Tab-delimited input for Luciphor 2

Luciphor2 is capable of scoring PSMs derived from any search engine so long as the data follows this tab-delimited syntax:

srcFile scanNum charge PSMscore peptide modSites

Each field is tab-separated. One row per Peptide-to-Spectrum Match (PSM). Descriptions of what each field is follows along with an example of what a valid value might look like.

  • srcFile: This is the name of the file that contains the spectrum indicated on this row.
    Example:phospho_sample_1.mzML
  • scanNum: This is the scan number of the spectrum to read in from the spectrum file. This value must be an integer. Example:12345
  • charge: The charge state of the PSM. This value must be an integer.
    Example:3
  • PSMscore: This is the search engine score assigned to the PSM. This can be a result from any of the popular search engines (MASCOT, SEQUEST, X!Tandem, Comet, etc..).
    Be aware that some types of search engine scores are scaled by luciphor2 prior to use. For instance: Expect values (common to X!Tandem or Comet) are converted to -log(expect) internally by Luciphor2.
    If you want to use your score 'as is', keep the SELECTION_METHOD field in the input file set to 0.
    Example:103.908
  • peptide: This is the amino acid sequence of the PSM. It must consist only of the 20 letters that make up the amino acid alphabet.
    Example:ELVISTCLESK
  • modSites: This is a string that indicates what variable modifications go on what residues of the peptide.
    The syntax is: pos=mass_of_modified_AA
    Multiple modifications on the same peptide are comma separated.
    No spaces are allowed.
    The first residue in a peptide is position 0 and the rest increment from there.
    For N-terminal or C-terminal modifications use -100 or 100 respectively for the value of 'pos' and then list the mass shift of the terminal modification.

    Example:
    Pretend the modified peptide sequence is: n42-ELVIST[181]CLES[167]K
    This peptide has an N-terminal acetylation event and two phosphorylations.
    The correct modSite syntax for this peptide is: -100=42.001,5=181.014,9=166.9983

    Here is a sample of what a correctly written input file might look like: 
    srcFile	scanNum	charge	PSMscore	peptide	modSites
ppeptidemix1_CID_Orbi.mgf	1975	2	0.0	AAVLQR	-100=42.010565
ppeptidemix1_CID_Orbi.mgf	1448	2	0.0	TICHCR	2=160.030649,4=160.030649
ppeptidemix1_CID_Orbi.mgf	1422	2	0.0	TICHCR	2=160.030649,4=160.030649
ppeptidemix1_CID_Orbi.mgf	1428	2	0.0	TLTFER	2=181.01401
ppeptidemix1_CID_Orbi.mgf	1416	2	0.0	TICHCR	2=160.030649,4=160.030649
ppeptidemix1_CID_Orbi.mgf	1434	2	0.0	TLTFER	2=181.01401
ppeptidemix1_CID_Orbi.mgf	1847	2	0.0	LTVIKAK	1=181.01401
ppeptidemix1_CID_Orbi.mgf	1585	2	0.0019	MADQLLR	0=147.0354
ppeptidemix1_CID_Orbi.mgf	2036	2	0.6504	TSPLNFK	0=181.01401
ppeptidemix1_CID_Orbi.mgf	2019	2	0.6568	TSPLNFK	0=181.01401
ppeptidemix1_CID_Orbi.mgf	2030	2	0.7434	TSPLNFK	0=181.01401
ppeptidemix1_CID_Orbi.mgf	2041	2	0.656	TSPLNFK	0=181.01401
ppeptidemix1_CID_Orbi.mgf	2014	2	0.8305	TQIGPYK	0=181.01401
ppeptidemix1_CID_Orbi.mgf	2024	2	0.621	TSPLNFK	0=181.01401
ppeptidemix1_CID_Orbi.mgf	1431	2	0.0	TTSSSTR	3=166.998359,4=166.998359
ppeptidemix1_CID_Orbi.mgf	1425	2	0.0037	TSSSTTR	4=181.01401,5=181.01401
ppeptidemix1_CID_Orbi.mgf	1260	2	0.0	VPEPGSIK	5=166.998359
ppeptidemix1_CID_Orbi.mgf	2034	2	0.0	YELYSR	3=243.02966
ppeptidemix1_CID_Orbi.mgf	2022	2	0.0281	SEPAGDVR	0=166.998359
ppeptidemix1_CID_Orbi.mgf	2671	2	0.0	RKKLMPK	4=147.0354
ppeptidemix1_CID_Orbi.mgf	3251	2	0.0	RKRSYK	3=166.998359
ppeptidemix1_CID_Orbi.mgf	3537	2	0.0	KRRYSK	4=166.998359
ppeptidemix1_CID_Orbi.mgf	3105	2	0.2703	LLKKLMR	5=147.0354
ppeptidemix1_CID_Orbi.mgf	3014	2	0.0	GKGPLMSSS	8=166.998359
ppeptidemix1_CID_Orbi.mgf	2434	2	0.0	KCIGVAATK	1=160.030649
ppeptidemix1_CID_Orbi.mgf	1649	2	0.0016	ALMSAPTPR	2=147.0354
ppeptidemix1_CID_Orbi.mgf	1809	2	0.1522	YSLTVAVK	1=166.998359
ppeptidemix1_CID_Orbi.mgf	1803	2	0.7919	YSLTVAVK	0=243.02966
ppeptidemix1_CID_Orbi.mgf	1823	2	0.4559	YSLTVAVK	0=243.02966
ppeptidemix1_CID_Orbi.mgf	1732	2	0.9993	YSLTVAVK	0=243.02966