TPP SpectraST Failed to open input file

[Nikita Boeren]

Dear All,

I have been setting up the TPP workflow and encountered an issue for which I ask your help. 

When using SpectraST to combine all spectra to generate a spectral library, I observe an error in my output, namely: "Failed to open input file ... mzXML"

What I find remarkable is that it only says something about mzXML files, while my centroid input files are mzML. Also, I performed every step in the same directory and all files are present in this folder, as not to encouter this issue that it cannot locate my input files (otherwise I get Failed to open input files for all extensions: mzML, mzXML, mzML.gz mzXML.gz). Despite this remark in the output lines, it adds spectra to the generated library, and it finished without error.

I have attached screen shots of the command prompt and of the created output files from SpectraST (no empty files are created). 

Some additional information:

- Comet search on mzML files is performed via Petunia GUI

- Workflow after search: PeptideProphet, iProphet, Mayu for cutoff score, then to SpectraST

- CMD is run as admin

- TPP version 5.2.0

Can someone explain to me why this is happening and how to fix/continue? Why does it say it fails to open input files?

Thanks in advance!

Nikita Boeren

[David Shteynberg]

Hi Nikita,

I think that message is somewhat misleading.  I recently looked at the code because I had a similar question.  The fact is that spectrast looks for all types of datatypes of files supported by the RAMP parser interface it uses.  It asks the parsers for all filetypes it can read (starting with mzXML) and tried reading them all one by one until it can find a file it can read.  When it cannot find the file of the filetype it is currently trying it prints this error and tries the next type of file (it tries mzXML, mzML, mzXML.gz, mzML.gz, and mz5 in this order) , it will print a message for each datatype it tries and fails on and another one Spectrast will report as an actual error if it cannot read any of them.  Since mzML is more widely used at this point, we will change the code to start by checking the mzML files first so you will not see this message in the future when you have mzML files.  For you, this message can be safely ignored since the mzML files are readable and you have a message from Spectrast at the bottom that it finished without error.

Thanks for using the TPP and asking your analysis questions here.  Let us know if you have any other concerns.

Cheers,

-David

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