Sequence contains no elements

[dtabb73]

Hi, all.

I have reproduced a problem when I run the 1.1.8305 release on my test file.

My script for execution looks like this:

"C:\Program Files\Informed-Proteomics-1.1.8305\ProMex.exe" -i 20151116_F_MaD_Ecolik12pool_ACNplate_ET5hcD10_01bis.raw
"C:\Program Files\Informed-Proteomics-1.1.8305\MSPathFinderT.exe" -i 20151116_F_MaD_Ecolik12pool_ACNplate_ET5hcD10_01bis.raw -d uniprot-proteome_UP000000625.fasta -ic 0 -mod IP-PTMs.txt -tda 0

(This RAW file isn't public, but any of the experiments from PXD019247 would probably be a fine replacement for it.)

My IP-PTMs.txt file looks like this:

NumMods=3

# Static
# C2H3NO,C,opt,any,Carbamidomethyl

# Variable
O1,    M, opt, any,         Oxidation
H-2,   C, opt, any,         Disulfide
C2H2O1,*, opt, Prot-N-term, Acetyl

The error output looks like the following: Calculating spectral E-values for target-spectrum matches Estimated matched sequences: 673 Processing, 0 proteins done, 0.0% complete, 1.4 sec elapsed Processing, 54 proteins done, 8.0% complete, 17.2 sec elapsed Processing, 104 proteins done, 15.5% complete, 32.9 sec elapsed Processing, 152 proteins done, 22.6% complete, 48.0 sec elapsed Processing, 195 proteins done, 29.0% complete, 63.0 sec elapsed Processing, 243 proteins done, 36.1% complete, 78.2 sec elapsed Processing, 294 proteins done, 43.7% complete, 94.1 sec elapsed Processing, 341 proteins done, 50.7% complete, 109.4 sec elapsed Processing, 434 proteins done, 64.5% complete, 140.7 sec elapsed Processing, 504 proteins done, 74.9% complete, 170.8 sec elapsed Processing, 572 proteins done, 85.0% complete, 200.8 sec elapsed Processing, 646 proteins done, 96.0% complete, 231.0 sec elapsed Total Progress: 53.33%, 0d 0h 5.00m elapsed, Current Task: Calculating spectral E-values for target-spectrum matches, estimated remaining: 0d 0h 4.37m Target-spectrum match E-value calculation elapsed Time: 262.8 sec

---

Exception while processing: Sequence contains no elements

Stack trace: MSPathFinderT.Program.ProcessFiles InformedProteomics.TopDown.Execution.IcTopDownLauncher.RunSearch InformedProteomics.TopDown.Execution.MzidResultsWriter.WriteResultsToMzid InformedProteomics.TopDown.Execution.MzidResultsWriter.CreateMzidSettings System.Linq.Enumerable.First[TSource]

Exception while processing: Sequence contains no elements Stack trace: MSPathFinderT.Program.ProcessFiles-:-InformedProteomics.TopDown.Execution.IcTopDownLauncher.RunSearch-:-InformedProteomics.TopDown.Execution.MzidResultsWriter.WriteResultsToMzid-:-InformedProteomics.TopDown.Execution.MzidResultsWriter.CreateMzidSettings-:-System.Linq.Enumerable.First[TSource]

[dtabb73]

Upon further investigation, I believe the problem was caused by my adding whitespace in the PTM configuration file IP-PTMs.txt!