MS/MS index file retrieving error through AWS

[qqwang-berkeley]

Hello,

I have been trying to use the standalone tool to search proteins against the CPTAC proteome datasets, and somehow continued to encounter the following errors:

[1;31m2025-05-29 18:12:41 [ERROR] main.java.pg.S3Interface[download:65] - Error when retrieving MS/MS index file!
[1;31m2025-05-29 18:12:41 [ERROR] main.java.pg.S3Interface[download:65] - Error when retrieving MS/MS index file!
ESC[mcom.amazonaws.services.s3.model.AmazonS3Exception: Forbidden (Service: Amazon S3; Status Code: 403; Error Code: 403 Forbidden;

I tried multiple CPTAC datasets and the results are the same. Are there limitation in access the index files from AWS s3?

Thanks!

Qingqing

[wenbostar]

This is likely due to the download limit described at #84 (comment)

[qqwang-berkeley]

In that case, I would like to follow up on #84's last comment - what would you recommend as an alternative if we need to use Pepquery2 when the download limit is on? Do you suggest we keep a local copy of the ms indexed files?

[wenbostar]

I'm happy to help with building local index. Could you please let me know for which datasets you want to build local index?

Bo

[qqwang-berkeley]

We are trying to use the deep 29 healthy tissue dataset (Project PXD010154 on PRIDE). I saw the instructions of how to index raw files locally using "index" command. The Project PXD010154 has > 1000 raw files. Do you recommend us to download them all and index locally ourselves? Or is there another more efficient way to get these many files indexed for search locally? Thank you!

[stsour]

@wenbostar do you know how long the download limit period is?

[wenbostar]

I'm not sure. @zhiaos may know about this.

[yashanazirbutt]

Is there any copy of ms indexed files elsewhere that can be used?