Ursgal Results

The main Ursgal result file format is a comma separated value file (CSV). This is a table format that can be easily viewed and further processed. In general, each row contains a PSM and each column contains distinct properties of that PSM. The number of columns can vary depending on the engines (unodes) that have been run, but the most unified columns and other common columns are briefly described here.

Raw data location

Location and file name of the file (.mgf or .mzML) that contains the MS information leading to the identification of the PSM

Spectrum ID

ID of the mass spectrum leading to the identification of the PSM

Spectrum Title

Information about the spectrum leading to the identification of the PSM in the format ‘<file_name>.<spectrum_id>.<spectrum_id>.<charge>’

Retention Time (s)

Retention time corresponding to the mass spectrum leading to the identification of the PSM

Sequence

Peptide sequence matched to the spectrum

Protein ID

Protein ID corresponding to the peptide sequence matched to the spectrum. If multiple Protein IDs correspond to the same peptide sequence, they are separated by ‘<|>’

Sequence Start

Start of the peptide sequence in the corresponding protein sequence. Counting starts at 1 (not 0). Multiple start points are separated by ‘;’ and start points of multiple corresponding proteins are separated by ‘<|>’

Sequence Stop

Stop of the peptide sequence in the corresponding protein sequence. Multiple stop points are separated by ‘;’ and stop points of multiple corresponding proteins are separated by ‘<|>’

Sequence Pre AA

Amino acid before the start of the peptide sequence in the corresponding protein sequence. If a pre aa does not exist (start of the protein), this is indicated by ‘-‘. Multiple pre aa are separated by ‘;’ and pre aa of multiple corresponding proteins are separated by ‘<|>’

Sequence Post AA

Amino acid after the end of the peptide sequence in the corresponding protein sequence. If a post aa does not exist (end of the protein), this is indicated by ‘-‘. Multiple post aa are separated by ‘;’ and post aa of multiple corresponding proteins are separated by ‘<|>’

Charge

Charge of the (precursor) ion leading to the identification of the PSM.

Exp m/z

Experimental m/z of the (precursor) ion leading to the identification of the PSM.

uCalc m/z

Theoretical m/z of the peptide (including modifications) calculated by Ursgal. This can vary from the ‘Calc m/z’ which is reported by the engine corresponding to the PSM.

uCalc mass

Theoretical mass of the peptide (including modifications) calculated by Ursgal.

Accuracy (ppm)

Accuracy of the PSM based on the ‘uCalc m/z’ and ‘Exp m/z’

Modifications

Modifications of the peptide sequence given in the following format: ‘<modification_name>:<position>’ The modification name is given as PSI-MS name, the position corresponds to the position of the modification in the peptide. Position 0 corresponds to N-terminal modifications, position peptide_length+1 corresponds to C-terminal modifications. Multiple modifications within the same peptide sequence are separated by ‘;’

Mass Difference

Mass Difference (between the matched peptide and the precursor mass) as reported by open modification search engines. Multiple modifications within the same peptide sequence are separated by ‘;’

Mass Difference Annotations

Annotations of mass differences as reported by engines processing mass differences from open modification search engines. Multiple annotations within the same peptide sequence are separated by ‘;’

Complies search criteria

True or False, indicating if any conflicts with specified search parameters were identified. Conflicts are repoted in the column ‘Conflicting uparam’

Enzyme Specificity

Indicated whether the matched peptide sequence originated from full enzymatic cleavage, semienzymatic cleave or nonspecific cleavage.

Is decoy

True or False, indicating whether the protein sequence corresponding to the PSM is a decoy sequence.

PEP

Posterior error probability of the PSM as determined by engines performing statistical post-processing.

q-value

q-value of the PSM as determined by engines performing statistical post-processing.

combined PEP

Combined PEP reported by the combined PEP approach used to combine results from multiple search engines. The basis for the combined PEP is the Bayes PEP which is calculated from the PEPs of each PSM reported by individual search engines.

Search Engine

Indicates which engine(s) reported the PSM.