Re: [proteowizard-support] mzPresent issues

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Hi John,

I assume you copied that red text from an earlier version of msconvert. It was updated in March to use a key/value system, and indeed the 
m/z list is the only required parameter. The new format is:
mzPresent <mz_list> [mzTol=<tolerance> (0.5 mz)] [type=<type> (count)] [threshold=<threshold> (10000)] [orientation=<orientation> 
(most-intense)] [mode=<include|exclude (include)>]
This filter includes or excludes spectra depending on whether the specified peaks are present.
    <mz_list> is a list of mz values of the form [mz1,mz2, ... mzn] (for example, "[100, 300, 405.6]"). Spectra which contain peaks within 
<tolerance> of any of these values will be kept.
    <tolerance> is specified as a number and units (PPM or MZ). For example, "5 PPM" or "2.1 MZ".
    <type>, <threshold>, and <orientation> operate as in the "threshold" filter (see above).
    <include|exclude> is optional and has value "include" (the default) or "exclude".  If "exclude" is used the filter drops spectra that 
match the various criteria instead of keeping them.

So yours should be:
mzPresent [366.14] mzTol=.02mz type=bpi-relative threshold=1

Hope this helps,
-Matt

On 11/9/2017 2:24 PM, Froehlich, John wrote:
>
> Hi there,
>
> I was on the paper for the mzPresent tool development, and I’m writing today because I can’t seem to get it to work within msaccess.
>
> I am trying to use mzPresent within the msaccess tool to generate a tsv file. I had some issue, so I started trying to use mzPresent 
> within the msconvert setup. Following these directions (below), would not generate an MGF file, however:
>
> “mzPresent <tolerance> <type> <threshold> <orientation> <mz_list> [<include_or_exclude>]
> This filter is similar to the "threshold" filter, with a few more options.
> <tolerance> is specified as a number and units (PPM or MZ). For example, "5 PPM" or "2.1 MZ".
> <type>, <threshold>, and <orientation> operate as in the "threshold" filter (see above).
> <mz_list> is a list of mz values of the form [mz1,mz2, ... mzn] (for example, "[100, 300, 405.6]"). Data points within <tolerance> of any 
> of these values will be kept.
> <include_or_exclude> is optional and has value "include" (the default) or "exclude". If "exclude" is used the filter drops data points 
> that match the various criteria instead of keeping them.”
>
> It seems that the <mz_list> has to come first, contrary to what we see on the directions? For example, trying this in the CMD window fails:
>
> C:\Users\ch145448>msconvert --mgf "C:\Users\ch145448\Dropbox\LAB_SHARE\GLAZER\RAW_Files\JF_IGDHilic_Tryp_Gfrac3.raw" --filter "mzPresent 
> .02 MZ bpi-relative 1 most-intense [366.14] include"
>
> format: MGF
>
> outputPath: .
>
> extension: .mgf
>
> contactFilename:
>
> filters:
>
>   mzPresent .02 MZ bpi-relative 1 most-intense [366.14] include
>
> filenames:
>
> C:\Users\ch145448\Dropbox\LAB_SHARE\GLAZER\RAW_Files\JF_IGDHilic_Tryp_Gfrac3.raw
>
> processing file: C:\Users\ch145448\Dropbox\LAB_SHARE\GLAZER\RAW_Files\JF_IGDHilic_Tryp_Gfrac3.raw
>
> Error writing run 1 in "JF_IGDHilic_Tryp_Gfrac3.raw":
>
> [SpectrumListFactory::filterCreator_mzPresent()] mzPresent filter expected a list of mz values like
>
> "[100,200,300.4]"
>
> However, putting the <mz_list> first does generate an mgf file, but the MGF file will not change regardless of what values of <tolerance> 
> or <threshold> we use.  Do you know what the defaults of <tolerance> or <threshold> might be? It seems that I am not actually passing 
> these parameters on correctly.
>
> C:\Users\ch145448>msconvert --mgf "C:\Users\ch145448\Dropbox\LAB_SHARE\GLAZER\RAW_Files\JF_IGDHilic_
>
> Tryp_Gfrac3.raw" --filter "mzPresent [366.14] .02 MZ bpi-relative 1 include"
>
> format: MGF
>
> outputPath: .
>
> extension: .mgf
>
> contactFilename:
>
> filters:
>
>   mzPresent [366.14] .02 MZ bpi-relative 1 include
>
> filenames:
>
> C:\Users\ch145448\Dropbox\LAB_SHARE\GLAZER\RAW_Files\JF_IGDHilic_Tryp_Gfrac3.raw
>
> processing file: C:\Users\ch145448\Dropbox\LAB_SHARE\GLAZER\RAW_Files\JF_IGDHilic_Tryp_Gfrac3.raw
>
> writing output file: .\JF_IGDHilic_Tryp_Gfrac3.mgf
>
> the full mgf is about 2 times larger than the one that gets mzPresent filtered.  So it must be doing something, I just can’t get it to 
> work properly.  Do you have any advice on something else to try?
>
> Version info:
>
> ProteoWizard release: 3.0.11417 (2017-10-3)
>
> ProteoWizard MSData: 3.0.11392 (2017-9-18)
>
> ProteoWizard Analysis: 3.0.11417 (2017-10-3)
>
> Build date: Oct  4 2017 00:40:40
>
> **
>
> Thanks!
>
> -John
>
> /John Froehlich/
>
> /Instructor/
>
> /(617) 919-2022 (x42022)/
>
> /Enders 1054/
>
>
>
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