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ProteomicsRescuing discarded spectra: Full comprehensive analysis of a minimal proteome.
A common problem encountered when performing large-scale mass spectrometry proteome analysis is the loss of information due to the high percentage of unassigned spectra. To determine the causes behind this loss we have analyzed the proteome of one of the smallest living bacteria that can be grown ax...
ORGANISM(S): Mycoplasma pneumoniae (strain ATCC 29342 / M129) 
2016-01-05 | PXD002779 | Pride
Translation errors : mass spectroscopy Post-translational modifications (ptms) Protein identification Proteome coverage Unassigned spectra 
ProteomicsA mass-tolerant database search identifies a large proportion of unassigned spectra in shotgun proteomics as modified peptides
Less than half of all MS/MS spectra acquired in shotgun proteomics typically result in a confident peptide match. Here we present an ultra-tolerant Sequest database search that allowed peptide matching even with modifications of unknown masses up to ±500 Da. From an HEK293 cell proteome-wide datas...
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
2016-06-19 | MSV000079841 | MassIVE
UnknownA mass-tolerant database search identifies a large proportion of unassigned spectra in shotgun proteomics as modified peptides.
Not available
S-EPMC4515955 | biostudies-literature
ProteomicsOrganisms with alternative genetic codes resolve unassigned codons via mistranslation and ribosomal rescue
Organisms possessing genetic codes with unassigned codons raise the question of how cellular machinery resolves such codons and how this could impact horizontal gene transfer. Here, we use a genomically recoded Escherichia coli to examine how organisms address translation at unassigned UAG codons, w...
ORGANISM(S): Escherichia coli 
2018-09-18 | PXD009643 | Pride
E coli Lc-ms/ms 
ProteomicsA mass-tolerant database search identifies a large proportion of unassigned spectra in shotgun proteomics as modified peptides
Less than half of all MS/MS spectra acquired in shotgun proteomics typically result in a confident peptide match. Here we present an ultra-tolerant Sequest database search that allowed peptide matching even with modifications of unknown masses up to ±500 Da. From an HEK293 cell proteome-wide datase...
ORGANISM(S): Homo sapiens (Human) 
2015-06-03 | PXD001468 | Pride
Sequest Large scale Modifications Proteomics 
UnknownAutomatic 13C chemical shift reference correction for unassigned protein NMR spectra.
Not available
S-EPMC6209040 | biostudies-literature
UnknownExperimental Protein Structure Verification by Scoring with a Single, Unassigned NMR Spectrum.
Not available
S-EPMC4786943 | biostudies-literature
UnknownDeuterated protein folds obtained directly from unassigned nuclear overhauser effect data.
Not available
S-EPMC4819401 | biostudies-literature
UnknownRapid classification of protein structure models using unassigned backbone RDCs and probability density profile analysis (PDPA).
Not available
S-EPMC2699457 | biostudies-literature
ProteomicsHalf decimal place rule
Many MS2 spectra in bottom-up proteomics experiments remain unassigned. To improve proteome coverage, we applied the half decimal place rule (HDPR) to remove non-peptidic molecules. The HDPR considers the ratio of the first digit after the decimal point to the full molecular mass and results in a re...
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
2017-03-29 | MSV000080727 | MassIVE
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