Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

A Labrador PeptideAtlas - resource for proteomics research in dogs

ABSTRACT: The domestic dog, Canis lupus familiaris, plays a vital role as companion or service animal, and the well-being and healthy aging of dogs is gaining importance. Proteins are key actors in cells, tissues and body fluids, and the ability to measure their composition and abundance is crucial to understand biological processes. We report a mass spectrometry-based proteomics approach analyzing canine tissue, plasma and urine to develop two comprehensive resources to advance the study of the dog proteome. Firstly, we developed a canine PeptideAtlas covering 49% of the predicted UniProt KB proteome and secondly, a spectral assay library for targeted applications by data-independent acquisition (DIA) that enables the identification and quantification of 11,792 proteins (11,564 protein groups) of the dog proteome (56%). We demonstrate the performance of the library with gradients of different length and quantify 10,140 proteins in tissue and 385 proteins in plasma.

INSTRUMENT(S):

ORGANISM(S): Canis Familiaris (dog) (canis Lupus Familiaris)

TISSUE(S): Heart, Spleen, Urine, Large Intestine, Stomach, Brain, Blood Plasma, Liver, Lung, Kidney, Skin, Muscle, Adipose Tissue, Pancreas, Small Intestine

SUBMITTER: Ulrike Kusebauch

LAB HEAD: Robert L.

PROVIDER: PXD052932 | Pride | 2025-12-16

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	RawData_QExactive_plasma_urine.zip	Other
	RawData_timsTOF_plasma_DDA.zip	Other
	RawData_timsTOF_tissue_PAC_DDA.zip	Other
	RawData_timsTOF_tissue_STrap_DDA.zip	Other
	UP000805418_2023-09-25_ENS-ROS_Cfam_1.0_CONTAM_targetdecoy.fasta	Fasta

Items per page:

1 - 5 of 28

Similar Datasets

A Labrador DIA spectral assay library - resource for proteomics research in dogs

Project description:The domestic dog, Canis lupus familiaris, plays a vital role as companion or service animal, and the well-being and healthy aging of dogs is gaining importance. Proteins are key actors in cells, tissues and body fluids, and the ability to measure their composition and abundance is crucial to understand biological processes. We report a mass spectrometry-based proteomics approach analyzing canine tissue, plasma and urine to develop two comprehensive resources to advance the study of the dog proteome. Firstly, we developed a canine PeptideAtlas covering 49% of the predicted UniProt KB proteome and secondly, a spectral assay library for targeted applications by data-independent acquisition (DIA) that enables the identification and quantification of 11,792 proteins (11,564 protein groups) of the dog proteome (56%). We demonstrate the performance of the library with gradients of different length and quantify 10,140 proteins in tissue and 385 proteins in plasma.

2025-12-16 | PXD052902 | Pride

Quantitative proteomic analysis of human malignant ascites

Project description:Ascites is a valuable source of cancer biomarkers, because it contains a variety of secreted and shed proteins from cancerous cells. Conversely, most proteomic studies on ascites have focused on ovarian cancer and provided insufficient depth for biomarker discovery. Further, no proteomic analysis of ascites from gastric cancer has been reported. To this end, we profiled the human ascites proteome to obtain a pool of biomarker candidates using comprehensive proteomic strategies. Subsequently, label-free quantitation was performed to compare the abundance of proteins between benign disease and gastric cancer patients.

2018-04-16 | PXD004501 | Pride

Proteomic profiling of Labeo Rohita; a widely cultivated fish

Project description:The aim of this study was to develop a Peptide Atlas repository for Labeo rohita. Using LC-MS/MS, we have performed in-depth proteomics analysis of 19 different sample types, including 17 tissue samples, plasma from female fish and embryo 4-day post fertilization. Whole analysis resulted in the identification of more than 6015 confident canonical proteins along with ~3000 non canonical peoteins corresponding to more than 150 thousands peptides. This proteomic dataset would complement the recently published genome to accelerate further research.

2022-01-10 | PXD026377 | Pride

Borrelia PeptideAtlas: A proteome resource of common Borrelia burgdorferi isolates for Lyme community

Project description:Lyme disease is a result from an infection by the spirochete Borrelia burgdorferi, and is the leading vector-borne disease in North America. Due to the genomic and proteomic variability of different B. burgdorferi isolates, the study and further comparison of their proteome is key to understand the biology and infectivity of these spirochetes. Mass spectrometry-based proteomics was used to assemble peptide datasets of laboratory isolates B31, MM1, B31-ML23, and the infective isolates B31-5A4, B31-A3, and 297, as well as other public datasets, and is publicly available as the Borrelia PeptideAtlas (http://www.peptideatlas.org/builds/borrelia/). These datasets include information on total proteome, secretome, and membrane proteome of the B. burgdorferi.

2024-09-03 | PXD046281 | Pride

Borrelia PeptideAtlas: A proteome resource of common Borrelia burgdorferi isolates for Lyme community

2025-05-06 | PXD042072 | Pride

Comparative analysis of the adaptation of Staphylococcus aureus to internalization by different types of human non-professional phagocytic host cells

Project description:We comparatively analyzed survival and physiological adaptation of S. aureus HG001 to two human lung epithelial cell lines (S9 and A549), and human embryonic kidney cells (HEK 293). Combining enrichment of bacteria from host-pathogen assays by cell sorting and quantitation of the pathogen´s proteome by mass spectrometry we characterized S. aureus adaptation during the initial phase between 2.5 h and 6.5 h post-infection.

2014-09-01 | PXD001003 | Pride

Proteome-wide evaluation of plasma depletion methods vis-à-vis fractionation techniques

Project description:Human plasma is one of the most widely used tissues in clinical analysis, and plasma-based biomarkers are used for monitoring patient health status and/or response to medical treatment to avoid unnecessary invasive biopsy. Data driven plasma proteomics has suffered from a lack of throughput and detection sensitivity, largely due to the complexity of the plasma proteome, and in particular the enormous quantitative dynamic range, estimated to be between 9-13 orders of magnitude between the lowest and highest abundance protein. A major challenge is to identify workflows which can achieve depth of plasma proteome coverage, while minimizing the complexity of sample workup and maximizing sample throughput. In this study, we have performed intensive depletion of high abundant plasma proteins or enrichment of low abundant proteins using Hu6, Hu14 and ProteoMiner followed by SDS PAGE and C18 prefractionation techniques. We compared the performance of each of these fractionation approaches to identify the method which satisfies requirements for analysis of clinical samples, and to include good plasma proteome coverage in combination with reasonable sample output. In this study, we have reported that gel-based prefractionation approaches can replace expensive and time-consuming chromatographic separation, thereby significantly accelerating analysis time. In addition, we showed that a variety of methodologies can achieve similarly high proteome coverage, allowing flexibility depending on project specific needs. These considerations are important in the effort to accelerate plasma proteomics research so as to provide efficient, reliable and accurate diagnoses for the population as a whole.

2021-02-17 | PXD022469 | Pride

Mouse organ specific spectral library and DIA analysis of the plasma proteome

Project description:The plasma proteome is highly dynamic and variable, composed of proteins derived from surrounding tissues and cells. To investigate the complex processes that contribute to the plasma proteome homeostasis we developed a mass spectrometry based proteomics strategy to infer the origin of proteins detected in murine plasma. The strategy relies on the construction of a comprehensive protein tissue atlas from cells and highly vascularized organs using shotgun mass spectrometry. The protein tissue atlas was transformed to a spectral library for highly reproducible quantification of tissue specific proteins directly in plasma using SWATH-like data-independent mass spectrometry analysis. We show that the method can determine drastic changes of tissue specific protein profiles in blood plasma from mouse animal models with sepsis. The strategy can be extended to several other species advancing our understanding of the complex processes that contribute to the plasma proteome homeostasis.

2015-11-23 | PXD002896 | Pride

Quantitative proteomic analysis of the hemolymph from Bithynia siamensis goniomphalos infected with Opisthorchis viverrini

Project description:We have performed a quantitative proteomic analysis of the hemocytes and plasma proteins from O. viverrini-infected Bithynia siamensis goniomphalos snails using SWATH-MS. The dataset contains validation SWATH-MS data and Skyline results plus the sample-specific libraries.

2016-10-17 | PXD004121 | Pride

Glucose-dependent insulinotropic polypeptide effects in type 1 diabetes

Project description:Glucose-dependent insulinotropic polypeptide (GIP) has been proposed to exert insulin-independent effects on lipid and bone metabolism. We investigated the effect of a 6-day s.c. GIP infusion on circulating lipids, white adipose tissue (WAT), brown adipose tissue (BAT), hepatic fat content, and inflammatory markers in patients with type 1 diabetes. In a randomized, placebo-controlled, double-blind, crossover study, 20 men with type 1 diabetes underwent a 6-day continuous s.c. infusion with GIP (6 pmol/kg/min) and placebo (saline), with an interposed seven-day washout period. Each intervention period involved three study days: Day 0 (baseline measurements, a baseline abdominal adipose tissue biopsy and blood sampling), Day 1 (fasting blood sample after 24 hours infusion), and Day 6 (fasting blood sample, an abdominal adipose tissue biopsy).

2022-11-08 | PXD034803 | Pride