Double or sequential digest using Kojak in combination with PeptideProphet

[nzsuzsanna]

Hi,

I tried to analyze my DSS and DMTMM cross-linking data using  Kojak and PeptideProphet.

Kojak run properly, however Peptideprophet claims for Trypsin GluC digestion, which is not defined. Kojak could handle it.

Why does PeptideProphet need the enzyme info at all?

Is this possible to define for PeptideProphet the TryGluC "enzyme"? i could not find it in the 

I read in the bioRxiv Mendes et al publication 'An integrated workflow for cross-linking/mass spectrometry" , that ".....we and the developers of these tools could not pair Kojak with PeptideProphet for sequential digestion."

Thanks for answers in advance.

best

Zsuzsi

[Michael Hoopmann]

Hi Zsuzsi,

Could you try renaming your enzyme, "trypsin_gluc" ?  I think that is the secret enzyme name that PeptideProphet recognizes for that enzyme combination. Sorry for the trouble, I'll have dig through the code to see who is at fault (Kojak or PeptideProphet) for not properly interpreting the enzyme combination.

As for the bioRxiv publication, I'm not sure if anyone on that author list tried to contact us, so it seems there is an error or exaggeration in that statement... We appreciate you made the effort.

Cheers,

Mike

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[nzsuzsanna]

Hi Mike,

many thanks for your prompt answer. I tried and indeed if I defined my sequential digest  in Kojak as you suggeste as "trypsin_gluc", then the PeptideProphet can analyze the pep.xml file. Many thanks.

Zsuzsi

Am Mittwoch, 11. September 2019 01:57:20 UTC+2 schrieb Michael Hoopmann:

Hi Zsuzsi,

Could you try renaming your enzyme, "trypsin_gluc" ?  I think that is the secret enzyme name that PeptideProphet recognizes for that enzyme combination. Sorry for the trouble, I'll have dig through the code to see who is at fault (Kojak or PeptideProphet) for not properly interpreting the enzyme combination.

As for the bioRxiv publication, I'm not sure if anyone on that author list tried to contact us, so it seems there is an error or exaggeration in that statement... We appreciate you made the effort.

Cheers,

Mike

On Tue, Sep 10, 2019 at 7:30 AM nzsuzsanna <zsuzsanna....@gmail.com> wrote:

Hi,

I tried to analyze my DSS and DMTMM cross-linking data using  Kojak and PeptideProphet.

Kojak run properly, however Peptideprophet claims for Trypsin GluC digestion, which is not defined. Kojak could handle it.

Why does PeptideProphet need the enzyme info at all?

Is this possible to define for PeptideProphet the TryGluC "enzyme"? i could not find it in the 

I read in the bioRxiv Mendes et al publication 'An integrated workflow for cross-linking/mass spectrometry" , that ".....we and the developers of these tools could not pair Kojak with PeptideProphet for sequential digestion."

Thanks for answers in advance.

best

Zsuzsi

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