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ProteomicsDe novo sequencing of antibody light chain proteoforms from patients with multiple myeloma
In multiple myeloma diseases, monoclonal immunoglobulin light chains (LCs) are abundantly produced, with as a consequence in some cases the formation of deposits affecting various organs, such as kidney, while in other cases to remain soluble up to concentrations of several g.L-1 in plasma. The exac...
ORGANISM(S): Homo sapiens (Human) 
2021-08-11 | PXD025884 | Pride
Proteoforms Top-down proteomics Antibody Bottom-up proteomics De novo sequencing Light chain disease 
ProteomicsTemplate-based assembly of proteomic short reads for de novo antibody sequencing and repertoire profiling
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.
ORGANISM(S): Homo sapiens (Human) 
2022-07-21 | PXD031941 | Pride
De novo  antibody  serum 
TranscriptomicsDe Novo Transcriptomic Analysis of Hydrogen Production in the Green Alga Chlamydomonas moewusii through RNA-Seq
Background: Microalgae can make a significant contribution towards meeting global renewable energy needs in both lipid-based liquid biofuel and hydrogen biofuel. The development of energy-related products and chemicals from algae could be accelerated with improvements in systems biology tools, and r...
ORGANISM(S): Chlamydomonas moewusii 
2013-09-04 | E-GEOD-46225 | biostudies-arrayexpress
ProteomicsMS-based sequencing of the anti-FLAG-M2 antibody
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...
ORGANISM(S): Homo sapiens (Human) Mus musculus (Mouse) 
2021-01-11 | PXD023419 | Pride
Antibody Stepped hcd Ethcd De novo sequencing 
ProteomicsDeep Coverage and Extended Sequence Reads Obtained with a Single Archaeal Protease Expedite de novo Protein Sequencing by Mass Spectrometry
Label-free protein sequencing is critically enabled by bottom-up, mass spectrometry-based proteomics workflows. Applications such as antibody sequencing or antigen discovery require de novo reconstruction of peptide and protein sequences. While trypsin has long served as the gold-standard protease i...
ORGANISM(S): Homo sapiens (Human) 
2026-03-17 | PXD063988 | Pride
Hta-proteases Hybrid fragmentation by eacid De novo antibody sequencing Bottom-up proteomics 
ProteomicsDe Novo Sequencing of Polyclonal Antibodies by Integrating Intact Mass, Top-Down and Bottom-Up Mass Spectrometry
Antibodies are specialized proteins produced by the adaptive immune system to identify and neutralize harmful antigens. Antibody-based diagnostics and therapeutics have advanced rapidly, with recombinant antibodies derived from monoclonal antibodies (mAbs) becoming the preferred standard due to thei...
ORGANISM(S): Homo sapiens (Human) 
2025-10-31 | PXD063526 | Pride
Intact mass De novo sequencing Top-down Bottom-up Polyclonal antibody sequencing 
ProteomicsMonoclonal antibody LC-MS/MS - Precision de novo peptide sequencing using mirror proteases of Ac-LysargiNase and trypsin for large-scale proteomics
Precision de novo peptide sequencing using mirror proteases of Ac-LysargiNase and trypsin for large-scale proteomics
ORGANISM(S): Hermarchus sp. HER2 
2019-01-11 | PXD008690 | Pride
Mirror spectra Monoclonal antibody Lc-ms/ms 
ProteomicsNext Generation Protein Sequencing
NGPS is a method for de-novo, full-length protein sequencing in high throughput. The method is based on cleavage of the protein at semi-random sites by microwave-assisted acid hydrolysis (MAAH), enrichment of LC-MS/MS amenable peptides from the hydrolysate by solid-phase-extraction, LC-MS/MS analysi...
ORGANISM(S): Bos taurus (Bovine) Equus caballus (Horse) 
2017-04-03 | PXD003804 | Pride
Full length Maah De-novo Ngps Microwave 
ProteomicsMultienzyme deep learning models improve peptide de novo sequencing by mass spectrometry proteomics
Generating and analyzing overlapping peptides through multienzymatic digestion is an efficient procedure for de novo protein using from bottom-up mass spectrometry (MS). Despite improved instrumentation and software, de novo MS data analysis remains challenging. In recent years, deep learning models...
ORGANISM(S): Homo sapiens (Human) 
2023-01-16 | PXD037803 | Pride
Monoclonal antibody Mass spectrometry De novo sequencing Deepnovo 
ProteomicsDe novo sequencing of an unknown monoclonal antibody using BU-MS and elucidation of the neutralizing antibody-Streptolysin O complex via cross-linking and hydrogen-deuterium exchange mass spectrometry
The identification of protective epitopes in bacterial pathogens using mass spectrometry proteomics is essential for advancing vaccine design, especially against the backdrop of increasing antibiotic resistance. Our study introduces an innovative strategy, leveraging multi-modal mass spectrometry te...
ORGANISM(S): Mus musculus (Mouse) Streptococcus pyogenes MGAS315 
2024-05-06 | PXD047461 | Pride
Host-pathogen interaction  antibody-antigen binding  mass spectrometry  structural proteomics 
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