SequenceWindow, Ile over-representation on the n-term side

[pisistrato]

Hi,

I was inspecting the files generated in the tmt-report folder. I noticed a suspicious over-representation of Ile in the SequenceWindow on the n-term side, i.e. before the detected peptide sequence. Can you comment on how that is calculated? It might be real, but I was expecting a Leu to be over-represented...

[fcyu]

It just uses the sequence of the assigned protein in the fasta file.

Best,

Fengchao

[pisistrato]

Since it was very strange, I checked the sequences manually, this is what I see

ProteinID	SequenceWindow	Start	SequenceWindowFromFasta	Fasta
A0A8I5KX85	TAPVQAPPAP	148	TAPVQAPPAP	xxxxxMAETEERSLDNFFAKRDKKKKKERSNRAASAAGAAGSAGGSSGAAGAAGGGAGAGTRPGDGGTASAGAAGPGAATKAVTKDEDEWKELEQKEVDYSGLRVQAMQISEKEEDDNEKRQDPGDNWEEGGGGGGGMEKSSGPWNKTAPVQAPPAPVIVTETPEPAMTSGVYRPPGARLTTTRKTPQGPPEIYSDTQFPSLQSTAKHVESRKDKEMEKSFEVVRHKNRGRDEVSKNQALKLQLDNQYAVLENQKSSHSQYNxxxxx
A0A8I5KX85	AIKIQLDNQY	239	ALKLQLDNQY	xxxxxMAETEERSLDNFFAKRDKKKKKERSNRAASAAGAAGSAGGSSGAAGAAGGGAGAGTRPGDGGTASAGAAGPGAATKAVTKDEDEWKELEQKEVDYSGLRVQAMQISEKEEDDNEKRQDPGDNWEEGGGGGGGMEKSSGPWNKTAPVQAPPAPVIVTETPEPAMTSGVYRPPGARLTTTRKTPQGPPEIYSDTQFPSLQSTAKHVESRKDKEMEKSFEVVRHKNRGRDEVSKNQALKLQLDNQYAVLENQKSSHSQYNxxxxx
A0A8I5KX85	NQAIKLQLDN	237	NQALKLQLDN	xxxxxMAETEERSLDNFFAKRDKKKKKERSNRAASAAGAAGSAGGSSGAAGAAGGGAGAGTRPGDGGTASAGAAGPGAATKAVTKDEDEWKELEQKEVDYSGLRVQAMQISEKEEDDNEKRQDPGDNWEEGGGGGGGMEKSSGPWNKTAPVQAPPAPVIVTETPEPAMTSGVYRPPGARLTTTRKTPQGPPEIYSDTQFPSLQSTAKHVESRKDKEMEKSFEVVRHKNRGRDEVSKNQALKLQLDNQYAVLENQKSSHSQYNxxxxx
A0A8I5KX85	FPSIQSTAKH	199	FPSLQSTAKH	xxxxxMAETEERSLDNFFAKRDKKKKKERSNRAASAAGAAGSAGGSSGAAGAAGGGAGAGTRPGDGGTASAGAAGPGAATKAVTKDEDEWKELEQKEVDYSGLRVQAMQISEKEEDDNEKRQDPGDNWEEGGGGGGGMEKSSGPWNKTAPVQAPPAPVIVTETPEPAMTSGVYRPPGARLTTTRKTPQGPPEIYSDTQFPSLQSTAKHVESRKDKEMEKSFEVVRHKNRGRDEVSKNQALKLQLDNQYAVLENQKSSHSQYNxxxxx

The first one is correct, the others are not. FYI, Start refers to the starting positon excluding the xxxxx

[fcyu]

The second one is also correct because there is a peptide ALKLQLDNQY in the protein. We don't distinguish I and L when mapping peptides to proteins because they have the identical mass.

Best,

Fengchao

[pisistrato]

Indeed, ALKLQLDNQY would be right, but FragPipe reports AIKIQLDNQY. To me it seems that all L are converted to I in the fasta file used to create the SequenceWindow.

Case closed :)

On Thu, Jul 18, 2024, 21:59 Fengchao @.***> wrote:

The second one is also correct because there is a peptide ALKLQLDNQY in the protein. We don't distinguish I and L when mapping peptides to proteins because they have the identical mass.

Best,

Fengchao

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[fcyu]

Yes, this is a known bug: https://github.com/Nesvilab/philosopher/issues/430

[fcyu]

Fixed in https://github.com/Nesvilab/philosopher/pull/517

Huge thanks to @hollenstein

Best,

Fengchao