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I'm trying to replicate the figure given in this paper using this table which they have given.

Figure 5

So what i understand from the figure is they have calculated the zscore between two condition and plotted the same.

Now How is the length of each bar which is the peptide here is variable is it the zscore or the actual peptide length?

Small subset of the data

dput(head(d2))
structure(list(Peptide = structure(1:6, .Label = c("AAHLPAEFTPAVH", 
"AAHLPAEFTPAVHASLD", "AAWGKVG", "AEFTPAVHA", "AEFTPAVHASLDKFLASVSTVLTSKYR", 
"AFSDGLAH", "AFSDGLAHLD", "AFSDGLAHLDNLK", "AGEYG", "AHAGEYG", 
"AHAGEYGAEALE", "AHAGEYGAEALERMF", "AHAGEYGAEALERMFLSFPTTK", 
"AHGKKVLG", "AHLDNLK", "AHLPAEFTPAVH", "AHLPAEFTPAVHASLD", "AHLPAEFTPAVHASLDKF", 
"AHVDDMPNA", "AHVDDMPNALS", "ALSDLH", "ALWGKVNVDEVG", "ALWGKVNVDEVGGEA", 
"ALWGKVNVDEVGGEALG", "ALWGKVNVDEVGGEALGRLL", "ANALAHKYH", "ASLDKF", 
"ASLDKFLA", "ASLDKFLASVS", "ASLDKFLASVSTVLT", "ASLDKFLASVSTVLTS", 
"ASLDKFLASVSTVLTSKYR", "ATLS", "AVAHVDD", "AVAHVDDMPN", "AVAHVDDMPNA", 
"AVAHVDDMPNAL", "AVAHVDDMPNALS", "AVAHVDDMPNALSA", "AYQKVVAGVANALAHK", 
"DALT", "DALTN", "DDMPNA", "DDMPNALS", "DEVG", "DEVGGEA", "DEVGGEALG", 
"DEVGGEALGRLL", "DGLA", "DGLAH", "DGLAHLD", "DGLAHLDNLK", "DKLHVD", 
"DKLHVDPEN", "DKLHVDPENF", "DKLHVDPENFR", "DKLHVDPENFRL", "DKLHVDPENFRLL", 
"DKLHVDPENFRLLG", "DKTNVK", "DLH", "DLS", "DLSTPD", "DLSTPDA", 
"DMPNALS", "DPENF", "DPENFR", "DPVNF", "DPVNFK", "EFTPAVH", "EFTPAVHASLD", 
"EFTPAVHASLDKFLASVSTVLTSKYR", "EFTPPVQ", "EFTPPVQA", "EFTPPVQAA", 
"ESFG", "ESFGDL", "ESFGDLSTPDAVM", "ESFGDLSTPDAVMG", "EVGG", 
"EVGGEALG", "FDLS", "FESF", "FESFG", "FESFGDLS", "FESFGDLSTPDAVMGNPKVK", 
"FGDL", "FGDLS", "FPHF", "FPHFD", "FPHFDL", "FPHFDLS", "FPT", 
"FPTT", "FPTTKT", "FPTTKTY", "FPTTKTYFPHF", "FSDGLA", "FSDGLAH", 
"FSDGLAHLD", "FSDGLAHLDNLK", "FTPAVH", "FTPAVHASLD", "FTPAVHASLDKFLASVSTVLT", 
"FTPPVQ", "FTPPVQA", "FTPPVQAA", "GAFSDGLA", "GAFSDGLAH", "GAFSDGLAHLDNLK", 
"GEALG", "GEYG", "GGEAL", "GKKVL", "GKKVLG", "GKVNVD", "GKVNVDE", 
"GKVNVDEVG", "GKVNVDEVGGEA", "GKVNVDEVGGEAL", "GKVNVDEVGGEALG", 
"GKVNVDEVGGEALGRL", "GKVNVDEVGGEALGRLL", "GLAHLDNLK", "GNPKV", 
"GNPKVK", "GNVL", "GRLL", "GTFAT", "GVANALAHKYH", "HAGEYG", "HAGEYGAEALE", 
"HAGEYGAEALERMF", "HFDLS", "HHFG", "HKYH", "HLD", "HLDNLK", "HLPAE", 
"HLPAEF", "HLPAEFTPAVH", "HLPAEFTPAVHASLD", "HLTPEEK", "HVDD", 
"HVDDMP", "HVDDMPN", "HVDDMPNA", "HVDDMPNAL", "HVDDMPNALS", "HVDDMPNALSA", 
"HVDDMPNALSALS", "HVDP", "HVDPEN", "HVDPENF", "HVDPENFR", "HVDPENFRL", 
"HVDPENFRLLG", "KAAWGKVG", "KEFTPPVQ", "KEFTPPVQA", "KEFTPPVQAA", 
"KEFTPPVQAAYQ", "KLHVDPENFRLLG", "KTYFP", "KTYFPH", "KTYFPHF", 
"KTYFPHFD", "KVNVDEVGG", "KVNVDEVGGEA", "KVNVDEVGGEALG", "LDNL", 
"LDNLK", "LGAFSDGLA", "LHVDP", "LHVDPENF", "LHVDPENFRLLG", "LKGTFATL", 
"LLVVYPWTQRF", "LPAE", "LPAEF", "LPAEFTPAVH", "LPAEFTPAVHASLD", 
"LPAEFTPAVHASLDK", "LPAEFTPAVHASLDKF", "LSALS", "LSFPTTK", "LSFPTTKT", 
"LSFPTTKTY", "LSFPTTKTYFPHF", "LSFPTTKTYFPHFDL", "LSFPTTKTYFPHFDLS", 
"LSFPTTKTYFPHFDLSHG", "LSTPDA", "LTPEEK", "LTPEEKSAVT", "LTPEEKSAVTA", 
"LTPEEKSAVTAL", "LTPEEKSAVTALW", "LTPEEKSAVTALWG", "LTPEEKSAVTALWGKVNVD", 
"LTPEEKSAVTALWGKVNVDEVG", "LTPEEKSAVTALWGKVNVDEVGGEA", "LTPEEKSAVTALWGKVNVDEVGGEALG", 
"LVVYPWTQRF", "LVVYPWTQRFF", "LWGKVNVDEVGGEALG", "NAVAHVDD", 
"NAVAHVDDMPNA", "NAVAHVDDMPNAL", "NAVAHVDDMPNALS", "NAVAHVDDMPNALSA", 
"NAVAHVDDMPNALSALS", "NAVAHVDDMPNALSALSDL", "NAVAHVDDMPNALSALSDLHAHKLR", 
"NVDEVG", "NVDEVGG", "NVDEVGGEA", "NVDEVGGEALG", "PADKTNVK", 
"PAEF", "PAEFTPAVH", "PAEFTPAVHASLD", "PAVH", "PDAV", "PDAVM", 
"PDAVMG", "PEE", "PEEK", "PEEKSAVT", "PEEKSAVTAL", "PENF", "PENFR", 
"PENFRLLG", "PHF", "PHFD", "PHFDL", "PHFDLS", "PKVK", "PNAL", 
"PNALS", "PPVQ", "PPVQA", "PPVQAA", "PVNF", "PVNFK", "PVQ", "PVQA", 
"PWTQ", "PWTQRF", "PWTQRFF", "QVKGHGKKVADALTN", "RVDPVNF", "SDGLA", 
"SDGLAHLDN", "SDGLAHLDNLK", "SDLH", "SFGD", "SFGDL", "SFGDLS", 
"SFGDLSTPDAVMG", "SLDKF", "SPADK", "SPADKTNVK", "SVSTVLT", "TKTYFPHF", 
"TNVK", "TPAVH", "TPAVHASLD", "TPAVHASLDKFLASVSTVLT", "TPDAVM", 
"TPDAVMG", "TPDAVMGNPKVK", "TPEEKSAVT", "TPEEKSAVTAL", "TPEEKSAVTALW", 
"TPPVQ", "TSKY", "TVLT", "TYFP", "TYFPH", "TYFPHF", "TYFPHFD", 
"TYFPHFDLS", "VAHVDD", "VAHVDDMPNA", "VAHVDDMPNALS", "VAHVDDMPNALSA", 
"VDDMP", "VDDMPN", "VDDMPNA", "VDDMPNAL", "VDDMPNALS", "VDEVG", 
"VDEVGG", "VDEVGGEA", "VDEVGGEALG", "VDPENF", "VDPENFR", "VDPENFRL", 
"VDPENFRLL", "VDPENFRLLG", "VDPVN", "VDPVNF", "VDPVNFK", "VDPVNFKL", 
"VDPVNFKLL", "VDPVNFKLLS", "VHL", "VHLT", "VHLTP", "VHLTPE", 
"VHLTPEE", "VHLTPEEK", "VHLTPEEKSAVT", "VHLTPEEKSAVTAL", "VHLTPEEKSAVTALWGKVNVD", 
"VHLTPEEKSAVTALWGKVNVDE", "VHLTPEEKSAVTALWGKVNVDEVG", "VHLTPEEKSAVTALWGKVNVDEVGGEA", 
"VHLTPEEKSAVTALWGKVNVDEVGGEALG", "VHLTPEEKSAVTALWGKVNVDEVGGEALGRLL", 
"VKAAWGKVGAHAGEY", "VLSP", "VLSPA", "VLSPAD", "VLSPADK", "VLSPADKT", 
"VLSPADKTN", "VLSPADKTNVK", "VLSPADKTNVKAA", "VLSPADKTNVKAAWGKVG", 
"VNVDE", "VNVDEVG", "VNVDEVGG", "VNVDEVGGEA", "VNVDEVGGEAL", 
"VNVDEVGGEALG", "VNVDEVGGEALGRL", "VVAGVANALA", "VVYPWTQRF", 
"VVYPWTQRFF", "VVYPWTQRFFE", "VVYPWTQRFFESFGDLS", "VYPWTQRF", 
"VYPWTQRFF", "VYPWTQRFFE", "WGKVG", "WGKVNVD", "WGKVNVDE", "WGKVNVDEVG", 
"WGKVNVDEVGGEA", "WGKVNVDEVGGEAL", "WGKVNVDEVGGEALG", "WGKVNVDEVGGEALGRL", 
"WGKVNVDEVGGEALGRLL", "YFPHFDLS", "YPWT", "YPWTQ", "YPWTQR", 
"YPWTQRF", "YPWTQRFF", "YPWTQRFFE"), class = "factor"), C2 = c(-1.13005927266738, 
-1.15451123584162, -0.771975424114207, -0.891503793435265, 0.686928914375861, 
-1.15469327326147), C4 = c(0.770515719059141, 0.559148858503814, 
1.12965461223673, 1.08129555353272, 0.46033682419062, 0.58089396147208
), C6 = c(0.359543553608241, 0.595362377337809, -0.357679188122518, 
-0.18979176009746, -1.14726573856648, 0.573799311789392)), row.names = c(NA, 
6L), class = "data.frame")

Any suggestion or help would be really appreciated

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1 Answer 1

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The length of the bars and their placement on the x-axis represents the length of the peptide and mapping to the source protein, respectively. The coloring represents the average difference in peptide MS intensity between the control and two experiments.

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  • $\begingroup$ so i need the length information isnt it which is not given in that paper .. $\endgroup$
    – kcm
    Nov 17, 2021 at 11:11
  • $\begingroup$ it can be done using ggplot i mean mapping the length of the peptide? $\endgroup$
    – kcm
    Nov 17, 2021 at 11:15
  • 1
    $\begingroup$ Maybe I am not following your question, but you get the peptide lengths from the peptides sequences. What you are missing from the table you link to is the source protein sequences, HBb and Hba. The placement of the peptide in the source protein is your x value of the bars, and the length of the peptide is the height of the bar. $\endgroup$
    – birey
    Nov 17, 2021 at 12:56
  • $\begingroup$ "What you are missing from the table you link to is the source protein sequences, HBb and Hba." yes this one . "The placement of the peptide in the source protein is your x value of the bars, and the length of the peptide is the height of the bar." color mapping is the zscore which i do have .. $\endgroup$
    – kcm
    Nov 17, 2021 at 13:41

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