no html in 2.reports folder

[Markus]

Hello everyone,

I just started using pLink and unfortunately ran into a problem right away.

When I process the example everything works fine. However, when I try my own data pLink processes until the end but does not generate the html report in the 2.reports folder. Instead I am finding three .xls files there: [samplename].complexLink.xls, [samplename].interLink.xls, [samplename].loopLink.xls (most of them empty except for the complexLinks). There is also no subfolder with the samplename but instead a folder named details that carries a couple of .xls files with identified peptides, etc. I processed the same mgf files with another crosslinking software where everything worked fine.

I did not change much in the pLink.ini file and tried to run most of the parameters on default. Obviously I am doing something wrong. Sorry if this is a beginner's mistake but I hope somebody has some suggestions.

Many thanks in advance
Markus

[Shengbo Fan]

Hi,

I guess you may used the Linker SS_0, which is specially designed for disulfide bond identification, and it will not generate 2.report folder, instead, as seen, three xls files. This function is not publicly available now so the user guide haven't contained it. May try to use SS if disulfide bond is needed. See if that will work.

[Markus]

Dear Shengbo Fan,

many thanks for your reply. Unfortunately, I did not use the SS_0 linker but rather the DSS. Below you will find the ini file that I used for processing perhaps that would help to track the problem.

Thanks a lot,
Markus

[pLink]
sample.num=1
sample1.spectra.instrument=HCD
sample1.spectra.format=mgf
sample1.spectra.path=D:\software\plink\bd4z3\
sample1.spectra.title=bd4z3

enzyme.name=Trypsin
database.path=D:\Software\plink\top6proteinIDs.fasta
database.name=top6proteins
max_miss_site=2

mod.fixed.total=1
mod.fixed.1=Carbamidomethyl_C
mod.variable.total=1
mod.variable.1=_Oxidation_M_15.995
mod.variable.2=_Deamidation_NQ_0.984014

linker.total=1
linker.name1=DSS

noninterexport=true
drawpsm=true

# for combinatorial mode peptide_tol_total could only be 1
peptide_tol_total=5
peptide_tol1=50
peptide_tol_type1=ppm
peptide_tol_base1=0.000000
peptide_tol_base_type1=Da
peptide_tol2=50
peptide_tol_type2=ppm
peptide_tol_base2=1.007825035
peptide_tol_base_type2=Da
peptide_tol3=50
peptide_tol_type3=ppm
peptide_tol_base3=2.01565007
peptide_tol_base_type3=Da
peptide_tol4=50
peptide_tol_type4=ppm
peptide_tol_base4=3.023475105
peptide_tol_base_type4=Da
peptide_tol5=50
peptide_tol_type5=ppm
peptide_tol_base5=4.03130014
peptide_tol_base_type5=Da

# -------------------notes----------------------
# type of base is Da
filter_peptide_tol_base=0,1.007825035,2.01565007,3.023475105,4.03130014
filter_peptide_tol_lb=-10,-10,-10,-10,-10
filter_peptide_tol_ub=10,10,10,10,10
filter_peptide_tol_type=ppm
# filter_peptide_tol_base=0
# filter_peptide_tol_lb=-10
# filter_peptide_tol_ub=10
# filter_peptide_tol_type=ppm

evalue_max=1
processor_num=1

# -------------------notes----------------------
# type of report
show_peptide_tol_type=ppm

bin.path=D:\software\plink\pLink_release\

output.path=D:\software\plink\bd4z3\top6\

[Shengbo Fan]

OK I see, thanks for the feedback, this helps us find a bug. This problem is due to recently updates, and the logic is when the linker name contains the "SS", it will use the new flow. And in fact DSS is not disulfide bond.

Would be fixed in the next version. For now, the easiest way is modify the name of DSS, like DS. Modify the xlink.ini and rename DSS to DS, and use linker.name1=DS to search will work.

Sorry for the inconvenience. 

[Markus]

I changed the name as you suggested and now everything works! I am glad I could contribute to find a bug, many thanks for your efforts and this great piece of software!