Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

MASH Explorer: A Universal Software Environment for Top-Down Proteomics

ABSTRACT: MASH Explorer, a universal, comprehensive, and user-friendly software environment for top-down proteomics. MASH Explorer integrates multiple spectral deconvolution and database searching algorithms into a single, universal platform which can process top-down proteomics data from various vendor formats, for the first time. It addresses the urgent need in the rapidly growing top-down proteomics community and is freely available to all users worldwide. With the critical need and tremendous support from the community, we envision this MASH Explorer software package will play an integral role in advancing top-down proteomics to realize its full potential for biomedical research.

INSTRUMENT(S): maXis

ORGANISM(S): Homo Sapiens (human)

SUBMITTER: Zhijie Wu

LAB HEAD: Dr. Ying Ge

PROVIDER: PXD020615 | Pride | 2021-09-09

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	Fchalf.ascii	Other
	Fchalf_ETD.xml	Xml
	Fd.ascii	Other
	Fd1.ascii	Other
	Fd1_ETD.xml	Xml

Items per page:

1 - 5 of 28

Publications

MASH Explorer: A Universal Software Environment for Top-Down Proteomics.

Wu Zhijie Z Roberts David S DS Melby Jake A JA Wenger Kent K Wetzel Molly M Gu Yiwen Y Ramanathan Sudharshanan Govindaraj SG Bayne Elizabeth F EF Liu Xiaowen X Sun Ruixiang R Ong Irene M IM McIlwain Sean J SJ Ge Ying Y

Journal of proteome research 20200824 9

Top-down mass spectrometry (MS)-based proteomics enable a comprehensive analysis of proteoforms with molecular specificity to achieve a proteome-wide understanding of protein functions. However, the lack of a universal software for top-down proteomics is becoming increasingly recognized as a major barrier, especially for newcomers. Here, we have developed MASH Explorer, a universal, comprehensive, and user-friendly software environment for top-down proteomics. MASH Explorer integrates multiple s ...[more]

PMID: 32786689

Publication: 1/2

Similar Datasets

Chip-SIP analysis of Monterey Bay surface waters incubated with organic carbon substrates

Project description:October 2013 surface seawater collected from Monterey Bay was incubated with 1 micromolar 13C labeled glucose, starch, acetate, lipids, protein, or amino acids for 12 hours. Community RNA was extracted and hybridized to a Roche Nimblegen microarray and analyzed by NanoSIMS to obtain isotope ratio data for all probe spots. Two Chips for fluorescence, and 15 Chips for different substrates from samples incubated for 12 or 36 hours.

2015-07-23 | E-GEOD-71228 | biostudies-arrayexpress

Endogenous Cell Type-Specific DISC1 Interactomes Reveal Protein Networks Associated to Neurodevelopmental Disorders

Project description:Disrupted in schizophrenia 1 (DISC1) has been implicated in contributing to a number of psychiatric diseases and neurodevelopmental phenotypes such as the proliferation and differentiation of neural progenitor cells. While there has been significant effort directed towards understanding the function of DISC1 through the determination of its protein-protein interactions within an in-vitro setting, endogenous interactions involving DISC1 within a cell-type specific setting relevant to neural development remain unclear.

2018-07-04 | PXD007103 | Pride

Global Proteomics Profiling of LPS Stimulated IMM cells

Project description:Immortalized mouse macrophages (IMMs) were stimulated with 100 ng/ml lipopolysaccharide (LPS) for 0, 30, and 60 min. The samples were analyzed using LC-MS for global proteomics.

2024-02-27 | PXD046656 | Pride

Project description:Top-down and Bottom-up

| PRJNA1117895 | ENA

Multi-omic diagnostics of prostate cancer in the presence of benign prostatic hyperplasia

Project description:There is an unmet need for improved diagnostic testing and risk prediction for cases of prostate cancer (PCa) to improve care and reduce overtreatment of indolent disease. Here we have analysed the serum proteome and lipidome of 262 study participants by liquid chromatography-mass spectrometry, including participants with a diagnosis of PCa, benign prostatic hyperplasia (BPH), or otherwise healthy volunteers, with the aim of improving biomarker specificity. Although a two-class machine learning model was able to separate PCa from controls with sensitivity of 0.82 and specificity of 0.95, adding BPH resulted in a statistically significant decline in specificity for prostate cancer to 0.76, with half of BPH cases being misclassified by the model as PCa. A small number of biomarkers differentiating between BPH and prostate cancer were identified, including proteins in MAP Kinase pathways, as well as in lipids containing oleic acid; these may offer a route to greater specificity. These results highlight, however, that whilst there are opportunities for machine learning, these will only be achieved by use of appropriate training sets that include confounding comorbidities, especially when calculating the specificity of a test.

2024-01-26 | PXD046530 | Pride

Synaptic GAP and GEF Complexes Cluster Proteins Essential for GTP Signaling

Project description:GTPase-activating proteins (GAPs) and guanine exchange factors (GEFs) play essential roles in regulating the activity of small GTPases. Several GAPs and GEFs have been shown to be present at the postsynaptic density (PSD) within excitatory glutamatergic neurons and regulate the activity of glutamate receptors. However, it is not known how synaptic GAP and GEF proteins are organized within the PSD signaling machinery, if they have overlapping interaction networks, or if they associate with proteins implicated in contributing to psychiatric disease. Here, we determine the interactomes of three interacting GAP/GEF proteins at the PSD, including the RasGAP Syngap1, the ArfGAP Agap2, and the RhoGEF Kalirin. We describe the functional properties of each interactome and show that these GAP/GEF proteins are highly associated with and cluster other proteins directly involved in GTPase signaling mechanisms. We also utilize Agap2 as an example of GAP/GEFs localized within multiple neuronal compartments and determine additional interactions involving Agap2 outside of the PSD. Functional analysis of PSD and non-PSD interactomes illustrates both common and unique functions of Agap2 determined by its subcellular location.

2022-02-22 | PXD006326 | Pride

Pseudomonas putida SQ1 pull-down

Project description:Pseduomonas putida SQ1 cell lysates grown on sulfoquinovose (SQ) were labelled with activity-based probe 3 and labelled proteins pulled-down using streptavidin beads. An on-bead digest was performed and the resulting peptides analysed by LCMS/MS.

2024-07-10 | PXD047091 | Pride

Effect of LINC00899 depletion on histone mark enrichment in HeLa cells

Project description:LncRNAs represent a major transcriptional output of the human genome, but the function of many of these elements is unknown. In this experiment, we have used the ‘CUT&RUN’ technique to quantify the changes in histone mark enrichment across the genome upon depletion of the lncRNA LINC00899 in HeLa cells. LINC00899 is of interest as its depletion results in mitotic delay, suggesting a role in mitotic progression. The CUT&RUN procedure uses antibodies to target a nuclease to the relevant protein binding site, cleaving the surrounding DNA for sequencing and yielding output equivalent to that of ChIP-seq. This experiment contains 2 replicate batches where each batch contains a sample with LINC00899 knocked down by RNA interference (RNAi); a RNAi negative control; a sample with LINC00899 knocked down with locked nucleic acid antisense oligonucleotides (LNA); and a LNA negative control. This was performed using antibodies against H3K4me3, H3K27ac, H3K36me3 and H3K27me3, as well as an IgG (goat-derived anti-rabbit) control. All samples in each batch were generated at the same time. Within each batch, all CUT&RUN experiments with the same knockdown were performed on nuclei obtained from the same cell culture. Independent cell cultures were used for experiments with different knockdown or in different batches.

2019-03-29 | E-MTAB-7419 | biostudies-arrayexpress

The beta-catenin interactome in a vascular smooth muscle cell model

Project description:Canonical Wnt/β-catenin signalling is an essential regulator of various cellular functions throughout development and adulthood. Aberrant Wnt/β-catenin signalling also contributes to various pathologies including cancer, necessitating an understanding of cell context dependent mechanisms regulating this pathway. Since protein-protein interactions underpin β-catenin function and localization, we sought to identify novel β-catenin interacting partners by affinity purification coupled with tandem mass spectrometry in vascular smooth muscle cells (VSMCs), where β-catenin is involved in both physiological and pathological control of cell proliferation. Here, we report novel components of the VSMC β-catenin interactome.

2018-10-25 | PXD010421 | Pride

Identifying the glycoproteome of Burkholderia thailandensis following knockdown of glycosylation using CRISPR interference - loading control for glycopeptide enrichment

Project description:To interrogate the glycoproteome following knockdown of pglL and subsequent knockdown of glycosylation in Burkholderia thailandensis through Zwitterionic Hydrophilic Interaction Liquid Chromatography (ZIC-HILIC) glycopeptide enrichment – loading control pre-enrichment

2023-03-20 | PXD037748 | Pride

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data