Issues when running Scout

[alessiodiianni]

Hi, I am trying to test your new software on an already published BSA dataset cross-linked with DSBU (Ihling et al. 2021, Anal. Chem.). After changing the settings and selecting the .mgf file and the .fasta file, I get this error message:

###################################################
Scout - v. 1.4.10
Engineered by Clasen et al. - LPEC / Brazil & The Liu Lab / Germany
###################################################
Starting run at C:\Users\MS_data\DSBU.
Database: BSA.fasta.
=============
Search parameters:
=============
Database file: BSA.fasta
Fasta batch size: 30000
Raw directory: C:\Users\MS_data\DSBU
Spectra saved in the results: False
Add contaminants: True
Add decoys: True
Fragment bin tolarance: 0.02
Fragment bin tolarance: 0
Max fragment bin m/z: 1800
Min fragment bin m/z: 200
Deconvolution for MS Searching: False
Deconvolution for Ion Pair Searching: True
Cross-linker: DSBU
Mass: 196.0848
Target N-term: True
Light fragment: 85.05276381
Heavy fragment: 111.03202835
Reaction residue(s): K
Enzyme: Trypsin
Enzyme specificity: FullySpecific
Isotopic possibilities precursor: 1
Min peptide length: 6
Max peptide length: 60
Max variable modifications per peptide: 2
Min peptide mass: 500
Max peptide mass: 6000
Max miscleavages: 3
Ppm error on MS1 level: 10
Ppm error on MS2 level: 20
Static Modification(s):
1)  Name: Carbamidomethyl
Mass: 57.02146
Target residues: C
N-term: False
C-term: False
Variable Modification(s):
1)  Name: Oxidation of Methionine
Mass: 15.9949
Target residues: M
N-term: False
C-term: False
===================
Post processing parameters:
===================
Use only unique XLs into PPIs: False
Separate protein intra- and inter-crosslinks: True
FDR:
CSM level: 0.01
Residue pair level: 0.01
PPI level: 0.01
===============
INFO: Starting search...
===============
ERROR: It's not possible to read C:\Users\MS_data\DSBU\BSA_DSBU25_1.mgf
ERROR - PerformSearch method: It's not possible to assemble the search pack.
at ScoutCore.QueryLogic.SearchPackFactory.AssembleSearchPack(String rawFile	ScoutParameters parameters)
at ScoutCore.PSMEngines.Tripper.Tripper.PerformSearch(String fastaFile	String rawFile)
Input string was not in a correct format.

ERROR - SearchFile method: It's not possible to perform search with the file: C:\Users\MS_data\DSBU\BSA_DSBU25_1.mgf. at ScoutCore.PSMEngines.Tripper.Tripper.PerformSearch(String fastaFile | String rawFile) |   |   |   |   |   |   |   |   |   |   |   at ScoutCore.ScoutEngine.SearchFile(String rawFile | String fastaFile) |   |   |   |   |   |   |   |   |   |   |   at ScoutCore.QueryLogic.SearchPackFactory.AssembleSearchPack(String rawFile | ScoutParameters parameters) |   |   |   |   |   |   |   |   |   |   at ScoutCore.PSMEngines.Tripper.Tripper.PerformSearch(String fastaFile | String rawFile) |   |   |   |   |   |   |   |   |   |   |   Input string was not in a correct format.

My PC has 20 logical cores and 32 GB RAM. Could you help me out with this??

[diogobor]

Hello,

The issue happened when Scout tried to read the mgf file. This file contains a different pattern for precursor mass. We fixed the mgf reader, and we will release a new version of Scout soon.

Meanwhile, you can use the Bruker Raw file (.d) to perform your search.

Best, Diogo

[alessiodiianni]

I tried to use also the .d file Bruker folder but it gives me similar troublesOn Jan 30, 2024, at 18:32, Diogo Borges @.***> wrote: Hello, The issue happened when Scout tried to read the mgf file. This file contains a different pattern for precursor mass. We fixed the mgf reader, and we will release a new version of Scout soon. Meanwhile, you can use the Bruker Raw file (.d) to perform your search. Best, Diogo

—Reply to this email directly, view it on GitHub, or unsubscribe.You are receiving this because you authored the thread.Message ID: @.***>

[diogobor]

Hello, Ok. We fixed this issue for Bruker files (and mgf). The next version will be released soon.

Best, Diogo