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UnknownPeptide-Spectrum Match Validation with Internal Standards (P-VIS): Internally-Controlled Validation of Mass Spectrometry-Based Peptide Identifications.
Not available
S-EPMC7775876 | biostudies-literature
ProteomicsP-VIS: internally-controlled validation of mass spectrometry-based peptide identifications
Peptide-Spectrum Match (PSM) Validation with Internal Standards (P-VIS) is an objective approach to validating individual PSMs. A biological sample is analyzed by LC-MS/MS and the data are searched using a traditional approach such as a database search or de novo sequencing. A PSM of interest is ide...
ORGANISM(S): Homo sapiens (Human) Mus musculus (Mouse) 
2020-09-21 | PXD020901 | Pride
Peptidomics Hybrid insulin peptides Peptide-spectrum match Post-translational modification Validation Immunotherapy Peptide splicing Immunopeptidomics 
UnknownImproving quantitation accuracy in isobaric-labeling mass spectrometry experiments with spectral library searching and feature-based peptide-spectrum match filter.
Not available
S-EPMC10465558 | biostudies-literature
UnknownA peptide-spectrum scoring system based on ion alignment, intensity, and pair probabilities.
Not available
S-EPMC4117239 | biostudies-literature
TranscriptomicsIntegration of next-generation sequencing and proteomics data: application to the discovery of new coding events in the human spermatozoa
Proteomics and transcriptomics data were integrated in order to identify hard-to-reach uncharacterized proteins which are known to be particularly numerous in human spermatozoa. MS-identifications were launched both against UniprotKB and translated predicted ORF databases generated from four differe...
ORGANISM(S): Homo sapiens 
2025-12-30 | E-MTAB-11518 | biostudies-arrayexpress
UnknownAIRPred: A Deep Learning Model Predictor for Peptide Intensity Ratios in Cross-Linking Mass Spectrometry Improves Cross-Link Spectrum Matching.
Not available
S-EPMC12658862 | biostudies-literature
ProteomicsEstimating the Contribution of Proteasomal Spliced Peptides to the HLA-I Ligandome
Spliced peptides are short protein fragments spliced together in the proteasome by peptide bond formation. True estimation of the contribution of proteasome-spliced peptides (PSPs) to the global Human Leukocyte Antigen (HLA) ligandome is critical. A recent study suggested that PSPs contribute up to ...
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
2020-11-13 | MSV000086452 | MassIVE
ProteomicsEstimating the Contribution of Proteasomal Spliced Peptides to the HLA-I Ligandome
Spliced peptides are short protein fragments spliced together in the proteasome by peptide bond formation. True estimation of the contribution of proteasome-spliced peptides (PSPs) to the global Human Leukocyte Antigen (HLA) ligandome is critical. A recent study suggested that PSPs contribute up to ...
ORGANISM(S): Homo sapiens (Human) 
2018-09-03 | PXD010793 | Pride
Lc-msms Immunopeptidomics Proteasomal splicing Hla-i peptides 
ProteomicsJUMPg: an Integrative Proteogenomics Pipeline Identifying Unannotated Proteins in Human Brain and Cancer Cells
Proteogenomics is an emerging approach to improve gene annotation and interpretation of proteomics data. Here we present JUMPg, an integrative proteogenomics pipeline including customized database construction, tag-based database search, peptide-spectrum match filtering, and data visualization. JUMP...
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
2017-03-16 | MSV000080641 | MassIVE
ProteomicsAccurately Assigning Peptides to Spectra When Only a Subset of Peptides Are Relevant
The standard proteomics database search strategy involves searching spectra against a peptide database and estimating the false discovery rate (FDR) of the resulting set of peptide-spectrum matches. One assumption of this protocol is that all the peptides in the database are reDR control strategies ...
ORGANISM(S): Ricinus communis Homo sapiens (Human) Saccharomyces cerevisiae (Baker's yeast) 
2021-06-17 | PXD022778 | Pride
Ups1 Ricin Yeast Castor Human 
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