Hi. I wonder why deltaCn values from out file and from peptideprophet shtml are different. I observed the following:
1. when the best hit and the second best hit in a out file are very similar (identical sequence except PTM), shtml DeltaCn is calculated with reference to the third best hit. example> in some out file #1 P.C*HCCA.P deltCn=0.0000 #2 P.CHCC*A.P deltCn=0.0046 #3 R.HC*CCA.E deltCn=0.0558 then, deltaCn in shtml is 0.0558. 2. when the second best and the third best hit are very similar, shtml DeltaCn is calculated with the next best hit. example> #1 r.fqspagtealfe...@isvadsan@YSC*VYVDLKPPFGGSAPSER.L deltCn=0.0000 #2 c.eecgkafnqstnltrhkrihtaekpykceecgkafnh...@.l deltCn=0.0028 #3 c.eecgkafnqstnltrhkrihtaekpykceecgk...@hpxn.l deltCn=0.0220 #4 Q.KFPKPLPQEYQYFDELSGIPAEDLPYYGGSVEIADYC*PFS.Q deltCn=0.1644 then, deltaCn in shtml is 0.1644. 3. there is no sequence homology from the best hit to a reference hit, but shtml DeltaCn is calculated with the reference hit. example> #1 e.qgxtdymgads...@ikr.k deltCn=0.0000 #2 L.LC*ELLYESEFDSQLW.I deltCn=0.0296 #3 a.ekic*eytytdie...@g.k deltCn=0.0417 then, deltaCn in shtml is 0.0417. 4. when there are very small number of hits, shtml DeltaCn is calculated with some not-shown hit. example> #1 I.LAXXXYEGLKEFZBCB.Z deltCn=0.0000 #2 B.ZAQLSLM#QLYLTNKSD.N deltCn=0.3882 The out file has only these two hits. then, deltaCn in shtml is 1. What is the rules for calculating shtml DeltaCn? --~--~---------~--~----~------------~-------~--~----~ You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To post to this group, send email to spctools-discuss@googlegroups.com To unsubscribe from this group, send email to spctools-discuss+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en -~----------~----~----~----~------~----~------~--~---
