Instrument index not available for requested device Parameter name: instrumentIndex

Instrument index not available for requested device Parameter name: instrumentIndex malikshagufa93  2023-07-16 17:20


I am trying to build spectral library using peptide atlas raw files dataset but i am facing issues multiple issues with 4 datasets particularly, I have attached the screenshots of the file.
I would like to send the raw files dataset for you to evaluate. Please help me to fix this issue.
Below are the 4 dataset:- PXD003772, PXD030951, PXD010664, PXD008969.

Nick Shulman responded:  2023-07-16 21:19
One user who ran into the error "Instrument index not available for requested device" later told us that it happened because the .raw file was damaged when they downloaded it to their computer.

Where did you download your .raw files from?
I see that I can download the file "Natalia_TMT6_2_240min_1pt5.raw" from here:

I downloaded that file and there did not seem to be anything wrong with that .raw file.
I would recommend that you try downloading that file again and see if the file that you downloaded the second time is identical to the file that you downloaded the first time.
-- Nick
malikshagufa93 responded:  2023-07-16 21:26

 I have downloaded those files separately on my computer and have verified the files but the error is still the same.
Nick Shulman responded:  2023-07-16 21:34
Can you send us your files?
We would like you to send us your Skyline document, some of your .raw files, and the FASTA file that you provided to the "File > Import > Peptide Search" wizard.

In Skyline, you can use the menu item:
File > Share
to create a .zip file containing your Skyline document.

You can upload that .zip file, your .raw file(s) and your FASTA file here:

Your Skyline document is probably empty because you were trying to do "File > Import > Peptide Search" into an empty document, but it will still be useful for us to see that document because it will tell us some things about your settings and the version of Skyline that you are using.
-- Nick
Nick Shulman responded:  2023-07-18 22:01
Thank you for uploading those .raw files.
I am able to reproduce the error that you are hitting.

The file which caused problems for me was "Natalia_TMT6_240m_1.raw".
In the screenshot that you posted, "PXD003772 EROOR.png", you can see that it successfully finished searching "Natalia_TMT6_2_240min_1pt5.raw".

The error "Instrument index not available..." happens when it tries to read the next file in the list of files that you told it to search, which was probably "Natalia_TMT6_240m_1.raw".

I believe the file "Natalia_TMT6_240m_1.raw" is completely unreadable. My guess is that the authors of the paper did not upload the entire file to the FTP site. That file is probably supposed to be twice as big as it actually is, and it is impossible to get any data out of that file.

I would recommend contacting the authors of the paper and asking if they have a version of that file which is not corrupted.
-- Nick