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ProteomicsDISMS2: A flexible algorithm for direct proteome-wide distance calculation of LC-MS/MS runs
The classification of samples on a molecular level has manifold applications, from cancer biology, where the goal is to classify patients according to effective treatments, to phylogenetics to identify evolutionary relationships between species. In such scenarios modern molecular methods are based o...
ORGANISM(S): Homo sapiens (Human) Mus musculus (Mouse) Saccharomyces cerevisiae (Baker's yeast) Drosophila melanogaster (Fruit fly) Caenorhabditis elegans 
2017-03-13 | PXD004824 | Pride
Distance measurements Spectral comparisions Lc-ms/ms 
ProteomicsCyclophilin A is not acetylated at Lysine-82 and Lysine-125 in resting and stimulated platelets
Cyclophilin A (CyPA), a member of the family of cyclophilins, is widely expressed by all prokaryotic and eukaryotic cells. Upon activation, CyPA can also be released from platelets, and engages in extracellular functions via interaction with the CD147 receptor that contribute to cardiovas...
ORGANISM(S): Homo sapiens (Human) Mus musculus (Mouse) 
2022-02-22 | PXD027289 | Pride
Acetylation Cyca Ptm 
ProteomicsSpLICE: A reference database enabling in depth proteome and PTM analysis of mouse immune cells
Spectral libraries fulfill multiple functions in biological and analytical applications. For biologists, these libraries provide a valuable resource to verify the presence and abundance of proteins or pathways within a selected cell type thus determine the feasibility of further experiments. Despite...
ORGANISM(S): Mus musculus (Mouse) 
2025-03-06 | PXD059683 | Pride
T-cell Bmdm Ptm Spectral library Glycoproteomics Bmdc Cd8 Splice Cd4 B-cell Immune cells 
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 
ProteomicsProteogenomics of colorectal cancer liver metastases
Colorectal cancer (CRC) is the third most common and second most deadly cancer worldwide. Treatments for metastatic CRC (mCRC) are still largely based on toxic chemotherapy regimens, but important insights into tumor biology enabled the development of targeted cancer therapies. Here, we describe a p...
ORGANISM(S): Homo sapiens (Human) 
2019-12-04 | PXD014222 | Pride
Human Lc-msms Prm Colorectal cancer Proteogenomics 
ProteomicsCombination of proteogenomics with peptide de novo sequencing identifies new genes and hidden posttranscriptional modifications
Proteogenomics, the combination of proteomics, genomics and transcriptomics, has considerably improved genome annotation in under-studied phylogenetic groups, where homology information is missing. Yet, it can also be advantageous when re-investigating well-annotated genomes. Here, we apply an advan...
ORGANISM(S): Sordaria macrospora 
2019-09-25 | PXD014240 | Pride
Lc-msms De novo peptide sequencing Rna editing Sordaria macrospora Proteogenomics 
ProteomicsHighly sensitive phosphoproteomics by tailoring solid-phase extraction to electrostatic repulsion-hydrophilic interaction chromatography
The dataset contains the data of key experiments for developing a novel and highly sensitive bottom-up phosphoproteomics strategy termed ERLIC-SCX/RP-LC-MS. We compared two SPE types (RP, SCX) for an ERLIC run with 7 fractions. The results were used to design a workflow for highly sensitive bottom-u...
ORGANISM(S): Homo sapiens (Human) 
2014-12-02 | PXD001381 | Pride
Phosphoproteomics Phosphopeptide enrichment Lc-ms Solid-phase extraction Scx Protein phosphorylation Rp 
ProteomicsDual-compartment shotgun proteomics unravel thermal stress responses in reef-calcifiers and their photosymbionts
The proliferation of coral reef organisms, such as the key ecological engineers and carbonate producers’ large benthic foraminifera (LBF), greatly relies on the mutual association with photosymbiotic algae. With respect to global change impacts such as ocean warming, evaluating stress and acclimatiz...
ORGANISM(S): Amphistegina Bacillariophyta 
2018-02-27 | PXD008015 | Pride
Large benthic foraminifera Thermal stress Label-free quantitation Lc-msms 
ProteomicsPeriostin as a blood biomarker of muscle cell fibrosis, cardiomyopathy and disease severity in myotonic dystrophy type 1
Myotonic dystrophy type 1 (DM1) is the most common form of adult-onset muscular dystrophy and is caused by an repeat expansion [r(CUG)exp] located in the 3' untranslated region of the DMPK gene. Symptoms include skeletal and cardiac muscle dysfunction and fibrosis. In DM1, there is a lack of establi...
ORGANISM(S): Mus musculus (Mouse) 
2023-05-02 | PXD024107 | Pride
Dm1 biomarker Dmsxl Dmpk Clinical proteomics Ctg-trinucleotide expansion Steinert’s disease 
ProteomicsERLIC-based strategies for combined quantitative proteome and phosphoproteome analysis with limited sample amounts
The study aims the development of a sensitive strategy for combined quantitative proteomics and phosphoproteomics. 3 ERLIC-based strategies, applicable for low-sample-amount experiments (~150 µg per condition), were evaluated and compared . Three samle sets have been uploaded. 16 fractions ERLIC-1-S...
ORGANISM(S): Homo sapiens (Human) 
2015-02-25 | PXD001241 | Pride
Protein phosphorylation Erlic Quantitative proteomics Multidimensional separation 
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