Spectrast: peptides with modifications are removed when converting NIST .msp formatted library to .splib.

[Ray]

Hi,

I was trying to convert the NIST consensus human hcd library (.msp format) to splib format with spectrast built from TPP 5.2.

After running the command:

spectrast -cNhuman_hcd human_hcd_tryp_best.msp

The resulting human_hcd.sptxt file contains significantly less spectra (273,137) than the original human_hcd_tryp_best.msp file (398,373). It seems that all peptides with modifications are discarded.

For example, in human_hcd_tryp_best.msp file, there is an entry: AAAAAAVGPGAGGAGSAVPGGAGPCATVSVFPGAR/3_2(0,A,Acetyl)(24,C,CAM)

But there is not such peptide in the output human_hcd.sptxt file. Did I miss some command-line arguments when converting the library?

Thank you.

Ray

[Wenguang]

Hi Ray,

Maybe try with -M option, which allows you to define customized modification types. You can find more details about -M option from SpectraST wiki.

Best,

Wenguang

[Henry Lam]

Ray,

This is because SpectraST does not recognize this way of specifying modification in "new" NIST files.

If you are comfortable compiling your own TPP, try downloading SpectraSTMspLibImporter.cpp from the latest "trunk" version of TPP, replace and re-compile. This should fix the problem. 

Henry

[Henry Lam]

Ray,

Sorry -- you also need to replace:

Peptide.cpp

Peptide.hpp

FileUtils.cpp

FileUtils.hpp

Hopefully that should work. Please let me know if it still doesn't.

Henry