Hello, I'm trying to incorporate Mascot search results into a TPP analysis, but am having great trouble doing so. I'm working with TPP (installed a couple of months ago) on the linux command line but running Mascot (2.5) on a windows server.
When I run the .dat output from Mascot through Mascot2XML I get various errors: First the program reads the amino acid masses and modifications then I get this: *Incomplete file name. No file loaded:* * warning: cannot open "" for reading scan numbers.* then lots of errors of this type: *Warning: could not find scan numbers of spectrum A1.5108.5108.2(intensity=4388884.9462)* *Set to 0000* And finally this: *error writing file /home/mpimp-golm.mpg.de/skeffington/winhome/linux/Pacbio_data1_2017/120718_analysis5/search_stability/converter/Wed_Aug_29_10-57-47_2018.spectrum30.00000.00000.2.dta: Numeric group ID too large* I've tried two methods of generating the mgf input to Mascot: first peak picking with progenesis and export as mgf, and secondy converting the RAW file to mzML with MSconvert and then convering this to a mgf with MzXML2Search. Both times the .dat file exported from Mascot gives the above errors. The .dat file definitely has unix text encoding. Looking at some previous posts issues with this step weren't enough for me to solve it (something to do with scan numbers and title fields...) An example file can be downloaded from here: https://we.tl/t-reBlJEnXAc but I've copy pasted examples of the format of the different sections of the file below in case that's easier. Any help would be very much appreciated! Thanks, Alastair sequences=39303 sequences_after_tax=39303 residues=13344484 distribution=39254,0,1,1,15,8,14,2,4,1,2,1 decoy_type=1 distribution_decoy=39274,0,0,1,8,5,7,3,2,1,2 exec_time=337 date=1535490575 time=23:09:35 queries=80990 min_peaks_for_homology=6 max_hits=50 version=2.5.1 fastafile=D:/inetpub/mascot/sequence/Ehux_JGIbest_NCMC/current/Ehux_JGIbest_NCMC_110817.fasta release=Ehux_JGIbest_NCMC_110817.fasta taskid=153549023801 --gc0p4Jq0M2Yt08jU534c0p Content-Type: application/x-Mascot; name="summary" qmass1=398.226814 qexp1=200.120683,2+ qmatch1=0 qplughole1=0.000000 qmass2=398.226814 qexp2=200.120683,2+ qmatch2=0 qplughole2=0.000000 qmass3=398.226860 qexp3=200.120706,2+ qmatch3=0 qplughole3=0.000000 qmass4=399.221954 qexp4=200.618253,2+ qmatch4=0 qplughole4=0.000000 qmass5=399.222074 qexp5=200.618313,2+ qmatch5=0 qplughole5=0.000000 qmass6=399.222328 qexp6=200.618440,2+ qmatch6=0 ... q20941_p4=2,1060.617508,-0.002194,3,ARMARVTIK,26,00010000000,4.49,0001002000000000000,0,0;"jgi|Emihu1|229675|gm1.15700096":0:180:188:1 q20941_p4_terms=R,H q20941_p4_primary_nl=00020000000 q20941_p5=1,1060.606277,0.009037,4,LNVMLTRAK,42,00001000000,3.59,0000002000000000000,0,0;"jgi|Emihu1|44663|gw1.52.19.1":0:149:157:1 q20941_p5_terms=R,R q20941_p5_primary_nl=00001000000 .... q63508_p1_terms=K,- q63508_p1_primary_nl=000100000000000000000 q63509_p1=-1 q63510_p1=-1 q63511_p1=0,1992.930984,0.017676,9,ETEGMDEVTLGTEANLLR,60,00000100000000000000,7.65,2000002010000000000,0,0;"jgi|Emihu1|463299|estExtDG_fgeneshEH_pg.C_230161":0:45:62:1 q63511_p1_terms=K,M\ ... title=A1%2e48180%2e48180%2e2%20%28intensity%3d1550626%2e6695%29 scans=48180 rtinseconds=4637.902 index=39202 charge=2+ mass_min=66.398610 mass_max=770.192020 int_min=3319 int_max=3.549e+006 num_vals=141 num_used1=-1 Ions1=86.096660:3.549e+006,199.179960:1.199e+006,357.248570:4.584e+005,444.280060:2.021e+005,487.322240:1.532e+005,600.369630:3.986e+005,713.455020:3.884e+004,770.192020:7872,147.112400:4.108e+005,197.127910:2.67e+005,317.216950:1.678e+005,430.301210:8.45e+004,529.345640:1.558e+004,588.369870:1.166e+005,714.459470:9704,72.081130:2.477e+005,215.138400:2.403e+005,358.251280:1.064e+005,426.269350:7.395e+004,550.296200:1.485e+004,601.372070:1.069e+005,673.825260:7357,129.101970:2.476e+005,227.174790:2.282e+005,365.180540:7.352e+004,445.283690:5.422e+004,543.350650:1.115e+004,602.376530:2.686e+004,688.241390:7128,70.065490:2.41e+005,175.118500:1.172e+005,298.174900:4.843e+004,454.265870:1.403e+004,469.551240:7739,74.060400:1.876e+005,260.196080:1.153e+005,308.159150:4.422e+004,452.285550:1.292e+004,502.667720:7425,120.080620:1.568e+005,200.183460:1.14e+005,311.170010:4.379e+004,442.264250:1.148e+004,130.086000:1.566e+005,211.143750:1.035e+005,284.196290:4.02e+004,396.259830:1.11e+004,136.075380:1.516e+005,183.148790:1.027e+005,329.180820:3.99e+004,383.191410:9470,87.100010:1.442e+005,171.112180:9.939e+004,337.186160:3.741e+004,427.275510:8092,66.398610:7476,69.070260:2.981e+004,71.068760:7072,71.847320:6862,73.084510:1.178e+004,84.044650:1.004e+005,84.081050:1.141e+005,87.093630:9692,93.159360:6454,95.283780:7634,100.701740:8448,101.071040:2.914e+004,101.107370:1.525e+004,102.055060:6.669e+004,110.071190:3.968e+004,113.070880:5.693e+004,115.086430:7442,121.083990:1.449e+004,124.039130:1.091e+004,128.682070:6426,129.065540:3.012e+004,131.081120:1.371e+004,131.089710:8456,141.065400:5.452e+004,141.101940:1.45e+004,143.117430:7.816e+004,148.115490:1.053e+004,155.081120:1.101e+004,157.096530:4.699e+004,157.129850:4876,157.133100:3.958e+004,158.092270:9042,159.076220:4.93e+004,159.090820:7016,166.963810:7044,169.096510:1.182e+004,170.116810:6923,171.148670:4.607e+004,177.101940:1.231e+004,184.152160:7317,185.091710:6.211e+004,185.123340:3319,185.127880:3.533e+004,185.164430:1.273e+004,187.071200:9269,189.122920:8.606e+004,199.107360:7783,201.549090:3.6e+004,202.117870:1.31e+004,209.127430:8030,212.102580:7999,213.158710:8006,225.122740:5.26e+004,226.118640:9989,228.133470:4.721e+004,229.154480:1.473e+004,233.091510:1.15e+004,239.174640:9244,240.133970:1.139e+004,242.186170:4.089e+004,243.134110:8297,244.128800:3.847e+004,244.165070:5.539e+004,245.185180:3.016e+004,251.102390:8286,254.149260:1.123e+004,255.143660:6924,270.180480:2.275e+004,273.119570:7401,278.148990:8556,280.164400:3.296e+004,301.187160:8614,306.159450:8586,312.191350:1.242e+004,313.222900:2.622e+004,315.201870:1.506e+004,323.171140:1.431e+004,326.170290:2.886e+004,339.202150:9492,339.238100:3.735e+004,341.181240:2.631e+004,345.224520:9916,391.875700:7250,403.229950:7642,410.580260:7000,438.265170:7058 --gc0p4Jq0M2Yt08jU534c0p Content-Type: application/x-Mascot; name="query10199" title=A1%2e70680%2e70680%2e2%20%28intensity%3d375254%2e7564%29 scans=70680 rtinseconds=6914.338 index=7468 charge=2+ mass_min=63.842020 mass_max=644.440980 int_min=1827 int_max=4.968e+005 num_vals=105 num_used1=-1 Ions1=86.096690:4.968e+005,185.128020:1.034e+005,288.202120:3.243e+004,401.286380:6.386e+004,529.344060:9.373e+004,642.428220:8.514e+004,157.133160:2.682e+005,175.118550:9.25e+004,355.232360:1.979e+004,402.289310:1.288e+004,512.317380:2.341e+004,643.430240:3.278e+004,70.065510:4.716e+004,242.149150:5.654e+004,271.175420:1.637e+004,384.259920:8715,530.346620:1.705e+004,644.440980:2124,120.080800:3.751e+004,235.106700:2.773e+004,268.165340:9687,408.559200:2663,511.335450:1.032e+004,72.081180:3.3e+004,199.179870:2.649e+004,303.947940:6403,366.178410:2520,513.322940:1.02e+004,131.117550:2.633e+004,197.648350:1.781e+004,272.176420:3824,563.330140:8138,158.136580:2.275e+004,227.174800:1.427e+004,303.931000:2849,531.352230:5067,87.100110:1.905e+004,197.636980:1.292e+004,356.237340:2786,494.307340:4680,87.044280:1.535e+004,170.059630:1.177e+004,298.211940:2697,527.353580:2742,158.092240:1.53e+004,214.154650:9927,265.176760:2483,492.291170:2626,63.842020:2005,66.224640:1899,69.070110:2143,73.266720:2197,82.290240:1866,83.052990:2068,84.044690:1.026e+004,84.081000:8933,84.667250:2618,87.093480:2158,92.023680:2293,101.070970:1.013e+004,102.054810:3958,103.413090:2339,110.071080:2344,112.086830:8846,113.070780:2407,115.086500:7391,116.070680:3806,129.102020:1.159e+004,130.064680:2253,130.085600:3336,132.080470:3841,136.075440:3968,143.117680:5118,147.112550:1.107e+004,156.112780:3412,159.091320:1.044e+004,160.095310:2344,171.112260:2262,175.086440:3021,176.122380:5062,183.148970:2888,185.165280:2258,186.131880:8686,197.127960:3542,197.640200:1827,217.097080:3722,224.138460:3149,225.123030:9809,236.110140:3376,243.152860:4158,249.098460:2229,253.189440:2157,255.148860:2580,256.170380:4852,260.195710:4951,261.368990:2484,263.102390:4062,279.784480:2370,294.600830:2052,332.843440:1898,337.220180:2177,340.478580:1972,355.045900:2028,475.631710:2415,491.980320:2140 --gc0p4Jq0M2Yt08jU534c0p Content-Type: application/x-Mascot; name="query10200" .... query72071=2915761 query72072=2915776 query72073=2915791 query72074=2915806 query72075=2915821 query72076=2915836 query72077=2915851 query72078=2915866 query72079=2915881 query72080=2915896 query72081=2915911 query72082=2915926 query72083=2915941 query72084=2915956 query72085=2915971 query72086=2915986 .... -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. 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