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ProteomicsTurboRAW2MGF: Removing isobaric-related ions improves the peptide/protein identification
Isobaric labelling technique coupled with high resolution mass spectrometry has been widely employed in the proteomics workflows requiring relative quantification. For each high resolution tandem mass spectrum (MS/MS), it can be used not only to quantify the peptide from different samples by reporte...
ORGANISM(S): Homo sapiens (Human) Rattus norvegicus (Rat) 
2015-01-30 | PXD000994 | Pride
Isobaric labelling Ltq-orbitrap Preprocessing Peptide identification Itraq 
ProteomicsA Collision-induced Dissociation Cleavable Isobaric Tag for Peptide Fragment Ion-based Quantification in Proteomics
Fragment ion-based proteome quantification methods quantify peptides based on unique peptide fragment ions avoiding the issue of ratio distortion that is commonly observed for reporter ion-based quantification approaches. Herein, we present a novel approach that relies on a collision-induced dissoci...
ORGANISM(S): Saccharomyces cerevisiae (Baker's yeast) 
2020-08-17 | PXD018790 | Pride
Isotopic labelling Proteomics Cid cleavable tag Fragment ion-based quantification Isobaric labelling 
ProteomicsCoupling microdroplet-based sample preparation, multiplexed isobaric labeling, and nanoflow peptide fractionation for deep proteome profiling of tissue microenvironment
Existing spatially-resolved proteomics technologies cannot provide deep proteome coverage due to limited sensitivity and poor sample recovery. Herein, we seamlessly combined laser capture microdissection with a low-volume sample processing technology that includes a microfluidic device named microPO...
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
2024-01-25 | MSV000093925 | MassIVE
ProteomicsExtending the Comprehensiveness of Immunopeptidome Analyses Using Isobaric Peptide Labeling
Defining the repertoire of peptides presented by the major histocompatibility complex class I (MHC I) is a key step towards the identification of relevant antigens for cancer immunotherapy. However, the identification of the cancer-specific antigens is a significant analytical challenge in view of t...
ORGANISM(S): Homo sapiens (Human) 
2020-11-16 | PXD017918 | Pride
Tmt Minor antigens Mhc Tumor specific antigens Faims 
UnknownSelective Maleylation-Directed Isobaric Peptide Termini Labeling for Accurate Proteome Quantification.
Not available
S-EPMC7271076 | biostudies-literature
ProteomicsStrain-specific peptide (SSP) standard: A genetically encoded quality control standard for isobaric tagging strategies
Isobaric tag-based sample multiplexing strategies are extensively used for global protein abundance profiling. However, such analyses are often confounded by ratio compression resulting from the co-isolation, co-fragmentation, and co-quantification of co-eluting peptides, termed “interference.” Rece...
ORGANISM(S): Mus musculus (Mouse) 
2021-04-03 | PXD023203 | Pride
Tmtpro16 Faims Eclipse Rts-ms3 Sps-ms3 Founder strains 
UnknownStrain-Specific Peptide (SSP) Interference Reference Sample: A Genetically Encoded Quality Control for Isobaric Tagging Strategies.
Not available
S-EPMC8210951 | biostudies-literature
UnknownLTQ-iQuant: A freely available software pipeline for automated and accurate protein quantification of isobaric tagged peptide data from LTQ instruments.
Not available
S-EPMC3025484 | biostudies-literature
ProteomicsExtensive Peptide Fractionation and y1 Ion-based Interference Detection Enable Accurate Quantification by Isobaric Labeling and Mass Spectrometry
Isobaric labeling quantification by mass spectrometry (MS) has emerged as a powerful technology for multiplexed large-scale protein profiling, but measurement accuracy in complex mixtures is confounded by the interference from co-isolated ions, resulting in ratio compression. Here we report that the...
ORGANISM(S): Escherichia coli 
2022-02-28 | PXD005797 | Pride
Isobaric labeling Proteomics Tmt Mass spectrometry And ratio compression Itraq Lc-ms/ms 
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
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