Re: [spctools-discuss] PTMProphet MSFragger modification mass discrepancy

2020-03-18 Thread 'David Shteynberg' via spctools-discuss 
Thanks Alex.  I suspect it is a possible bug in PTMProphet. Can you see
what step of your analysis created these additional mods on C?  I would
help me narrow down the places to look.

Cheers,
David

On Wed, Mar 18, 2020 at 11:56 AM Alex Zelter  wrote:

> Hi David,
> Thanks for the fast response!
>
> My list of commands are as follows (after running MSFragger):
>
> tpp/bin/InteractParser   interact.pep.xml FraggerOutput.pepXML
> tpp/bin/DatabaseParser   interact.pep.xml
> tpp/bin/RefreshParserinteract.pep.xml
> /path/to/database/fastaFile.fasta
> tpp/bin/PeptideProphetParser interact.pep.xml ACCMASS DECOYPROBS
> DECOY=random NONPARAM MASSWIDTH=520 MINPROB=0
> tpp/bin/InterProphetParser   interact.pep.xml interact.ipro.pep.xml
> tpp/bin/PTMProphetParser MASSDIFFMODE interact.pep.xml
> tpp/bin/PTMProphetParser MASSDIFFMODE interact.ipro.pep.xml
>
> I'm happy to share the full set of files with you if that helps.
>
> Thanks!
> Alex
>
> On Wednesday, March 18, 2020 at 11:42:22 AM UTC-7, David Shteynberg wrote:
>>
>> Hi Alex,
>>
>> This seems like a bug that should be fixed.  Are you running PTMProphet
>> at any point in your analysis pipeline?
>>
>> Thanks,
>> -David
>>
>> On Wed, Mar 18, 2020 at 11:38 AM Alex Zelter  wrote:
>>
>>> I am running PTMProphet (TPP v5.2.1-dev Flammagenitus, Build
>>> 202003100907-8034) on MSFragger (MSFragger version MSFragger-2.3) output
>>> and ending up with strange results in specific cases.
>>>
>>> For example, for a specific PSM, 52782, MSFragger outputs:
>>>
>>> >> uncalibrated_precursor_neutral_mass="2288.8486" assumed_charge="3"
>>> spectrum="QEP2_2018_0812_AZ_033_az736_AZ.52782.52782.3" end_scan="52782"
>>> index="41840" precursor_neutral_mass="2288.8384"
>>> retention_time_sec="6104.521">
>>> 
>>> >> calc_neutral_pep_mass="1817.8188" peptide_next_aa="A"
>>> num_missed_cleavages="2" num_tol_term="2" num_tot_proteins="5"
>>> tot_num_ions="56" hit_rank="1" num_matched_ions="23"
>>> protein="sp|P02768|ALBU_HUMAN Serum albumin OS=Homo sapiens GN=ALB PE=1
>>> SV=2" peptide_prev_aa="K" is_rejected="0">
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>>
>>> This would indicate that C9 is +57, C10 is +57 and there is an
>>> additional unlocalized mass diff of +471.
>>>
>>> After running TPP I end up with output like this
>>> in interact.ipro.pep.xml for that scan:
>>>
>>> >> uncalibrated_precursor_neutral_mass="2288.8486" assumed_charge="3"
>>> spectrum="QEP2_2018_0812_AZ_033_az736_AZ.52782.52782.3" end_scan="52782"
>>> index="36796" precursor_neutral_mass="2288.8384"
>>> retention_time_sec="6104.521">
>>> 
>>> >> calc_neutral_pep_mass="1817.8188" peptide_next_aa="A"
>>> num_missed_cleavages="1" num_tol_term="2" num_tot_proteins="5"
>>> tot_num_ions="56" hit_rank="1" num_matched_ions="23"
>>> protein="sp|P02768|ALBU_HUMAN" peptide_prev_aa="K" is_rejected="0"
>>> protein_descr="Serum albumin OS=Homo sapiens GN=ALB PE=1 SV=2">
>>> 
>>> 
>>> 
>>> 
>>> ...
>>>
>>> So it seems to me that we now have a modification mass addition of +471
>>> on residues 6 9 and 10 rather than a mass addition of +471 on residue 6 and
>>> then an addition of +57 on residues 9 and 10.
>>>
>>> In cases where there is just a mass diff (open modification) and no
>>> defined variable modifications output is as expected. This situation seems
>>> to occur when both defined variable modifications and open modifications
>>> are present.
>>>
>>> I have confirmed the same behavior in older versions of MSFragger and
>>> TPP.
>>>
>>> Any ideas would be much appreciated!
>>> Thanks,
>>> Alex
>>>
>>> --
>>> You received this message because you are subscribed to the Google
>>> Groups "spctools-discuss" group.
>>> To unsubscribe from this group and stop receiving emails from it, send
>>> an email to spctools...@googlegroups.com.
>>> To view this discussion on the web visit
>>> https://groups.google.com/d/msgid/spctools-discuss/5a37d860-cd21-445a-a485-ed3684291f4d%40googlegroups.com
>>> 
>>> .
>>>
>> --
> You received this message because you are subscribed to the Google Groups
> "spctools-discuss" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to spctools-discuss+unsubscr...@googlegroups.com.
> To view this discussion on the web visit
> https://groups.google.com/d/msgid/spctools-discuss/4314cc4f-3944-4a51-bb34-dc43aae61848%40googlegroups.com
> 
> .
>

-- 
You received this message because you are subscribed to the Google Groups 
"spctools-discuss" group.
To unsubscribe from this group and stop receiving emails from it, send an email 
to spctools-discuss+unsubscr...@googlegroups.com.
To view this discussion on the web visit 
https://groups.google.com/d/msgid/spctools-discuss/

Re: [spctools-discuss] PTMProphet MSFragger modification mass discrepancy

2020-03-18 Thread Alex Zelter 
Hi David,
Thanks for the fast response!

My list of commands are as follows (after running MSFragger):

tpp/bin/InteractParser   interact.pep.xml FraggerOutput.pepXML
tpp/bin/DatabaseParser   interact.pep.xml
tpp/bin/RefreshParserinteract.pep.xml 
/path/to/database/fastaFile.fasta
tpp/bin/PeptideProphetParser interact.pep.xml ACCMASS DECOYPROBS 
DECOY=random NONPARAM MASSWIDTH=520 MINPROB=0
tpp/bin/InterProphetParser   interact.pep.xml interact.ipro.pep.xml
tpp/bin/PTMProphetParser MASSDIFFMODE interact.pep.xml
tpp/bin/PTMProphetParser MASSDIFFMODE interact.ipro.pep.xml

I'm happy to share the full set of files with you if that helps.

Thanks!
Alex

On Wednesday, March 18, 2020 at 11:42:22 AM UTC-7, David Shteynberg wrote:
>
> Hi Alex,
>
> This seems like a bug that should be fixed.  Are you running PTMProphet at 
> any point in your analysis pipeline?
>
> Thanks,
> -David
>
> On Wed, Mar 18, 2020 at 11:38 AM Alex Zelter > 
> wrote:
>
>> I am running PTMProphet (TPP v5.2.1-dev Flammagenitus, Build 
>> 202003100907-8034) on MSFragger (MSFragger version MSFragger-2.3) output 
>> and ending up with strange results in specific cases.
>>
>> For example, for a specific PSM, 52782, MSFragger outputs:
>>
>> > uncalibrated_precursor_neutral_mass="2288.8486" assumed_charge="3" 
>> spectrum="QEP2_2018_0812_AZ_033_az736_AZ.52782.52782.3" end_scan="52782" 
>> index="41840" precursor_neutral_mass="2288.8384" 
>> retention_time_sec="6104.521">
>> 
>> > calc_neutral_pep_mass="1817.8188" peptide_next_aa="A" 
>> num_missed_cleavages="2" num_tol_term="2" num_tot_proteins="5" 
>> tot_num_ions="56" hit_rank="1" num_matched_ions="23" 
>> protein="sp|P02768|ALBU_HUMAN Serum albumin OS=Homo sapiens GN=ALB PE=1 
>> SV=2" peptide_prev_aa="K" is_rejected="0">
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>>
>> This would indicate that C9 is +57, C10 is +57 and there is an additional 
>> unlocalized mass diff of +471.
>>
>> After running TPP I end up with output like this in interact.ipro.pep.xml 
>> for that scan:
>>
>> > uncalibrated_precursor_neutral_mass="2288.8486" assumed_charge="3" 
>> spectrum="QEP2_2018_0812_AZ_033_az736_AZ.52782.52782.3" end_scan="52782" 
>> index="36796" precursor_neutral_mass="2288.8384" 
>> retention_time_sec="6104.521">
>> 
>> > calc_neutral_pep_mass="1817.8188" peptide_next_aa="A" 
>> num_missed_cleavages="1" num_tol_term="2" num_tot_proteins="5" 
>> tot_num_ions="56" hit_rank="1" num_matched_ions="23" 
>> protein="sp|P02768|ALBU_HUMAN" peptide_prev_aa="K" is_rejected="0" 
>> protein_descr="Serum albumin OS=Homo sapiens GN=ALB PE=1 SV=2">
>> 
>> 
>> 
>> 
>> ...
>>
>> So it seems to me that we now have a modification mass addition of +471 
>> on residues 6 9 and 10 rather than a mass addition of +471 on residue 6 and 
>> then an addition of +57 on residues 9 and 10.
>>
>> In cases where there is just a mass diff (open modification) and no 
>> defined variable modifications output is as expected. This situation seems 
>> to occur when both defined variable modifications and open modifications 
>> are present.
>>
>> I have confirmed the same behavior in older versions of MSFragger and TPP.
>>
>> Any ideas would be much appreciated!
>> Thanks,
>> Alex
>>
>> -- 
>> You received this message because you are subscribed to the Google Groups 
>> "spctools-discuss" group.
>> To unsubscribe from this group and stop receiving emails from it, send an 
>> email to spctools...@googlegroups.com .
>> To view this discussion on the web visit 
>> https://groups.google.com/d/msgid/spctools-discuss/5a37d860-cd21-445a-a485-ed3684291f4d%40googlegroups.com
>>  
>> 
>> .
>>
>

-- 
You received this message because you are subscribed to the Google Groups 
"spctools-discuss" group.
To unsubscribe from this group and stop receiving emails from it, send an email 
to spctools-discuss+unsubscr...@googlegroups.com.
To view this discussion on the web visit 
https://groups.google.com/d/msgid/spctools-discuss/4314cc4f-3944-4a51-bb34-dc43aae61848%40googlegroups.com.

Re: [spctools-discuss] PTMProphet MSFragger modification mass discrepancy

2020-03-18 Thread 'David Shteynberg' via spctools-discuss 
Hi Alex,

This seems like a bug that should be fixed.  Are you running PTMProphet at
any point in your analysis pipeline?

Thanks,
-David

On Wed, Mar 18, 2020 at 11:38 AM Alex Zelter  wrote:

> I am running PTMProphet (TPP v5.2.1-dev Flammagenitus, Build
> 202003100907-8034) on MSFragger (MSFragger version MSFragger-2.3) output
> and ending up with strange results in specific cases.
>
> For example, for a specific PSM, 52782, MSFragger outputs:
>
>  uncalibrated_precursor_neutral_mass="2288.8486" assumed_charge="3"
> spectrum="QEP2_2018_0812_AZ_033_az736_AZ.52782.52782.3" end_scan="52782"
> index="41840" precursor_neutral_mass="2288.8384"
> retention_time_sec="6104.521">
> 
>  calc_neutral_pep_mass="1817.8188" peptide_next_aa="A"
> num_missed_cleavages="2" num_tol_term="2" num_tot_proteins="5"
> tot_num_ions="56" hit_rank="1" num_matched_ions="23"
> protein="sp|P02768|ALBU_HUMAN Serum albumin OS=Homo sapiens GN=ALB PE=1
> SV=2" peptide_prev_aa="K" is_rejected="0">
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
>
> This would indicate that C9 is +57, C10 is +57 and there is an additional
> unlocalized mass diff of +471.
>
> After running TPP I end up with output like this in interact.ipro.pep.xml
> for that scan:
>
>  uncalibrated_precursor_neutral_mass="2288.8486" assumed_charge="3"
> spectrum="QEP2_2018_0812_AZ_033_az736_AZ.52782.52782.3" end_scan="52782"
> index="36796" precursor_neutral_mass="2288.8384"
> retention_time_sec="6104.521">
> 
>  calc_neutral_pep_mass="1817.8188" peptide_next_aa="A"
> num_missed_cleavages="1" num_tol_term="2" num_tot_proteins="5"
> tot_num_ions="56" hit_rank="1" num_matched_ions="23"
> protein="sp|P02768|ALBU_HUMAN" peptide_prev_aa="K" is_rejected="0"
> protein_descr="Serum albumin OS=Homo sapiens GN=ALB PE=1 SV=2">
> 
> 
> 
> 
> ...
>
> So it seems to me that we now have a modification mass addition of +471 on
> residues 6 9 and 10 rather than a mass addition of +471 on residue 6 and
> then an addition of +57 on residues 9 and 10.
>
> In cases where there is just a mass diff (open modification) and no
> defined variable modifications output is as expected. This situation seems
> to occur when both defined variable modifications and open modifications
> are present.
>
> I have confirmed the same behavior in older versions of MSFragger and TPP.
>
> Any ideas would be much appreciated!
> Thanks,
> Alex
>
> --
> You received this message because you are subscribed to the Google Groups
> "spctools-discuss" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to spctools-discuss+unsubscr...@googlegroups.com.
> To view this discussion on the web visit
> https://groups.google.com/d/msgid/spctools-discuss/5a37d860-cd21-445a-a485-ed3684291f4d%40googlegroups.com
> 
> .
>

-- 
You received this message because you are subscribed to the Google Groups 
"spctools-discuss" group.
To unsubscribe from this group and stop receiving emails from it, send an email 
to spctools-discuss+unsubscr...@googlegroups.com.
To view this discussion on the web visit 
https://groups.google.com/d/msgid/spctools-discuss/CAGJJY%3D-3E-%3D4OqMEjuio3wngty4anoHp-9n658HQHspH1%3D-cCg%40mail.gmail.com.

[spctools-discuss] PTMProphet MSFragger modification mass discrepancy

2020-03-18 Thread Alex Zelter 
I am running PTMProphet (TPP v5.2.1-dev Flammagenitus, Build 
202003100907-8034) on MSFragger (MSFragger version MSFragger-2.3) output 
and ending up with strange results in specific cases.

For example, for a specific PSM, 52782, MSFragger outputs:















This would indicate that C9 is +57, C10 is +57 and there is an additional 
unlocalized mass diff of +471.

After running TPP I end up with output like this in interact.ipro.pep.xml 
for that scan:








...

So it seems to me that we now have a modification mass addition of +471 on 
residues 6 9 and 10 rather than a mass addition of +471 on residue 6 and 
then an addition of +57 on residues 9 and 10.

In cases where there is just a mass diff (open modification) and no defined 
variable modifications output is as expected. This situation seems to occur 
when both defined variable modifications and open modifications are present.

I have confirmed the same behavior in older versions of MSFragger and TPP.

Any ideas would be much appreciated!
Thanks,
Alex

-- 
You received this message because you are subscribed to the Google Groups 
"spctools-discuss" group.
To unsubscribe from this group and stop receiving emails from it, send an email 
to spctools-discuss+unsubscr...@googlegroups.com.
To view this discussion on the web visit 
https://groups.google.com/d/msgid/spctools-discuss/5a37d860-cd21-445a-a485-ed3684291f4d%40googlegroups.com.