Best Practices - Library Searching MassHunter

Hello, I am using an Agilent 8890 GC with a 7000D triple quadrupole. I have MassHunter version 10.0 with Quant and Qual software. I am acquiring regular MS scan data (not MRM) and want to build a library of reference compounds I've run on the instrument and search samples first for compounds in my custom library and then with NIST. As is often the case with this type of software there are multiple ways to essentially do the same thing. So I am wondering what is the simplest approach? I have options to use the Qual, Quant, PCDL, library editor, or unknowns analysis programs? Its unclear what the practical utility differences are between library editor, PCDL, and unknowns analysis programs? I have quite a bit of experience using quant software for analysis of targeted compounds in MRM modes but less experience using qualitative analysis for identifying unknown compounds. 

So far I have tried sending spectra from qualitative analysis to a PCDL library. However when I attempt to use that library it doesn't really work and there are a number of issues. I will illustrate the problem with an example. Lets say I run a reference standard and I want to build a PCDL library from sample and then search that same sample with the library I built. Here is the workflow: 

1- Open qualitative analysis under method editor set the identification workflow to search the NIST20 library. 

2- Open my data file. 

3- Extract peak spectrum and do a background subtraction manually. 

4- Right click on background subtracted spectra and identify the peak. I've tried all 3 ways including identify spectra, search library / DB for spectra, and add / edit manual identification. NIST usually gives the right answer so I used the search library / DB for identification. 

5- Send spectra to PCDL. 

6- Tell method editor to search my PCDL library first then search NIST. 

7- Reopen data file and tell the method editor to search my PCDL library followed by NIST. 

A number of issues are happening that are hindering this process. The first is that when I use the identify spectra or the search library / DB for spectra for the initial identification (step 4 above) the retention time from the NIST library is sent to the PCDL library. If I manually edit that retention time in the PCDL software and close the software and reopen the database it erases my manual entry and puts back the NIST entry. If I clear all retention times the PCDL library and manually enter retention time when I reopen the PCDL is just erases my manual entry and goes back to blank. So that is frustrating. 

Another issue is that if I search my sample in qualitative analysis program its supposed to first search my PCDL first  then NIST. But the results list (I set max 3 results) keeps prioritizing the NIST library and sometimes doesn't show my PCDL hit at all. So if I remove the NIST library and search with my PCDL it found nothing. So I had to tell it to ignore retention times and then it found the compound. But I want to search retention times in the long run so this work around isn't a solution. If I put NIST back it'll just ignore my library and give me NIST result. 

So I am almost ready to give up on PCDL and figure out another approach. This seems overly complicated. Any ideas? 

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