propogating retention time from .ms2 to .sptxt with spectrast

[Matthew Russell]

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]

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.