propogating retention time from .ms2 to .sptxt with spectrast

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Matthew Russell

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Jan 26, 2021, 12:22:08 AMJan 26
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Hi

I am trying to put together a processing pipeline from Waters MSe data to spectrast. I can process data with Waters own tools to generate a spectral library, and then use skyline and blib to convert to .ms2 format. I would like to put that as an input to spectrast to make a .sptxt / .splib file. However, when I do that the retention time information is not carried through to .sptxt file.

Is there a way to propagate retention time into the spectrast data files? I wondered if the retention time is not labelled the way spectrast expects in my .ms2 file. In which case I could fix it with a program like sed. Alternatively I wondered if I used the wrong switch. Any help would be very welcome.

The command line I used was essentially:

spectrast.exe -V -cNmyBaseName mySpectra.ms2

The first spectra in my .ms2 and .sptxt files is below showing the presence and then absence of the retention time information.

######
.ms2:

H CreationDate Mon Jan 18 22:01:43 2021
H Extractor BlibToMs2
H Comment Library D:/Repositories\p20_05_HaloSpecLibPaper_SciData\splib\halo.blib
S 1 1 1278.65
I RTime 84.7206
Z 2 2481.75
D seq AAAANPGSAKAIADLGGAEGALTQAMGR
D modified seq AAAANPGSAKAIADLGGAEGALTQAM[+15.99492]GR
693.35 39.0
822.42 85.0
1006.53 48.0
1209.62 100.0
679.31 36.0
792.40 52.0
863.41 67.0
1049.49 76.0
1031.49 66.0
1120.54 67.0
1103.50 67.0
1330.66 84.0

####
.sptxt:

Name: AAAANPGSAKAIADLGGAEGALTQAM[147]GR/2
LibID: 0
MW: 2557.2908
PrecursorMZ: 1278.6454
Status: Normal
FullName: K.AAAANPGSAKAIADLGGAEGALTQAM[147]GR.L/2 (CID-QTOF)
Comment: AvePrecursorMz=1279.4240 BinaryFileOffset=308 FracUnassigned=0.00,0/5;0.00,0/20;0.00,0/12 Fullname=X.AAAANPGSAKAIADLGGAEGALTQAM[147]GR.X/2 Mods=1/25,M,Oxidation NAA=28 NMC=1 NTT=2 Pep=Tryptic PepContext=1/AGLK_LNVV Prob=1.0000 Protein=1/fig|2745.389.peg.2815 ScanNum=1.1 Spec=CREATE
NumPeaks: 12
679.3100 3600.0 y6/-0.009
693.3500 3900.0 b9-18/0.019,b9-17/-0.965
792.4000 5200.0 y7/-0.003,y17-64^2/0.487
822.4200 8500.0 b10-17/0.010,b10-18/0.994
863.4100 6700.0 y8/-0.030
1006.5300 4800.0 b12-17/-0.002,b12-18/0.982
1031.4900 6600.0 y10-18/-0.004,y10-17/-0.988,y22^2/0.467,b24-44^2/-0.558,b24-45^2/-0.042,b24-46^2/0.450
1049.4900 7600.0 y10/-0.014,b13-45/-0.084
1103.5000 6700.0 y11-17/-0.015,y11-18/0.969
1120.5400 6700.0 y11/-0.002,y24-35^2/1.487
1209.6200 10000.0 b14/-0.002
1330.6600 8400.0 y14-17/0.018

Juergen Bartel

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Feb 22, 2021, 1:27:58 PMFeb 22
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Dear Matthew, did you find a solution for this? I have the exact same question as I also try use a recently generated skyline library in spectraST.
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