Classes for reading and writing spectral libraries

Mascot 2.6 and later support searching spectral libraries in parallel with a FASTA database.

See: Spectral library search on the Matrix Science public web site for an overview.

For help on reading spectral library results from Mascot Results files, see Spectral libraries

The classes described in this section are used for reading, parsing and writing spectral library files. These classes are not used for performing the library search, which is done by third party tools.

ms_spectral_lib_file is used to open and read a spectral library. The third parameter is used to specify whether to use and create an index file which will improve performance with searching for particular spectra within the library. See ms_spectral_lib_file::findEntries for details of how to lookup entries in the library.

When a spectral library is added to Mascot Server for searching, it converts the library to the NIST format using: ms_spectral_lib_file::saveAs function. It also sets the replaceProteinName parameter to 'true'. Mascot Server saves the spectrum peaklist checksum in results files so that the findEntries function can be used to lookup the spectrum reliably.

ms_spectral_lib_file::getEntryFromNumber can be used to return one ms_spectral_lib_entry object

Supported Spectral Library Formats

Mascot Parser Supports the following formats:

The NIST MSP format

The National Institute of Standards and Technology, NIST in the United States provides a number of libraries to be used with their search tool, MSPepSearch. They provide libraries in a binary format, and also in a text 'MSP' format. Mascot Parser can read and write libraries in MSP format. The format is documented here.

PRIDE files are essentially .msp files, but without any peak annotation. When the file is saved in NIST format, a "?" is added as peak annotation otherwise MSPepSearch can fail to find matches.

The ISB SpectraST format

These files typically have a .sptxt extension. The format is slightly different from the NIST MSP format. There are some details here.

The Name field can include a modification delta, for example: Name: K.AADQADESSPLLS[167]PS[167]NSNHPSEHPQQDLNNK.S/4
The PeakList entries are a slightly different format.
The line specifying the number of peaks is Num peaks: in an MSP file, but NumPeaks: in a SpectraST file.
There are normally comment lines at the top of the file.

X! Hunter Annotated Spectrum Library (ASL)

The format is described here

These files are converted to NIST MSP format before being submitted to MSPepSearch.