Navigating peptideSieve Tips/Tricks?

[sophie culos]

Hello,

I am trying to use peptideSieve for an in silico digestion to identify proteotypic peptides for MALDI.

I've attached a screenshot of what I've been inputting into the command line and the error I've been consistently getting. The output file is always blank,  and I'm not sure how to proceed.

Any help would be very much appreciated!

Cheers,

Sophie

[Luis Mendoza]

Hello Sophie,

I don't have much help to offer at this point, since we have not used that software in a very long time.  But one thing I notice from your screenshots is that the folder/directory name appears to have a space in "MS User", which is not present in the commands, e.g. "C:\Users\msuser\TPP\...".  Perhaps this is causing the errors you observe?

Cheers,

--Luis

--
You received this message because you are subscribed to the Google Groups "spctools-discuss" group.
To unsubscribe from this group and stop receiving emails from it, send an email to spctools-discu...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/spctools-discuss/3017c88a-3ac5-4c9d-a8f1-34e9da686575n%40googlegroups.com.

[David Shteynberg]

For what it is worth, yesterday I downloaded the PeptideSieve and ran it on my system commandline to generate non-empty output files successfully.  I used '/' in my path definitions, but I am not sure it that makes a difference.  Good luck!

To view this discussion on the web visit https://groups.google.com/d/msgid/spctools-discuss/CACyS9brV76SC0pD2K8wNwvB8xkf1dGwM2%2BCc-kgDWeOxTb89uw%40mail.gmail.com.

[sophie culos]

David, would you be at all willing to post the code that you were using? I'll give "/" a shot in my path definitions.

[David Shteynberg]

Sure!  This was my command:

To view this discussion on the web visit https://groups.google.com/d/msgid/spctools-discuss/9523f77b-7758-42fd-98fc-5211c0b255c8n%40googlegroups.com.

[sophie culos]

Thank you David, I got an error when I attempted something similar but it may have helped me narrow down what the problem could be. 

I have a few more questions, if that's alright? . Please excuse any misuse of nomenclature, I have very little computer science experience :)

- where your PeptideSieve.exe is located - is it in the bin?

- How is your FASTA file formatted and where is it located? Earlier errors had issue reading the file and I've been trying getting rid of the header etc. (picture attached)

- Where is your properties.txt located and are you using any of the supplementary materials? I'm hoping to use the MALDI supplementary material, and have it saved in the initial peptideSieve directory as "properties.txt" and "MALDI.txt" (and have tried using both without success)

I am very open to any and all suggestions about how to format/organize files correctly.

Cheers!

[David Shteynberg]

Yes! I am doing everything in the bin directory for the test to make it easier to specify paths.

My fasta file just looks like this.  Definition lines must start with ">" and precede the sequence data lines as so:

Running everything from the bin over commandline as follows:

Results are in TEST:

I hope this helps!

-David

To view this discussion on the web visit https://groups.google.com/d/msgid/spctools-discuss/30080cb3-19d5-4e2b-b923-02f632c16fd9n%40googlegroups.com.