Information on spectra considered for TMTintegrator-based quant

[michaelsteidel86]

Dear Fengchao/Alexey,

is there actually a way to extract information on which spectra were actually considered for TMTintegrator-based quan? This information would be highly useful in individual cases (i.e. which spectra were exluded in the outlier removel for individual protein quantification, etc)

Another related question: How do you calculate protein-level quant values in the Philosopher output?

Thanks in advance! Michael

[anesvi]

Regarding the first question, TMT-Integrator I think prints temporary files listing PSMs that are used for quantification, but they are deleted at the end. Hui-yin, is that the case? But yes, it would be nice to have a way to propagate this info. One possibility could be also for TMT-Integrator to write a new column to PSM.tsv called “TMT-Integrator_Used” with 1 if it was used. Although there may be some ambiguity too. A PSM may be removed for protein level calculation because its quant is an outlier, but I suppose it can be used for peptide-level quant if it is not called outlier tehre? Hui-yin, can you confirm?

The quant you see in the Philosopher output tables is based on summing the reporter ion intensities to the peptide/protein level. So it is similar to what Proteome Discoverer does. Similar filters are applied as in TMT-Integrator (purity score, min intensity, etc), but more PSMs are used. There is no outlier removal, and no removal of redundant PSMs that TMT-I does as a default option (repeated ID in the same MS run; TMT-I selects the one with highest intensity if a peptide ion sequences more than once in the same LC-MS/MS run).

Best Alexey

From: michaelsteidel86 @.> Sent: Thursday, October 13, 2022 10:13 AM To: Nesvilab/FragPipe @.> Cc: Subscribed @.***> Subject: [Nesvilab/FragPipe] Information on spectra considered for TMTintegrator-based quant (Issue #856)

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Dear Fengchao/Alexey,

is there actually a way to extract information on which spectra were actually considered for TMTintegrator-based quan? This information would be highly useful in individual cases (i.e. which spectra were exluded in the outlier removel for individual protein quantification, etc)

Another related question: How do you calculate protein-level quant values in the Philosopher output?

Thanks in advance! Michael

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[michaelsteidel86]

A potential solution to avoid any ambiguity in case of quantification at both peptide-level and protein-level could be to propagate this information in the TMT-integrator ouput (i.e. concatenated string pointing to spectra id's)

Another quite useful option could be the addition of the quant spectra count (in TMT integrator outputs), as an additional measure for quant confidence

[anesvi]

Yes, I am thinking maybe we can print a PSM table (but smaller, just scan ID_ a few columns) in the TMT-I folder showing if the scan was used for what analysis (e.g. if it was used for peptide/gene/protein/site level calculation). Hui-yin what do you think?

From: michaelsteidel86 @.> Sent: Thursday, October 13, 2022 10:36 AM To: Nesvilab/FragPipe @.> Cc: Nesvizhskii, Alexey @.>; Comment @.> Subject: Re: [Nesvilab/FragPipe] Information on spectra considered for TMTintegrator-based quant (Issue #856)

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A potential solution to avoid any ambiguity in case of quantification at both peptide-level and protein-level could be to propagate this information in the TMT-integrator ouput (i.e. concatenated string pointing to spectra id's)

Another quite useful option could be the addition of the quant spectra count (in TMT integrator outputs), as an additional measure for quant confidence

— Reply to this email directly, view it on GitHubhttps://github.com/Nesvilab/FragPipe/issues/856#issuecomment-1277715595, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AIIMM67KT3IWGWYGVYFT6WDWDAM5XANCNFSM6AAAAAAREKM22Q. You are receiving this because you commented.Message ID: @.@.>>

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[huiyinc]

Hi Alexey,

Yes, during the process, TMT-Integrator exports a temporary file of each input PSM table. In the temporary file, there is a column, called Is Used (TMT-I), to indicate if the PSM is used for quantitation. I think a simple solution is to add a parameter to let users decide if they want to keep the temporary files (default value: false).

Huiyin

Alexey Nesvizhskii @.***> 於 2022年10月13日 週四 晚上10:41寫道：

Yes, I am thinking maybe we can print a PSM table (but smaller, just scan ID_ a few columns) in the TMT-I folder showing if the scan was used for what analysis (e.g. if it was used for peptide/gene/protein/site level calculation). Hui-yin what do you think?

From: michaelsteidel86 @.> Sent: Thursday, October 13, 2022 10:36 AM To: Nesvilab/FragPipe @.> Cc: Nesvizhskii, Alexey @.>; Comment @.> Subject: Re: [Nesvilab/FragPipe] Information on spectra considered for TMTintegrator-based quant (Issue #856)

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A potential solution to avoid any ambiguity in case of quantification at both peptide-level and protein-level could be to propagate this information in the TMT-integrator ouput (i.e. concatenated string pointing to spectra id's)

Another quite useful option could be the addition of the quant spectra count (in TMT integrator outputs), as an additional measure for quant confidence

— Reply to this email directly, view it on GitHub< https://github.com/Nesvilab/FragPipe/issues/856#issuecomment-1277715595>, or unsubscribe< https://github.com/notifications/unsubscribe-auth/AIIMM67KT3IWGWYGVYFT6WDWDAM5XANCNFSM6AAAAAAREKM22Q>.

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-- Hui-Yin Chang, 張彙音 Assistant Professor Department of Biomedical Sciences and Engineering National Central University, Taiwan