Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Template-based assembly of proteomic short reads for de novo antibody sequencing and repertoire profiling

ABSTRACT: We developed a software package STITCH (https://github.com/snijderlab/stitch) to perform template-based assembly of de novo peptide reads from antibody samples. As a test case we generated de novo peptide reads from protein G purified whole IgG from COVID-19 patients.

INSTRUMENT(S): Orbitrap Fusion

ORGANISM(S): Homo Sapiens (human)

SUBMITTER: Joost Snijder

LAB HEAD: Joost Snijder

PROVIDER: PXD031941 | Pride | 2022-07-21

REPOSITORIES: pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	20200515_F1_Ag6_Peng0013_SA_IgG_14_chymo.raw	Raw
	20200515_F1_Ag6_Peng0013_SA_IgG_14_ela.raw	Raw
	20200515_F1_Ag6_Peng0013_SA_IgG_14_thermo.raw	Raw
	20200515_F1_Ag6_Peng0013_SA_IgG_14_tryp.raw	Raw
	20200515_F1_Ag6_Peng0013_SA_IgG_21_chymo.raw	Raw

Items per page:

1 - 5 of 10

Similar Datasets

MS-based sequencing of the anti-FLAG-M2 antibody

Project description:We demonstrate a method for direct de novo sequencing of monoclonal IgG from the purified antibody products. The method uses a panel of multiple complementary proteases to generate suitable peptides for de novo sequencing by LC-MS/MS in a bottom-up fashion. Furthermore, we apply a dual fragmentation scheme, using both stepped high-energy collision dissociation (stepped HCD) and electron transfer high-energy collision dissociation (EThcD) on all peptide precursors. The method achieves full sequence coverage of the monoclonal antibody Herceptin, with an accuracy of 98% in the variable regions. We applied the method to sequence the widely used anti-FLAG-M2 mouse monoclonal antibody, which we successfully validated by remodeling a high-resolution crystal structure of the Fab and demonstrating binding to a FLAG-tagged target protein in Western blot analysis. The method thus offers robust and reliable sequences of monoclonal antibodies.

2021-01-11 | PXD023419 | Pride

Sequencing the anti-MUC1 hybridoma antibody 139H2

Project description:Mucin 1 (MUC1) is a transmembrane mucin expressed at the apical surface of epithelial cells at different mucosal surfaces including breast and intestine. The MUC1 extracellular domain contains a variable number of tandem repeats (VNTR) of 20 amino acids, which are heavily O-linked glycosylated. Monoclonal antibodies against the MUC1 VNTR can be powerful tools because of their multiplicity of binding and possible applications in the diagnosis and treatment of MUC1-expressing cancers. One such antibody is the hybridoma mouse monoclonal 139H2 which is also widely used as a research tool to study non-cancer MUC1. Here we report direct mass spectrometry-based sequencing of hybridoma-derived 139H2 IgG, which enabled reverse engineering of a recombinant 139H2.

2024-03-18 | PXD043489 | Pride

Glycoproteomics profiling of recombinant SARS-CoV-2 stabilized Spike construct

Project description:N-linked glycans of recombinant SARS-CoV-2 Spike protein with stabilizing mutations were profiled by LC-MS/MS.

2021-07-28 | PXD025554 | Pride

Glycan shield of the ebolavirus envelope glycoprotein GP

Project description:The envelope glycoprotein GP of the ebolaviruses is essential for host cell attachment and entry. It is also the primary target of the protective and neutralizing antibody response in both natural infection and vaccination. GP is heavily glycosylated with up to 17 predicted N-linked sites, numerous O-linked glycans in its disordered mucin-like domain (MLD), and three predicted C-linked mannosylation sites. Glycosylation of GP is important for host cell attachment to cell-surface lectins, as well as GP stability and fusion activity. Moreover, it has been shown to shield GP from neutralizing activity of serum antibodies. Here, we use mass spectrometry-based glycoproteomics to profile the site-specific glycosylation patterns of ebolavirus GP, including N-, O-, and C-linked glycans.

2022-08-02 | PXD031459 | Pride

Quick and clean: Cracking E.coli’s code by LC-MS/MS, de novo sequencing, and dictionary search

Project description:In this study, we faced the challenge of deciphering a protein that has been designed and expressed by E.coli in such a way that the amino acid sequence encodes two concatenated English sentences. The sequence carried unknown modifications and cannot be found online. The letters ‘O’ and ‘U’ are both replaced by ‘K’ in the protein. To solve the challenge, we developped a workflow consisting of shotgun proteomics, de novo sequencing and a bioinformatic tool to search for words from the identified sequences. By using this workflow, we assembled the first complete English sentence and validated by searching against a customized sequence database.

2020-05-26 | PXD012015 | Pride

RNA-seq of 36 individuals with autism spectrum disorder

Project description:To assess the clinical impact of splice-altering noncoding mutations in autism spectrum disorder (ASD), we used a deep learning framework (SpliceAI) to predict the splice-altering potential of de novo mutations in 3,953 individuals with ASD from the Simons Simplex Collection. To validate these predictions, we selected 36 individuals that harbored predicted de-novo cryptic splice mutations; each individual represented the only case of autism within their immediate family. We obtained peripheral blood-derived lymphoblastoid cell lines (LCLs) and performed high-depth mRNA sequencing (approximately 350 million 150 bp single-end reads per sample). We used OLego to align the reads against a reference created from hg19 by substituting de novo variants of each individual with the corresponding alternate allele.

2018-11-25 | E-MTAB-7351 | biostudies-arrayexpress

Catharanthus Transcriptome and Gene Expression

Project description:In this study, we aim to present a global transcriptome analysis of medicinal plant, Catharanthus roseus. We generated about 343 million high-quality reads from three tissues (leaf, root and flower) using Illumina platform. We performed an optimized de novo assembly of the reads and estimated transcript abundance in different tissue samples. The transcriptome dynamics was studied by differential gene expression analyses among tissue samples. We collected different tissue samples from the mature plants. Total RNA isolated from these tissue samples was subjected to Illumina sequencing. The sequence data was further filtered using NGS QC Toolkit to obtain high-quality reads. The filtered reads were used for de novo assembly optimization. The reads were further mapped to the Catharanthus transcripts via CLC Genomics Workbench and differential gene expression analysis was performed using DESeq software.

2014-07-29 | E-GEOD-57326 | biostudies-arrayexpress

RNA-seq experiment of the amoeboflagellate Orciraptor agilis feeding on Mougeotia sp.

Project description:In this study transcriptomic data of three life history stages of Orciraptor agilis was generated: 1) Gliding cells in absence of food ('gliding'), 2) Cells attached to the cell wall of its algal prey during perforation ('fattacking'), 3) Cells after acquisition of the algal plastid material ('digesting'). Furthermore, RNA-seq of the algal prey Mougeotia sp. was also performed. A de novo transcriptome assembly of the algal reads was performed in order to identify and substract algal reads of the Orciraptor samples by mapping the Orciraptor reads to the algal transcriptome. After this filtering step the remaining Orciraptor reads from all libraries were pooled for a de novo transcriptome assembly of Orciraptor agilis. This transcriptome was the basis for a comparative transcriptomic study in which transcript expression was compared between the three life history stages.

2022-06-13 | E-MTAB-11291 | biostudies-arrayexpress

De novo assembly of siRNA immunity in wild plants

Project description:We describe an application of deep sequencing and de novo assembly of short RNA reads to investigate small interfering (si)RNAs mediated immunity in leaf samples from eight tree taxa naturally occurring in Wytham Woods, Oxfordshire, UK. BLAST search for homologues of contigs in the GenBank identified siRNA populations against a number of RNA viruses and a Ty1-copia retrotransposons in these tree species. Small RNA sequencing and de novo assembly

2012-06-01 | E-GEOD-22079 | biostudies-arrayexpress

RNA sequencing of 10 Aegilops tauschii accessions

Project description:To generate novel genetic markers, we performed RNA sequencing of 10 accessions of Ae. tauschii. Transcripts were deduced from de novo assembly of short reads for each accession.

2016-05-11 | E-MTAB-5071 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data