Problems to run Andromeda
349 views
Skip to first unread message
Alex
Jul 8, 2011, 11:23:03 AM7/8/11
to Andromeda Help
Hello everyone,
i got a problem to run the Andromeda-Application from my PC, without
geting an error.
When i load the Apar-/Apl-File and run Andromeda i get the following
message:
"GetProteinSet ended unexpected [...]"
My Apar-File looks like this:
protease=Trypsin/P
variable modifications=Oxidation (M),Acetyl (Protein N-term)
fixed modifications=Carbamidomethyl (C)
label modifications=;Arg10,Lys8
peptide mass tolerance=6
max combinations=512
peptide mass tolerance Unit=ppm
fragment mass tolerance=0.5
fragment mass tolerance Unit=Da
top peaks=6
max missed cleavages=2
fasta file="O:\NG4\programs\Spectral_Tools\Andromeda
\ipi.HUMAN.v3.68.fasta"
randomize=False
include contaminants=True
include water=True
include ammonia=True
dependent losses=True
special aas=KR
fragment all=False
higher charges=True
fragmentation type=CID
My Apl-File looks like this:
peaklist start
mz=318.194816248815
fragmentation=CID
charge=1
header=RawFile: 20070522_NH_Orbi2_HelaEpo_01.raw Index: 11289 _iso_
124.08831 240.9049
133.15234 886.8938
145.89978 258.8192
155.07605 744.2031
177.24826 1331.983
199.05032 1048.418
207.16418 341.4998
221.12369 1043.664
272.23712 773.4581
273.19226 631.176
282.30661 2449.862
283.27881 1466.312
290.29871 459.1101
350.35056 44.0538
353.08893 105.7582
371.49704 189.9874
389.40836 67.9984
415.37045 346.268
416.34976 98.6677
459.44257 646.9711
460.61075 87.73492
468.40329 68.68661
502.40927 30.98646
503.48285 395.6319
505.68625 28.63757
518.4632 11.84873
526.2218 23.73791
563.49554 25.1901
peaklist end
peaklist start
mz=349.183025197284
fragmentation=CID
charge=1
header=RawFile: 20070522_NH_Orbi2_HelaEpo_01.raw Index: 2787 _iso_
156.97345 199.5383
175.22302 310.0417
178.05371 91.77128
185.15698 204.5205
203.21915 213.2872
231.23459 156.8409
238.47775 154.2045
246.27255 308.486
248.75189 859.7328
303.00885 310.2423
306.39355 425.3981
311.48547 296.0198
312.44006 517.1763
319.74982 258.5357
375.50949 213.1348
378.31946 251.5619
382.73965 412.0713
383.55136 843.53
392.5679 152.4134
430.9534 263.0809
453.6774 144.2338
484.54584 241.0981
496.55289 519.6778
505.94101 91.39008
519.5459 282.4577
520.5127 73.6552
582.63116 26.47505
597.46246 23.34732
606.36932 23.98016
608.47906 34.28849
624.60907 42.8191
634.61591 24.38491
652.17731 22.15483
667.61267 107.9327
672.86938 14.04181
706.44641 12.69905
peaklist end
[...]
is there anybody who got an idea, how i can handle that error message?
Thanks and Greetings,
Alex
i got a problem to run the Andromeda-Application from my PC, without
geting an error.
When i load the Apar-/Apl-File and run Andromeda i get the following
message:
"GetProteinSet ended unexpected [...]"
My Apar-File looks like this:
protease=Trypsin/P
variable modifications=Oxidation (M),Acetyl (Protein N-term)
fixed modifications=Carbamidomethyl (C)
label modifications=;Arg10,Lys8
peptide mass tolerance=6
max combinations=512
peptide mass tolerance Unit=ppm
fragment mass tolerance=0.5
fragment mass tolerance Unit=Da
top peaks=6
max missed cleavages=2
fasta file="O:\NG4\programs\Spectral_Tools\Andromeda
\ipi.HUMAN.v3.68.fasta"
randomize=False
include contaminants=True
include water=True
include ammonia=True
dependent losses=True
special aas=KR
fragment all=False
higher charges=True
fragmentation type=CID
My Apl-File looks like this:
peaklist start
mz=318.194816248815
fragmentation=CID
charge=1
header=RawFile: 20070522_NH_Orbi2_HelaEpo_01.raw Index: 11289 _iso_
124.08831 240.9049
133.15234 886.8938
145.89978 258.8192
155.07605 744.2031
177.24826 1331.983
199.05032 1048.418
207.16418 341.4998
221.12369 1043.664
272.23712 773.4581
273.19226 631.176
282.30661 2449.862
283.27881 1466.312
290.29871 459.1101
350.35056 44.0538
353.08893 105.7582
371.49704 189.9874
389.40836 67.9984
415.37045 346.268
416.34976 98.6677
459.44257 646.9711
460.61075 87.73492
468.40329 68.68661
502.40927 30.98646
503.48285 395.6319
505.68625 28.63757
518.4632 11.84873
526.2218 23.73791
563.49554 25.1901
peaklist end
peaklist start
mz=349.183025197284
fragmentation=CID
charge=1
header=RawFile: 20070522_NH_Orbi2_HelaEpo_01.raw Index: 2787 _iso_
156.97345 199.5383
175.22302 310.0417
178.05371 91.77128
185.15698 204.5205
203.21915 213.2872
231.23459 156.8409
238.47775 154.2045
246.27255 308.486
248.75189 859.7328
303.00885 310.2423
306.39355 425.3981
311.48547 296.0198
312.44006 517.1763
319.74982 258.5357
375.50949 213.1348
378.31946 251.5619
382.73965 412.0713
383.55136 843.53
392.5679 152.4134
430.9534 263.0809
453.6774 144.2338
484.54584 241.0981
496.55289 519.6778
505.94101 91.39008
519.5459 282.4577
520.5127 73.6552
582.63116 26.47505
597.46246 23.34732
606.36932 23.98016
608.47906 34.28849
624.60907 42.8191
634.61591 24.38491
652.17731 22.15483
667.61267 107.9327
672.86938 14.04181
706.44641 12.69905
peaklist end
[...]
is there anybody who got an idea, how i can handle that error message?
Thanks and Greetings,
Alex
J. Cox
Jul 9, 2011, 7:00:36 AM7/9/11
to androme...@googlegroups.com
You might try to remove the 'search' folder once. This is containing the indices for the search. It could be that it contains corrupted files for some reason.
Reply all
Reply to author
Forward
0 new messages