BiblioSpec makes use of several file formats for input and output. Below are descriptions of these along with links to additional information.
In most cases libraries are built from database search result files. Supported formats are listed on the BlibBuild page.
For peptide or small molecule identifications 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 end with the '.ssl' extension and have a header line with the following column names in it (the score-type, score, and retention-time columns are optional):
file scan charge sequence score-type score retention-time
additional columns for small molecule use may be included (the sequence column should be omitted for small molecule libraries - here is a small example file):
adduct chemicalformula moleculename inchikey otherkeys
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 (e.g. vendor formats like .raw, .wiff, etc. or .ms2, .mzML, .mzXML, .mgf). 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.
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. The fourth column contains the peptide sequence, with the addition of any modifications given as a mass shift (the difference between the modified and unmodified residue) following the modified residues. For example,
Peptides with n-terminal modifications should have these mass shift follow the first residue.
The score-type column can be any of the following:
PEPTIDE PROPHET SOMETHING
MASCOT IONS SCORE
TANDEM EXPECTATION VALUE
PROTEIN PILOT CONFIDENCE
WATERS MSE PEPTIDE SCORE
OMSSA EXPECTATION SCORE
PROTEIN PROSPECTOR EXPECTATION SCORE
and the score column is a floating point value representing the spectrum's score of that type. The retention time column can be used to specify retention times in minutes; otherwise the values from the spectrum file will be used. Scores fall into three categories: probability that identification is correct, probability that identification is incorrect, or not a probability score. This information can be found in the ScoreTypes table.
BiblioSpec library files are in the sqlite3 format, usually with a ".blib" filename extension. Each library is a small database that you can search and manipulate with standard SQL commands using, for example, the sqlite3 command line tools or SQLite Expert Personal.
Details on the BiblioSpec SQLite schema can be found here.