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ProteomicsEnzyme and Chemical Assisted N-Terminal Blocked Peptides Analysis, ENCHANT, as a Selective Proteomics Approach Complementary to Conventional Shotgun Approach
Shotgun (bottom-up) approach has been widely applied in large-scale proteomics studies. The inherent shortages of shotgun approach lie in that the generated peptides often overwhelm the analytical capacity of current LC-MS/MS systems and that abundant proteins often hamper the identification of prot...
ORGANISM(S): Homo sapiens (Human) 
2017-11-30 | PXD007863 | Pride
Dia Single-charge ion inclusion N-terminal blocked peptides Cnbr-activated sepharose 4b 
ProteomicsN-terminal COFRADIC on cytosolic proteins of HEK293T cells - UniProt search
N-terminal proteoforms stem from the same gene but differ at their N-terminus, and most of these are found to be truncated, though some are N-terminally extended caused by ribosomes starting translation from codons in the annotated 5’UTR, and/or carry modified N-termini different from those of the c...
ORGANISM(S): Homo sapiens (Human) 
2023-06-08 | PXD039392 | Pride
Cytosol Hek293t cells N-terminal peptides 3 proteases Cofradic Atis Lc-ms/ms 
ProteomicsMetabolic regulation of N-terminal acetylation in yeast
N-terminal (Nt) acetylation, catalyzed by N-terminal acetyltransferases (NATs), has emerged as an important co-translational modification in eukaryotes, and involves the transfer of the acetyl moiety from acetyl-CoA (Ac-CoA) to the α-amino group of a nascent polypeptide. Here, we report the first gl...
ORGANISM(S): Saccharomyces cerevisiae (Baker's yeast) 
2018-09-07 | PXD004326 | Pride
Metabolism Acetyl coenzyme a Saccharomyces cerevisiae N-terminal acetylation N-terminomics 
ProteomicsPositional proteomics reveals differences in N-terminal proteoform stability.
To understand the impact of alternative translation initiation on a proteome, we performed the first large-scale study of protein turnover rates in which we distinguish between N-terminal proteoforms pointing to translation initiation events. Using pulsed SILAC combined with N-terminal COFRADIC we m...
ORGANISM(S): Homo sapiens (Human) 
2013-03-14 | PXD002091 | Pride
Nt-acetylation Protein stability Alternative translation initiation Initiator methionine processing Protein turnover N-terminal proteoform Human N-terminal cofradic 
ProteomicsAn OMICS perspective on N-terminal Methionine Excision
Excision of the N-terminal initiator methionine (iMet) from nascent peptide chains is an essential and omnipresent protein modification carried out by Methionine aminopetidases (MetAPs) and accounting for a major source of N-terminal proteoform diversity. While MetAP2 is known to be implicated in pr...
ORGANISM(S): Homo sapiens (Human) 
2018-01-10 | PXD006638 | Pride
Metap Metap1 Shotgun N-terminal proteomics Imet excision 
ProteomicsN-terminomics Proteogenomics - N-terminal proteomics assisted profiling of the unexplored translation initiation landscape in Arabidopsis thaliana
Proteogenomics is a research field where proteome data is used to improve gene annotation. To achieve this, customized protein databases are constructed to match proteomic data. We perform a proteogenomic analysis using N-terminal COFRADIC data in order to identify novel translational initiation sta...
ORGANISM(S): Arabidopsis thaliana (Mouse-ear cress) 
2017-04-24 | PXD004896 | Pride
Arabidopsis thaliana Proteogenomics N-terminal cofradic Ribosome profiling Positional proteomics Ribo-seq 
ProteomicsN-terminal COFRADIC on cytosolic proteins of HEK293T cells
Ribosome profiling revealed translation outside of canonical coding sequences (CDSs) including translation of short upstream open-reading frames (ORFs), long non-coding RNAs, ORFs in UTRs or ORFs in alternative reading frames. Ribo-seq but also bioinformatics-based prediction and RNA-sequencing repo...
ORGANISM(S): Homo sapiens (Human) 
2022-07-12 | PXD030601 | Pride
Cytosol Hek293t cells N-terminal peptides 3 proteases Cofradic Atis Lc-ms/ms 
ProteomicsArabidopsis thaliana N-terminal proteome,LC-MS
An extended ChaFRADIC workflow was applied to analyze the N-terminal proteome of Arabidopsis thaliana seedlings. Using iTRAQ protein labeling, a multi-enzyme digestion approach including trypsin, GluC, and subtilisin, a total of 200 μg per enzyme were used, and only 1/3 of each ChaFRADIC-enriched fr...
ORGANISM(S): Arabidopsis thaliana (Mouse-ear cress) 
2015-07-21 | PXD001855 | Pride
Arabidopsis thaliana Chafradic Itraq reagent Enrichment of n-terminal peptide 
ProteomicsChaFRADIC: A novel SCX-based approach for N-terminal Enrichment
Step 1: Cell lysis of yeast sphaeroblast (Saccharomyces cerevisiae) and carbamidomethylation. Step 2: Isotopic labeling with dimethylation (light + medium). Step 3: Proteolytic digestion with trypsin (ArgC specificity because of blocked lysines by dimethylation). Step 4: Enrichment via ChaFRADIC...
ORGANISM(S): Saccharomyces cerevisiae (Baker's yeast) 
2013-08-09 | PXD000292 | Pride
Chafradic Yeast Protease Peptidase Icp55 Cofradic N-terminal Degradomics 
ProteomicsImpact of NatC on N-terminal acetylome
The impact of NatC subunits NAA30, NAA35 and NAA38 on the human N-terminal acetylome. Analysis of HAP1 WT, NAA30 KO, NAA35 KO and NAA38 KO cells
ORGANISM(S): Homo sapiens (Human) 
2023-09-13 | PXD034992 | Pride
Lc-ms/ms Hap cells Natc Scx N-terminal enrichment 
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