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ProteomicsYPIC challenge 2018: A case study in characterizing an unknown protein sample
For the YPIC challenge 2018 contestants were invited to try to decipher two unknown English questions encoded by a synthetic protein expressed in E. coli. We present how we analyzed this unknown sample using a tryptic digest with dynamic exclusion disabled to increase the signal-to-noise ratio of t...
ORGANISM(S): Escherichia coli 
2019-06-11 | PXD014003 | Pride
Spectral clustering Spectral networking Ypic De novo Synthetic protein 
ProteomicsFast open modification spectral library searching through approximate nearest neighbor indexing
Open modification searching (OMS) is a powerful search strategy that identifies peptides carrying any type of modification by allowing a modified spectrum to match against its unmodified variant by using a very wide precursor mass window. A drawback of this strategy, however, is that it leads to a l...
ORGANISM(S): Homo sapiens (Human) Saccharomyces cerevisiae (Baker's yeast) 
2021-05-25 | PXD009861 | Pride
Ptm Open modification searching Spectral library 
ProteomicsExtremely fast and accurate open modification spectral library searching of high-resolution mass spectra using feature hashing and graphics processing units
Open modification searching (OMS) is a powerful search strategy to identify peptides with any type of modification. OMS works by using a very wide precursor mass window to allow modified spectra to match against their unmodified variants, after which the modification types can be inferred from the c...
ORGANISM(S): Homo sapiens (Human) Saccharomyces cerevisiae (Baker's yeast) 
2019-12-06 | PXD013641 | Pride
Proteomics Graphics processing unit Post-translational modification Mass spectrometry Feature hashing Approximate nearest neighbor indexing Spectral library Open modification searching 
MetabolomicsGNPS - NISTfecalRM_Astral_HypersilGoldC18_positive
NIST fecal reference material extracted with 50% MeOH and prepared in different dilutions and reconstitution solvents. The analysis was conducted using a Hypersil Gold (C18) in positive ionization mode on a Astral via different MS-modes (positive ionization mode).
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
2023-11-28 | MSV000093526 | GNPS
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