Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

MS-MS analysis of coomassie stained protein bands observed on the Alzheimer model active compound drug resin (102) versus control resin (74)

ABSTRACT: Pig brain was homogenized in column buffer supplemented with protease inhibitors and 10kx/g supernate prepared and flash frozen. Aliquot was thawed, 100ul applied to the 50ul bed volume drug resin (124) or control resin lacking the drug ligand (74) and incubated for 1hr at room temperature followed by 100 bed volumes of wash with column buffer. Free drug at 200uM in column buffer was used to elute bound proteins, and the drug resin stripped with 8M urea to remove proteins that may have stuck after elution. Samples 16-18 were the bands observed in the control resin. Samples 4-14 were the bands observed in the drug resin. Samples 1-3 were the bands observed in the 8M urea stripping of the drug resin and not observed upon similar stripping the control resin.

INSTRUMENT(S): sciex

ORGANISM(S): Sus Scrofa (ncbitaxon:9823)

SUBMITTER: Vishwanath R. Lingappa, MD, PhD

PROVIDER: MSV000099711 | MassIVE | Fri Oct 31 12:14:00 GMT 2025

SECONDARY ACCESSION(S): PXD070166

REPOSITORIES: MassIVE

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

TMT analysis of detergent-soluble and insoluble fractions from HEK293T cells in normal conditions and upon heat shock

Project description:HEK293T cells were cultured according to standard protocols and heat shocked at 42oC for 6 hours. Detergent-soluble and insoluble fractions from HEK293T cells were obtained following the procedures described before. Specifically, HEK293T cells were lysed in NP40 lysis buffer (Invitrogen #FNN0021) with protease inhibitors by gentle pipetting. The cell homogenate was centrifuged at 14000 rpm and the supernatant was retrieved (detergent-soluble fraction). The remaining pellet was washed twice in ice-cold NP40 lysis buffer and then resuspended in urea buffer (RIPA buffer with 8M urea). The samples were then centrifuged at 14000 rpm for 10 min to pellet any remaining cell debris. The resulting supernatant (detergent-insoluble fraction) was retrieved and analyzed as explained below.

2025-08-01 | PXD046967 | Pride

LC-MS/MS data from spider major ampullate silk fibers and glands

Project description:This project contains proteomic (LC-MS/MS) data from 27 samples. The samples are as follows: (1) Major ampullate glands dissolved in 8M Urea (3 replicates); (2) Major ampullate silk fibers dissolved in 8M Urea (3 replicates); (3) Major ampullate silk fibers dissolved in Hexafluoroisopropanol (3 replicates); (4) Major ampullate silk fibers dissolved in 9M Lithium Bromide (3 replicates); (5) Major ampullate silk fibers dissolved in 2M Urea (3 replicates); (6) Major ampullate silk fibers dissolved in 4M Urea (3 replicates); (7) Major ampullate silk fibers dissolved in 8M Urea (3 replicates); (8) Major ampullate silk fibers first dissolved in Formic acid and then in 2M Urea (2 replicates); (9) Major ampullate silk fibers first dissolved in Formic acid and then in 4M Urea (2 replicates); (10) Major ampullate silk fibers first dissolved in Formic acid and then in 8M Urea (2 replicates);

2024-07-16 | PXD052116 | Pride

Refinement of Protein Extraction Protocols for Human Peripheral Nerve Tissue

Project description:Our aim was to establish an effective method for protein extraction from freshly frozen human peripheral nerves and determine the minimum amount required for consistent protein extraction outcomes. Five extraction methods were compared using 8 M Urea and Ripa buffer, using either the Bullet Blender or Bioruptor. Out of the total 2619 identified proteins, protein extraction using Ripa buffer combined with either Bioruptor or the Bullet Blender resulted in the identification of 1582 (60%) and 1615 (62%) proteins, respectively. In contrast, using 8 M Urea and Bioruptor for protein extraction resulted in 1022 proteins (39%), whereas employing the Bullet Blender yielded 1446 proteins (55%). Sample amount, ranging from 0.6 to 10 mg, were prepared with consistent protein extraction outcome obtained for samples ≥ 1.2 mg. Combining Ripa and 8M Urea with Bullet Blender increased protein identification to 2126 (81%). Proteins were classified by their cell components, molecular functions, and biological processes. Furthermore, a subclassification of proteins involved in the extracellular matrix (ECM) was introduced. We recommend the use of Ripa buffer, in combination with 8 M Urea and Bullet Blender for extracting proteins from fresh-frozen human nerves weighing ≥ 1.2 mg.

2025-02-21 | PXD049366 | Pride

NET-seq analysis of pSer2-Pol II profile in shCTRL, shMETTL3 and shDDX21 HeLa cells

Project description:The chromatin fraction was isolated from 5x107 HeLa cells. Chromatin was digested in 100 mL of MNase (40 units/ mL ) reaction buffer for 3 min at 37 °C in a thermomixer (1,400 rpm). After addition of 10 L EGTA (25mM) to inactivate MNase, soluble digested chromatin was collected by 13,000 rpm centrifuge for 5 min. 10 mg of Pol II antibody was conjugated to magnetic protein A beads. The supernatant was diluted with 400 mL of NET-2 buffer and pSer2-Pol II antibody-conjugated beads were added. Incubated the IP reaction at 4 °C for 1 hr. The beads were washed with 1 mL of NET-2 buffer six times and 100 mL of 1xPNKT (1xPNK buffer and 0.05% Triton X-100) buffer once. Washed beads were incubated in 50 mL PNK reaction mix (1xPNKT, 1 mM ATP and 0.05 U/ml T4 PNK (NEB)) in Thermomixer at 37 °C, 1,400 rpm for 6 min. Beads were washed with 1 mL of NET-2 buffer once and RNA was extracted with Trizol reagent. RNA was suspended in urea Dye (7M Urea, 1xTBE, 0.1% BPB and 0.1% XC) and resolved on 6% TBU gel (Invitrogen) at 200 V for 5 min. Gels with 30-160 nt RNAs were collected. 0.2 mL tube was prepared with holes made with 25G needle and placed in a 1.5 mL tube. Gel fragments were placed in the layered tube and broken down by centrifugation at 12,000 rpm for 1 min. The small RNAs were eluted from gel using RNA elution buffer (1 M NaOAc and 1 mM EDTA) at 25 °C for 1 hr in Thermomixer (900 rpm). Eluted RNA was puriﬁed with SpinX column (Coster) with 2 glass ﬁlters (Millipore) and the ﬂow-through RNA was ethanol precipitated.

2019-10-15 | GSE134102 | GEO

cross linking mass spectrometry of Exo84 pulldown in Sec9 and Sec18 depletion mutants

Project description:Co-Immunoprecipitation with Crosslinking Using DSS for Exo84 Subunit Sample Preparation: Yeast strains expressing Exo84-3xGFP and FRB-tagged Sec18 or Sec9 were cultured in YPD at 30°C until OD600 0.8-1. Cells were harvested, washed with resuspension buffer (50 mM HEPES, 150 mM NaCl, protease inhibitors), and frozen in liquid nitrogen. Lysis was performed using a Freezer/Mill, followed by clarification via centrifugation. Crosslinking with DSS: Lysates were crosslinked with DSS (0.5 mM, 1h, RT) and quenched with glycine (100 mM, 15 min). Supernatants were clarified by centrifugation. Immunoprecipitation: GFP-Trap beads were used to capture Exo84 complexes. Lysates were pre-cleared with blocking beads (1h, 4°C) before incubation with GFP-Trap beads (overnight, 4°C). Beads were washed with a stringent buffer (2M NaCl, 8M urea, 1% Triton X-100) and PBS. Mass Spectrometry Sample Preparation: Immunoprecipitated complexes were reduced (DTT), alkylated (IAA), digested with trypsin (37°C, 8h), and desalted before LC-MS/MS. LC-MS/MS Analysis: Samples were analyzed on an Orbitrap Fusion Lumos coupled to an EASY-nLC 1200 with a 50 cm C18 column. Peptides were separated with a gradient from 5% to 40% acetonitrile over 60 min. MS1 scans were acquired at 120,000 resolution, and the Top Speed method was used for data-dependent MS2 acquisition with HCD fragmentation.

2026-01-21 | PXD061766 | Pride

Klebsiella pneumoniae x546,ATCC15380, TMT

Project description:Klebsiella pneumoniae x546,ATCC15380, TMT,The samples were ground into a powder in liquid nitrogen. Then the powder was suspended in lysis buffer [1% sodium deoxycholate (SDS), 8M urea]. The mixture was allowed to settle at 4 鎺矯 for 30 min during which the sample were vortexed at every 5 min, and treated by ultrasound at 40 kHz and 40 W for 2 min. After centrifugation at 16000 rpm at 4鎺矯 for 30 min, the concentration of protein supernatant was determined by Bicinchoninic acid (BCA) method by BCA Protein Assay Kit (Pierce, Thermo, USA). Protein quantification was performed according to the kit protocol(Chen et al., 2021)

2021-11-15 | PXD028396 | Pride

Hydrogen deuterium exchange epitope mapping of glycosylated epitopes enabled by online immobilized glycosidase

Project description:Numerous mAbs are known to recognize N-glycosylated epitopes or to bind in close proximity to an N-glycan site, however, glycosylated protein sites are typically obscured from HDX detection as a result of the inherent heterogeneity of glycans. To overcome this limitation, we covalently immobilized the glycosidase PNGase Dj on solid resin and incorporated it into an online HDX-MS workflow for post-HDX deglycosylation. The resin-immobilized PNGase Dj exhibits a robust tolerance to various buffer conditions, and is employed in a column format that can be readily adapted into a typical HDX-MS platform. Using this system, we were able to obtain full sequence coverage of the SARS-CoV-2 receptor binding domain (RBD) and to map the glycosylated epitope of the glycan-binding mAb S309 to the RBD.

2024-05-24 | PXD041204 | Pride

Identification of RNAs that co-purify with the Caulobacter sRNA, GsrN

Project description:Purpose: To identify RNAs that interact with GsrN, a small regulatory RNA from Caulobacter crescentus. Methods: Pseudomonas phage 7 (PP7) viral coat protein fused to maltose binding protein (MBP) was immobilized on amylose resin. PP7 coat protein binds to PP7 RNA hairpins (PP7hp). A strain expressing GsrN tagged with a genetically encoded PP7hp at base 37 (GsrN(37)-PP7hp) was captured on this column, washed, and eluted in biological triplicate (pos_rep). As a negative control, we incubated the PP7 coat protein column with independent duplicate lysates from a Caulobacter strain expressing PP7hp fused to a non-functional 3' isoform of GsrN (mock). We generated RNA-seq libraries for each of three independent GsrN(37)-PP7hp fractions, and the duplicate mock fractions. Results: We quantified levels of RNAs in the GsrN(37)-PP7hp (pos) fractions with fractions from parallel PP7hp-3'GsrN(mock) pull-downs by RNA-seq. From these data, we identified a group of RNAs that were enriched in the GsrN(37)-PP7hp fraction.

2017-10-26 | GSE106171 | GEO

CryoGrid-PIXUL-RNA: High throughput RNA isolation platform for tissue transcript analysis

Project description:We compared proteinase K buffer (PKBuffer) vs TRIzol vs column-based (PureLink RNA Micro kit) RNA isolation on frozen mouse organs methods using the high throughput CryoGrid system integrated with PIXUL sonicator. Mice were treated with intraperiteal injection of LPS (model of endotoxin induced sepsis) or PBS (control). After 12 hours mice were euthanized and brains, hearts, kidneys, and livers were harvested, immediately placed on ice, and then frozen in CryoTrays.

2022-03-31 | GSE199598 | GEO

Systematic Discovery of Deeply Conserved Plant Protein Complexes, Tomato

Project description:The associated files are mass spec data from HPLC mixed-bed ion exchange column fractions. Sample loaded was a native extract of tomato leaves.

2019-10-28 | PXD013004 | 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