SAGE search engine score is missing after psm re-scoring using percolator #288

WangHong007 · 2023-09-19T13:02:28Z

Description of the bug

SAGE's search engine score should be hyperscore, pyopenms could extrct it with idXMLs after searchengines step. But after psm re-scoring using percolator, it's missing in idXMLs.

idxml before psm re-scoring:

<PeptideIdentification score_type="hyperscore" higher_score_better="true" significance_threshold="0.0" MZ="988.485223533228918" RT="2776.47440000000006" spectrum_reference="controllerType=0 controllerNumber=1 scan=16570" >
	<PeptideHit score="4.372861652440132" sequence="LLGPSLTSTTPASSSSGSSSR" charge="2" aa_before="R" aa_after="G" start="363" end="383" protein_refs="PH_0" >
		<UserParam type="string" name="target_decoy" value="target"/>
		<UserParam type="string" name="ln(-poisson)" value="3.14389626700959"/>
		<UserParam type="string" name="ln(delta_best)" value="0.0"/>
		<UserParam type="string" name="ln(delta_next)" value="3.819337728782414"/>
		<UserParam type="string" name="ln(matched_intensity_pct)" value="3.5826106"/>
		<UserParam type="string" name="longest_b" value="9"/>
		<UserParam type="string" name="longest_y" value="18"/>
		<UserParam type="string" name="longest_y_pct" value="0.85714287"/>
		<UserParam type="string" name="matched_peaks" value="27"/>
		<UserParam type="string" name="scored_candidates" value="8222"/>
		<UserParam type="string" name="protein_references" value="unique"/>
	</PeptideHit>
	<UserParam type="string" name="PinSpecId" value="312"/>
</PeptideIdentification>

idxml after psm re-scoring:

<PeptideIdentification score_type="Posterior Error Probability" higher_score_better="false" significance_threshold="0.0" MZ="988.485223533228918" RT="2776.47440000000006" spectrum_reference="controllerType=0 controllerNumber=1 scan=16570" >
	<PeptideHit score="4.70852e-08" sequence="LLGPSLTSTTPASSSSGSSSR" charge="2" aa_before="R" aa_after="G" start="363" end="383" protein_refs="PH_7718" >
		<UserParam type="string" name="target_decoy" value="target"/>
		<UserParam type="string" name="ln(-poisson)" value="3.14389626700959"/>
		<UserParam type="string" name="ln(delta_best)" value="0.0"/>
		<UserParam type="string" name="ln(delta_next)" value="3.819337728782414"/>
		<UserParam type="string" name="ln(matched_intensity_pct)" value="3.5826106"/>
		<UserParam type="string" name="longest_b" value="9"/>
		<UserParam type="string" name="longest_y" value="18"/>
		<UserParam type="string" name="longest_y_pct" value="0.85714287"/>
		<UserParam type="string" name="matched_peaks" value="27"/>
		<UserParam type="string" name="scored_candidates" value="8222"/>
		<UserParam type="string" name="protein_references" value="unique"/>
		<UserParam type="float" name="MS:1001492" value="2.65249"/>
		<UserParam type="float" name="MS:1001491" value="7.304600000000001e-04"/>
		<UserParam type="float" name="MS:1001493" value="4.70852e-08"/>
	</PeptideHit>
	<UserParam type="string" name="PinSpecId" value="312"/>
</PeptideIdentification>

Command used and terminal output

No response

Relevant files

No response

System information

No response

The text was updated successfully, but these errors were encountered:

jpfeuffer · 2023-09-19T13:39:08Z

How is this with other search engines?

It might be because PSMFeatureExtractor can be and is skipped with Sage.

ypriverol · 2023-09-19T14:07:14Z

I guess we are not taking the SAGE output but the pin file from percolator?

WangHong007 · 2023-09-19T14:16:47Z

@jpfeuffer @ypriverol It should be SAGE seach output. Comet and MSGF+ got their search scores in MetaValue of every PeptideHit, but not SAGE.

jpfeuffer · 2023-09-19T14:29:14Z

How does an idXML for comet look like after PSMFeatureExtractor?

WangHong007 · 2023-09-19T14:38:57Z

Comet search engine score is xcorr -> MetaValue MS:1002252. It's already exist before psm re-scoring.

<PeptideIdentification score_type="Posterior Error Probability" higher_score_better="false" significance_threshold="0.0" MZ="474.761474031899979" RT="1815.299999999999955" spectrum_reference="controllerType=0 controllerNumber=1 scan=3727" >
	<PeptideHit score="0.990159" sequence="LSGATLQMK" charge="2" aa_before="K" aa_after="R" start="48" end="56" protein_refs="PH_1080" >
		<UserParam type="string" name="target_decoy" value="decoy"/>
		<UserParam type="string" name="MS:1002258" value="6"/>
		<UserParam type="string" name="MS:1002259" value="16"/>
		<UserParam type="string" name="num_matched_peptides" value="1060"/>
		<UserParam type="int" name="isotope_error" value="0"/>
		<UserParam type="float" name="MS:1002252" value="1.116"/>
		<UserParam type="float" name="MS:1002253" value="1.0"/>
		<UserParam type="float" name="MS:1002254" value="0.0"/>
		<UserParam type="float" name="MS:1002255" value="113.900000000000006"/>
		<UserParam type="float" name="MS:1002256" value="11.0"/>
		<UserParam type="float" name="MS:1002257" value="2.89"/>
		<UserParam type="string" name="protein_references" value="unique"/>
		<UserParam type="float" name="COMET:deltCn" value="1.0"/>
		<UserParam type="float" name="COMET:deltLCn" value="0.0"/>
		<UserParam type="float" name="COMET:lnExpect" value="1.061256502124341"/>
		<UserParam type="float" name="COMET:lnNumSP" value="6.966024187106113"/>
		<UserParam type="float" name="COMET:lnRankSP" value="2.397895272798371"/>
		<UserParam type="float" name="COMET:IonFrac" value="0.375"/>
		<UserParam type="float" name="MS:1001492" value="-0.641415"/>
		<UserParam type="float" name="MS:1001491" value="0.270715"/>
		<UserParam type="float" name="MS:1001493" value="0.990159"/>
	</PeptideHit>
</PeptideIdentification>

jpfeuffer · 2023-09-19T15:00:41Z

But this is after rescoring. I need to see before.

WangHong007 · 2023-09-19T15:20:18Z

<PeptideIdentification score_type="expect" higher_score_better="false" significance_threshold="0.0" MZ="474.761474031899979" RT="1815.299999999999955" spectrum_reference="controllerType=0 controllerNumber=1 scan=3727" >
	<PeptideHit score="2.89" sequence="LSGATLQMK" charge="2" aa_before="K" aa_after="R" start="48" end="56" protein_refs="PH_9943" >
		<UserParam type="string" name="MS:1002258" value="6"/>
		<UserParam type="string" name="MS:1002259" value="16"/>
		<UserParam type="string" name="num_matched_peptides" value="1060"/>
		<UserParam type="int" name="isotope_error" value="0"/>
		<UserParam type="float" name="MS:1002252" value="1.116"/>
		<UserParam type="float" name="MS:1002253" value="1.0"/>
		<UserParam type="float" name="MS:1002254" value="0.0"/>
		<UserParam type="float" name="MS:1002255" value="113.900000000000006"/>
		<UserParam type="float" name="MS:1002256" value="11.0"/>
		<UserParam type="float" name="MS:1002257" value="2.89"/>
		<UserParam type="string" name="target_decoy" value="decoy"/>
		<UserParam type="string" name="protein_references" value="unique"/>
	</PeptideHit>
</PeptideIdentification>

jpfeuffer · 2023-09-19T15:47:04Z

Yes so the problem is that we actually use the Comet e-value as main score.
So you are just lucky that you picked a score that is not a main score for the other search engines.

ypriverol · 2023-09-25T15:36:35Z

I think this problem is solved. You should take the data @WangHong007 from the SAGE id folder.

ypriverol · 2023-09-27T13:12:04Z

@timosachsenberg Im re-opening this PR because After testing http://ftp.pride.ebi.ac.uk/pub/databases/pride/resources/proteomes/quantms-benchmark/PXD004683/percolator/ the error remains. Can you double check why the hyperscore is not included in the percolator sage output?

Percolator SAGE output: http://ftp.pride.ebi.ac.uk/pub/databases/pride/resources/proteomes/quantms-benchmark/PXD004683/percolator/20150820_Haura-Pilot-TMT1-bRPLC01-2_sage_perc.idXML

jpfeuffer · 2023-09-27T13:28:38Z

according to pipeline_info it is still using the old container

ypriverol · 2023-09-27T13:29:20Z

This is percolator no?

jpfeuffer · 2023-09-27T13:30:54Z

yes PercolatorAdapter

jpfeuffer · 2023-09-27T13:32:46Z

https://github.com/bigbio/quantms/blob/dev/modules/local/openms/thirdparty/percolator/main.nf#L5

jpfeuffer · 2023-09-27T13:34:42Z

I honestly think we should just override the containers for all openms labelled processes until the release. I.e. make the dev profile active by default. Otherwise someone will always forget to change a process.

ypriverol · 2023-09-27T13:35:35Z

I actually think we should make variable the containers using in every-process a variable, would that be possible? Something like:

openms_conda_string = "bioconda::openms=2.9.1"
openms_singularity_string = "ghcr.io/openms/openms-executables-sif:latest"
openms_docker_string = "ghcr.io/openms/openms-executables:latest"

jpfeuffer · 2023-09-27T14:11:51Z

I don't like it very much. You will just get confused because suddenly conda uses something different from docker etc. It also confuses users with yet an additional THREE parameters.
The only thing you will ever want is dev or latest. Nothing else.

ypriverol · 2023-09-27T14:28:45Z

I have no idea what do you have in mind? How can you make a profile default, can you send me an example and I can do it.

ypriverol · 2023-09-27T14:58:05Z

You mean something like this:

https://github.com/nf-core/quantms/blob/dev/conf/dev.config

jpfeuffer · 2023-09-27T15:01:11Z

yes. just put it in base.config. The thing is just to remember to remove it when releasing

ypriverol · 2023-09-27T15:05:44Z

I was actually thinking to leave it there but then in the nextflow.config import it or not depending on the release cycle. Like in the nextflow.config

includeConfig 'conf/dev.config'

What do you think?

jpfeuffer · 2023-09-27T15:12:59Z

Yes but you need to find out if and how nextflow knows about its release cycle ;)
If it cannot know about it, then having to change one line every release it not much better than just changing 3 lines.

WangHong007 added the bug Something isn't working label Sep 19, 2023

ypriverol added the sage-support label Sep 19, 2023

ypriverol assigned timosachsenberg, jpfeuffer and WangHong007 Sep 19, 2023

jpfeuffer mentioned this issue Sep 19, 2023

Keep main score in PercolatorAdapter OpenMS/OpenMS#7090

Merged

5 tasks

ypriverol linked a pull request Sep 25, 2023 that will close this issue

update some process to openms dev #289

Merged

10 tasks

ypriverol closed this as completed in #289 Sep 25, 2023

ypriverol reopened this Sep 27, 2023

jpfeuffer closed this as completed Sep 27, 2023

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SAGE search engine score is missing after psm re-scoring using percolator #288

SAGE search engine score is missing after psm re-scoring using percolator #288

WangHong007 commented Sep 19, 2023

jpfeuffer commented Sep 19, 2023 •

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jpfeuffer commented Sep 27, 2023

SAGE search engine score is missing after psm re-scoring using percolator #288

SAGE search engine score is missing after psm re-scoring using percolator #288

Comments

WangHong007 commented Sep 19, 2023

Description of the bug

Command used and terminal output

Relevant files

System information

jpfeuffer commented Sep 19, 2023 • edited Loading

ypriverol commented Sep 19, 2023

WangHong007 commented Sep 19, 2023

jpfeuffer commented Sep 19, 2023

WangHong007 commented Sep 19, 2023 • edited Loading

jpfeuffer commented Sep 19, 2023

WangHong007 commented Sep 19, 2023

jpfeuffer commented Sep 19, 2023

ypriverol commented Sep 25, 2023

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