list of compounds tht is displyed in the Pthwy List view (see the figures on the next pge). Selected pthwys nd compounds in the list views re highlighted using ckground color. g Review the list of compounds in the Compounds List. Go to step 6 on pge 9 Compounds re dded to the Compound List ech time you click Select Highlighted or Select All. 8 Pthwys to PCDL Quick Strt Guide

9 Steps Detiled Instructions Comments 5 Option: Select compounds when Rection Prtners is the Selection Mode. c d e f Click Cler All in the Compound List pne to strt new compound list. Click Rection Prtners. Review the updted list of compounds in the Pthwy List. Select the first eleven (11) compounds in the Pthwy List. Click Select Highlighted. Review the list of compounds in the Compound List. Rection Prtners is not n option when WikiPthwys is the Pthwy Dt, Source. After you click Select Highlighted or Select All the originl selection in the Pthwys List is no longer highlighted. For this illustrtion the eleven compounds were re-selected to show the correltion. 6 Select compounds using custom Serch Text entry when ny Selection Mode is selected. Type tryptophn for the Serch Text. Review the list of pthwys in the Compounds List. The numer of pthwys is smller thn when viewed in step 3 on pge 7. Pthwys cn e filtered y severl text serches. Click Select Highlighted or Select All fter ech serch to uild your custom compound dtse sed on the selected pthwys. Pthwys to PCDL Quick Strt Guide 9

10 Steps Detiled Instructions Comments 7 Review unresolved compounds in your Compound List. c d e Click View Unresolved. Review the list of unresolved compounds in the Unresolved Compound Viewer dilog ox. Click OK. Review the list of compounds in the Compound List. Remove unresolved compounds from your Compound List. Mrk compounds to delete under the Del. column. Pthwys to PCDL provides you with n opportunity to mnully review the compounds in your Compound List tht my not hve strong correltion with the pthwy(s) you hve selected (unresolved compounds). The View Unresolved utton is ville when you hve unresolved compounds in your Compound List. After reviewing the unresolved compounds, you my retin them in your Compound List or remove them from the Compound List y mrking the compound row under the Del. column. When you mrk the compound under the Del. column it is immeditely removed. 8 Select the preferred source of the finl dtse compound nmes. Click BioCyc/MetCyc s the Prefer Compound Nmes from source. 10 Pthwys to PCDL Quick Strt Guide

11 Steps Detiled Instructions Comments 9 Crete your custom PCD/PCDL. Click Crete PCD. Select the folder to sve your PCD/PCDL dtse. c Type the nme for your PCD/PCDL dtse in File nme. d Click Sve. This step cretes your custom PCD/PCDL sed on the compounds involved in the pthwy selection(s) you hve mde. If your reference METLIN metolite dtse is PCD, your custom dtse does not contin MS/MS dt. If your reference METLIN metolite dtse is PCDL, your custom dtse contins MS/MS dt. e Click OK fter you hve reviewed the summry informtion descriing your custom PCD/PCDL. 10 Crete nother PCD/PCDL or exit Pthwys to PCDL. Crete nother PCD y returning to Select Source under Pthwy Dt. on pge 6. Click the close utton to exit Pthwys to PCDL if you re done creting your custom PCD/PCDL dtse(s). You hve completed creting your first custom PCD/PCDL dtse. You cn crete nother dtse or exit the softwre. Pthwys to PCDL Quick Strt Guide 11

12 BioCyc Pthwy/Genome Dtses Includes BioCyc Pthwy/Genome dtses from the Bioinformtics Reserch Group t SRI Interntionl, used under license. Cittion sed on use of BioCyc Users who pulish reserch results in scientific journls sed on use of dt from the EcoCyc Pthwy/Genome dtse should cite: Keseler et l, Nucleic Acids Reserch 39:D Users who pulish reserch results in scientific journls sed on use of dt from most other BioCyc Pthwy/Genome dtses should cite: Cspi et l, Nucleic Acids Reserch 40:D In some cses, BioCyc Pthwy/Genome dtses re descried y other specific pulictions tht cn e found y selecting the dtse nd then going to the Summry Sttistics pges under the Tools menu. The resulting pge sometimes contins cittion for tht dtse. 12 Pthwys to PCDL Quick Strt Guide

13 In this ook The Agilent G6825AA MssHunter Pthwys to PCDL Softwre - Quick Strt Guide presents the first steps to use the MssHunter Pthwys to PCDL Softwre. If you hve comments out this guide, plese send n e-mil to feedck_lcms@gilent.com. Agilent Technologies, Inc Revision A, Novemer 2012 *G * G Agilent Technologies