Skip to content

Output format

Jump to bottom Edit New page
Yasset Perez-Riverol edited this page May 17, 2020 · 2 revisions

The output format of LucXor is the following:

specId  peptide	predictedPep1	predictedPep2	numPPS	numRPS	pepProphet	deltaScore	pep1score	pep2score	globalFLR	localFLR
020320_TiO2_Phospho.609.609.2	KSPGSTSR	KsPGSTSR	KSPGsTSR	4	1	0.5414	3.9773	9.7787	5.8014	0.0107	0.0536
020320_TiO2_Phospho.1199.1199.2	KSGLSSR	KsGLSSR	KSGLsSR	3	1	0.7376	5.5098	8.8216	3.3118	0.0027	0.013

Columns Description:

  • specId: The spectrum identifier for the reported scoring PSM in the default output file. This is taken directly from the input pepXML file. This PSM is the most confidently scored PSM for the phospho-permutation associated with it. File Collection (extension is removed) . startScanNumber . endScanNumber . charge

  • peptide: The peptide sequence assigned to this PSM. This sequence will contain no modification information.

  • predictedPep1: The top-scoring LucXor phospho-permutation for this PSM.

  • predictedPep2: The second best scoring LucXor phospho-permutation for this PSM

  • numPSS: Number of Potential Phosphorylation Sites. This is the number of S, T, or Y residues in the peptide sequence that can undergo phosphorylation.

  • numRPS: Number of Reported Phosphorylation Sites. This is the number of S, T, or Y residues in the sequence that are reported to be phosphorylated in the peptide.

  • pepProphet: This is the score assigned to the PSM by the original search engine used to analyze the data. The field title actually varies based upon the parameters used in LucXor. Current possible values are 'pepProphet', 'mascot', 'xtandem', and 'sequest'.

  • deltaScore: The difference in the score between the top two phospho-permutations for the given PSM. This is the value upon which the FLR estimations are based. The larger this value is, the more confident you can be in the correctness of the phospho-permutation reported in the predictedPep_1 field.

  • pep1score: LucXor score of the best prediction

  • pep2score: LucXor score of the second-best prediction

  • globalFLR: Global False Localization Rate. This the global estimated false localization rate for the top-scoring phospho-permutation reported by Luciphor of the given PSM. This FLR is based upon the scores of all the reproted PSMs in the data. This value will be NA for any decoy-matched PSMs.

  • localFLR: Local False Localization Rate. This the local estimated false localization rate for the top-scoring phospho-permutation reported by Luciphor of the given PSM. This FLR is based upon the PSMs with similar delta scores. This value will be NA for any decoy-permutation PSMs.

  • nss: Number of Supporting Spectra. This is the number of PSMs whose top-scoring LucXor phospho-permutation was the same as the string reported in the predictedPep_1 field described above.

Add a custom footer
Add a custom sidebar
Clone this wiki locally