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ProteomicsApplication of de novo sequencing to large-scale complex proteomics datasets
Dependent on concise, pre-defined protein sequence databases, traditional search algorithms perform poorly when analyzing mass spectra derived from wholly uncharacterized protein products. Conversely, de novo peptide sequencing algorithms can interpret mass spectra without relying on reference datab...
ORGANISM(S): Bos taurus (Bovine) Saccharomyces cerevisiae (Baker's yeast) 
2016-01-12 | PXD003317 | Pride
De novo peptide sequencing Ms/ms Large-scale computational analysis Yeast Bos Mass spectrometry Proteomics 
ProteomicsCombining de novo peptide sequencing algorithms, a synergistic approach to boost both identifications and confidence in bottom-up proteomics
Complex MS-based proteomics datasets are usually analyzed by protein database-searches. While this approach performs considerably well for sequenced organisms, direct inference of peptide sequences from tandem mass spectra, i.e. de novo peptide sequencing, oftentimes is the only way to obtain inform...
ORGANISM(S): Radix auricularia Homo sapiens (Human) Mus musculus (Mouse) Saccharomyces cerevisiae (Baker's yeast) 
2019-09-25 | PXD005280 | Pride
False discovery rate Bottom-up proteomics De novo peptide sequencing Lc-ms/ms 
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 
ProteomicsNovoBoard: a comprehensive framework for evaluating the false discovery rate and accuracy of de novo peptide sequencing
De novo peptide sequencing is a fundamental research area in mass spectrometry (MS) based proteomics. However, those methods have often been evaluated using a couple of simple metrics that do not fully reflect their overall performance. Moreover, there has not been an established method to estimate ...
ORGANISM(S): Homo sapiens (Human) 
2024-08-28 | PXD055277 | Pride
False discovery rate De novo peptide sequencing 
ProteomicsComplementary CID and 351 nm UVPD tandem mass spectra enable effective de novo sequencing
This dataset accompanies a publication in which we present a strategy for acquisition and effective de novo peptide sequencing of complementary CID and 351 nm ultraviolet photodissociation (UVPD) MS/MS pairs. E. coli whole cell lysate is carbamylated to block lysine side chains, digested with trypsi...
ORGANISM(S): Escherichia Coli (ncbitaxon:562) 
2017-03-06 | MSV000080603 | MassIVE
ProteomicsIdentification of Unknown Biological Toxin Protein Using Mass Spectrometry: A Case Study on De Novo Sequencing of Ricin
Currently, the genomes of many toxin proteins remain unsequenced. Characterizing these toxin proteins and their active peptide segments is crucial for the development of detoxification agents and for discovering proteins with potential therapeutic applications. Existing methods for identifying and d...
ORGANISM(S): Ricinus communis 
2025-12-01 | PXD061213 | Pride
Unknown biological toxin protein Heuristic denovo protein sequencing Ricin toxin De novo sequencing Mass spectrometry 
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 
ProteomicsE. coli mirror 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 proteomicsPrecision de novo peptide sequencing using mirror proteases of Ac-LysargiNase and trypsin for large-scale proteomics
ORGANISM(S): Escherichia coli 
2019-01-11 | PXD008688 | Pride
Mirror spectrum pairs E. coli 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 
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 
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