BiblioSpec input and output file formats

BiblioSpec makes use of several file formats for input and output. Below are descriptions of these along with links to additional information

BlibBuild .ssl file

In most cases libraries are built from database search result files. For peptide identificatiosn that do not come from one of the supported database searches, BiblioSpec supports a generic tab-delimited text file format refered to as ssl (spectrum sequence list). Here is a small example file. An ssl file must begin with this header line

 
file	scan	charge	sequence	modifications

Each of the following lines contains information for one spectrum. The first column contains a full or relative path to a file containing the spectrum. The second column has an id for that spectrum, typically a scan number or index number. The third column is the charge state of the spectrum, followed by the peptide sequence. The final column contains the same sequence, this time with the addition of any modifications given as a mass shift (the difference between the modified and unmodified residue). For example,

TASEFDC[+57.0]SAIO[+16.0]AQDK

Known bug: There is currently no way to include the score or search type from this file.

Library files

BiblioSpec library files are in the sqlite3 format. Each library is a small database that you can search and manipulate with standard SQL commands using, for example, the sqlite3 command line tools. BiblioSpec does not require that you know any SQL, but should you be interested in using these files outside of the BiblioSpec context, we give you the schema.

The libraries consist of these tables: LibInfo, RefSpectra, SpectrumSourceFiles, ScoreTypes. Coming soon: the complete schema for each table with a description of each field.

Library as text (MS2)

BlibToMs2 allows you to view the spectra in your library in the .ms2 text format. This format is recongnized by proteowizard's msconvert and can be converted into other formats such as .mzXML.

In an .ms2 file there are four types of lines. Lines beginning with 'H' are header lines and contain information about how the data was collected as well as comments. They appear at the beginning of the file. Lines beginning with 'S' are followed by the scan number and the precursor m/z. Lines beginning with 'Z' give the charge state followed by the mass of the ion at that charge state. Lines beginning with 'D' contain information relevant to the preceeding charge state. BlibToMs2's output will include D-lines with the sequence and modified sequence. The file is arranged with these S, Z and D lines for one spectrum followed by a peak list: a pair of values giving each peaks m/z and intensity. Here is an example file

Report files

BlibSearch writes results to a tab-delimited text file refered to as the report file. The header (lines beginning with '#') contains details of the search parameters. Next is a line naming each of the fields. Subsequent rows summarize one query-library match. The fields are as follows:

• Query The identifier for the query spectrum.
• LibId The number of the library with the match. The header lines will list all libraries being searched and assign each a number referenced in this column.
• LibSpec The identifier for the library spectrum.
• rank The rank of the match for this query spectrum. By default, ranks 1-5 are printed. In case of a tie (two matches with the same score) both matches will be given the same rank.
• dotp The score given to this match (a dot product). Ranges from 0 (poor match) to 1 (two identical spectra).
• query-mz The precursor m/z of the query spectrum.
• query-z The charge of the query spectrum. If there was more than one in the spectrum file, they will be listed separated by comas.
• lib-mz The precursor m/z of the library spectrum.
• lib-z The charge of the library spectrum.
• copies The number of spectra in the redundant library for this same sequence and charge state.
• candidates The number of library spectra the query was compared to.
• sequence The peptide sequence of the library spectrum.

Parameter files

All BibliSpec tools (with the exception of BlibBuild and LibToSqlite3) will accept a parameter file in which additional options can be specified. See each tool's documentation page for the specific options allowed. The file should contain one option per line with the full option name and value separated by an equals sign (=). Here is an example parameter file.