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ProteomicsUltra high resolution linear ion trap Orbitrap mass spectrometer (Orbitrap Elite) facilitates top down LC MS/MS and versatile peptide fragmentation modes
Although only a few years old, the combination of a linear ion trap with an Orbitrap analyzer has become one of the standard mass spectrometers to characterize proteins and proteomes. Here we describe a novel version of this instrument family, the Orbitrap Elite, which is improved in three main area...
ORGANISM(S): Homo sapiens (Human) 
2013-10-10 | PXD000508 | Pride
Cid High-field orbitrap analyzer Hcd Top down Shotgun proteomics 
ProteomicsA ‘proteomic ruler’ for protein copy number and concentration estimation without spike-in standards
Absolute protein quantification using mass spectrometry (MS)-based proteomics delivers protein concentrations or copy numbers per cell. Existing methodologies typically require a combination of isotope-labeled spike-in references, cell counting and protein concentration measurements. Here we present...
ORGANISM(S): Mus musculus (Mouse) Homo sapiens (Human) 
2014-09-17 | PXD000661 | Pride
Copy numbers Absolute quantification 
ProteomicsProteomic portrait of human breast cancer progression identifies novel prognostic markers
Triplicate analysis of eleven breast cancer cell lines, each separated to 12 offgel fractions. Proteomes were quantified relative to heavy SILAC-labeled MCF7 cells that served as a spike-in standard. In this study, we used system-wide analysis of breast cancer proteomes to identify proteins that are...
ORGANISM(S): Homo sapiens (Human) 
2013-07-02 | PXD000309 | Pride
Breast cancer Proteomics Mass spectrometry 
ProteomicsMaxLFQ label-free quantification algorithm benchmark datasets
We developed a set of algorithms for label-free quantification, termed MaxLFQ, embedded into MaxQuant. This contains two datasets to benchmark MaxLFQ: The proteome benchmark dataset consists of of HeLa and E. coli lysates mixed at defined ratios. The dynamic range benchmark dataset consists of UPS1...
ORGANISM(S): Homo sapiens (Human) Escherichia coli 
2014-09-17 | PXD000279 | Pride
Benchmark datasets Label-free quantification Maxlfq Maxquant 
ProteomicsParallel accumulation – serial fragmentation combined with data-independent acquisition (diaPASEF)
Data independent acquisition modes isolate and concurrently fragment populations of different precursors by cycling through segments of a predefined precursor m/z range. Although these selection windows collectively cover the entire m/z range, overall only a few percent of all incoming ions in each ...
ORGANISM(S): Homo sapiens (Human) Saccharomyces cerevisiae (Baker's yeast) 
2020-12-17 | PXD017703 | Pride
Tims Pasef Dia Technical Ion mobility 
ProteomicsThe Proteome Landscape of the Kingdoms of Life
Proteins preform the vast majority of functions in all biological domains but their large-scale investigation has lagged behind for technological reasons. Since the first essentially complete eukaryotic proteome was reported1, advances in mass spectrometry (MS)-based proteomics2 have enabled increas...
ORGANISM(S): Homo sapiens (Human) 
2020-06-18 | PXD019483 | Pride
Lc-ms/ms 
ProteomicsThe Proteome Landscape of the Kingdoms of Life
Proteins preform the vast majority of functions in all biological domains but their large-scale investigation has lagged behind for technological reasons. Since the first essentially complete eukaryotic proteome was reported1, advances in mass spectrometry (MS)-based proteomics2 have enabled increas...
ORGANISM(S): Danio rerio (Zebrafish) (Brachydanio rerio) Arabidopsis thaliana (Mouse-ear cress) Mus musculus (Mouse) Drosophila melanogaster (Fruit fly) Gallus gallus (Chicken) Caenorhabditis elegans Sus scrofa domesticus (domestic pig) Dictyostelium discoideum (Slime mold) Bos taurus (Bovine) Vitis vinifera (Grape) Homo sapiens (Human) Triticum aestivum (Wheat) Escherichia coli Saccharomyces cerevisiae (Baker's yeast) Rattus norvegicus (Rat) 
2020-06-18 | PXD014877 | Pride
Machine learning Mass spectrometry Proteomics Bioinformatics Systems biology Phylogeny 
ProteomicsHs_Hela_Mitosis
HeLa S3 cells, double thymidine block and nocodazole arrest
ORGANISM(S): Homo Sapiens (human) 
2014-12-31 | PAe005289 | PeptideAtlas
ProteomicsHs_Hela_Tyr_Mitosis
HeLa S3 cells, Tyr phosphorylation, double thymidine block and nocodazole arrest
ORGANISM(S): Homo Sapiens (human) 
2014-12-31 | PAe005270 | PeptideAtlas
ProteomicsRapid and in-depth coverage of the (phospho-)proteome with deep libraries and optimal window design for dia-PASEF
Data-independent acquisition (DIA) methods have become increasingly attractive in mass spectrometry (MS)-based proteomics, because they enable high data completeness and a wide dynamic range. Recently, we combined DIA with parallel accumulation – serial fragmentation (dia-PASEF) on a Bruker trapped ...
ORGANISM(S): Homo sapiens (Human) 
2022-08-11 | PXD034128 | Pride
Pasef Egf Tims Data-independent acquisition Phosphoproteomics Systems biology 
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