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ProteomicsSpectral Library Search for Improved TMTpro Labelled Peptide Assignment in Human Plasma Proteomics
Clinical biomarker discovery is often based on the analysis of human plasma samples. However, the high dynamic range and complexity of plasma pose significant challenges to mass spectrometry-based proteomics. Current methods for improving protein identifications require laborious pre-analytical samp...
ORGANISM(S): Homo sapiens (Human) 
2023-10-24 | PXD042546 | Pride
Peptide identification  plasma proteomics  spectral library search  tmtpro 
MetabolomicsMetabolomic Profile of Diet-Induced Obesity Mice in Response to Human and Small Humanin-like Peptide 2 Treatment

INTRODUCTION: The mitochondrial-derived peptides (MDPs) are a novel group of natural occurring peptides that have important signaling functions and biological activity. Both humanin and small-humanin-like peptide 2 (SHLP2) have been reported to act as insulin sensitizers and modu...

2019-06-21 | MTBLS159 | MetaboLights
ProteomicsCavia porcellus spectral library
The guinea pig (cavia porcellus) is an excellent experimental model for translation to many aspects of human physiology and disease yet there is limited experimental information regarding its proteome. In an effort to overcome this gap in our knowledge, we generated a comprehensive spectral library ...
ORGANISM(S): Cavia Porcellus (ncbitaxon:10141) 
2018-12-07 | MSV000083199 | MassIVE
ProteomicsComprehensive spectral library from the pathogenic bacterium Streptococcus pneumoniae with focus on phosphoproteins
In this study, a comprehensive spectral library for S. pneumoniae with an emphasis on phosphopeptide spectra was compiled. In total, 76% of the theoretical S. pneumoniae proteins were stored in a spectral library. Additionally, in combination with classical database search algorithms and the spectra...
ORGANISM(S): Streptococcus Pneumoniae D39 
MSV000084269 | MassIVE
ProteomicsSimulated phosphopeptide spectral library for confident site localization
We have developed a new workflow to unambiguously localize phosphorylation sites on proteins. We demonstrate that spectral matching of phosphopeptide datasets against a library of the well-simulated spectra provided higher sensitivity for confident site localization than other tested programs. To co...
ORGANISM(S): Homo sapiens (Human) 
2015-03-17 | PXD000474 | Pride
Synthetic peptide Simulated spectral library Hela Phosphopeptide Lc-ms/ms 
ProteomicsSimulated spectral library searching on TripleTOF phosphopeptide datasets
Synthetic phosphopeptides and enriched K562 cell phosphopeptides were analyzed using a TripleTOF 6600 mass spectrometer before and after enzymatic dephosphorylation. Dephosphorylated peptides identified by X!Tandem database searching were subjected to spectral simulation of all possible single phosp...
ORGANISM(S): Homo Sapiens (human) 
2019-12-03 | PXD012433 | JPOST Repository
ProteomicsA primary human T-cell spectral library to facilitate large scale quantitative T-cell proteomics
Comprehensive spectral libraries are essential in sequential window acquisition of all theoretical mass spectra (SWATH-MS) based high throughput proteomic studies. Even though SWATH-MS assays provide robust quantitative proteomics data its applications to human T-cell studies are limited by the lack...
ORGANISM(S): Homo sapiens (Human) 
2020-10-19 | PXD019446 | Pride
Human Swath Spectral library Primary t-cells 
ProteomicsReproducibility, specificity and accuracy of DIA quantification - Spectral Libraries
For the complete description see the manuscript. Data dependent acquisition (DDA) is the method of choice for mass spectrometry based proteomics discovery experiments, data-independent acquisition (DIA) is steadily becoming more important. One of the most important requirement to perform a DIA analy...
ORGANISM(S): Mus musculus (Mouse) 
2019-11-08 | PXD012987 | Pride
Dia Label-free quantification Peptide identification Spectral library Data-independent acquisition 
ProteomicsConstructing a Tandem Mass Spectral Library for Forensic Ricin Identification
Ricin, a protein found in castor seeds, is a lethal toxin that is designated as a category 2 select agent. Because castor seeds are easy to obtain and the toxin can be easily extracted, cases of attempted ricin poisoning are relatively common. A shotgun proteomics method for ricin identification has...
ORGANISM(S): Ricinus communis 
2019-10-02 | PXD013711 | Pride
Forensic proteomics Spectral library Castor Ricin Lc-ms/ms 
ProteomicsProteome analysis of Jurkat cells for spectral library
In order to increase the spectral library to study the ocurrence of distinct peptide fragmetation patterns, we analyzed the whole cell proteome of Jurkat cells.
ORGANISM(S): Homo sapiens (Human) 
2019-02-25 | PXD005111 | Pride
Spectral library Fragmentation pattern Whole cell lysate 
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