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Mass spectrometric identification of lamprey VLRG protein

ABSTRACT: To determine if the immunoprecipitated protein was VLRG, it was resolved by SDS-PAGE, stained with Coomassie blue, and the target gel band was excised for LC-MS/MS analysis.

ORGANISM(S): Lethenteron Reissneri

SUBMITTER: Jialong Yang

PROVIDER: PXD072176 | iProX | Thu Dec 18 00:00:00 GMT 2025

REPOSITORIES: iProX

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Biotin-modified cardiac-hypertrophy-associated piRNA (CHAPIR) pulldown proteins

Project description:PIWI-interacting RNAs (piRNAs) are abundantly expressed during cardiac hypertrophy development, but their influence on pathological hypertrophy and the underlying mechanisms remains to be elucidated. Here, we identified a cardiac-hypertrophy-associated piRNA (CHAPIR), and we found that it regulates pathological hypertrophy. To investigate the molecular mechanisms by which CHAPIR regulates cardiomyocyte hypertrophy, we transfected the biotinylated CHAPIR into cardiomyocytes and performed streptavidin bead pull down assay. The CHAPIR pull-down materials and its control were resolved using SDS-PAGE gel and stained with coomassie blue. Then the entire gel lanes of the CHAPIR pull-down materials and its control were excised and send for liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis.

2024-07-04 | PXD020098 | Pride

Aurora A phosphorylates PKM2 at T45.

Project description:Flag-PKM2 was expressed in H1299 cells. Then the H1299 cells were treated with DMSO or 100nM MLN8237. Then, cell lysate was incubated with anti-Flag M2-agarose. Elutes were separated with 10% SDS-PAGE. The gel was stained with Coomassie Brilliant Blue. Visualized bands were excised and subjected to LC-MS/MS analysis. Then the phosphorylation sites of PKM2 were identified.

2023-03-11 | PXD036575 | Pride

SWATH-Proteomics of Mathurameha in High Glucose-Induced Endothelial Dysfunction

Project description:This study aimed to elucidate the mechanisms underlying the anti-diabetic effects of Mathurameha against high glucose-induced endothelial dysfunction by SWATH-MS. The EA.hy926 cells were treated with normal glucose, high glucose, or high glucose plus Mathurameha for 24 h. Proteins were extracted and resolved on 12% SDS-PAGE. Coomassie blue-stained gel were excised in the whole lane and subjected to in-gel tryptic digestion and SWATH-MS.

2024-05-31 | PXD052751 | JPOST Repository

Identification of proteins interacted with EphA2 in nasopharyngeal carcinoma cells by LC-MS / MS

Project description:To search proteins that interact with EphA2, EphA2 interactors were coimmunoprecipitated with anti-EphA2 antibody from 5-8F NPC cell extracts, separated on SDS-PAGE and stained with Coomassie blue , and non-immune IgG antibody instead of anti-EphA2 antibody served as control. All bands were excised, and subjected to in gel trypsin digestion and liquid chromatography and high-throughput mass spectrometry (LC-MS/MS) analysis.As a result, a total of1352 proteins including ANXA1 and Cbl were identified .

2021-09-08 | PXD015242 | Pride

The E. coli effector EspJ blocks Src kinase activity via amidation and ADP-ribosylation

Project description:In vitro ADP-ribosylated Src-K295M was separated by SDS-PAGE and the Coomassie stained protein band excised and digested with either trypsin, thermolysin or elastase. All digests were analysed by nanoLC-MS/MS using Higher-energy C-trap Dissociation (HCD) as well as Electron-Transfer Dissociation (ETD) fragmentation.

2014-12-19 | PXD001461 | Pride

Detection of transcription factors bound with the OL4 region of stx1a-CPR in PC12 NE

Project description:An affinity-purified protein band was cut from a Coomassie blue stained gel and trypsinized. Digested proteins were analyzed with a mass spectrometer system (LTQ-Orbitrap Velos mass spectrometer) coupled with a direct nanoLC system (DiNA, KYA Technologies). In order to access the NCBI database and analyze the data, the mascot search engine was used.

2024-02-21 | PXD049982 | JPOST Repository

GNPS Co-Purified His-Rich Putative Nickel Insertion Protein larC_Band in Gel

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2025-05-19 | MSV000097920 | GNPS

Human intracranial tumors LC-MS/MS

Project description:We found the reality that each Coomassie blue-stained 2D gel spot contained lots of protein species in analysis of in tissue proteome.

2017-12-11 | PXD004930 | Pride

U1 Small Nuclear Ribonucleoprotein Complex and RNA Splicing Alterations in Alzheimer Disease

Project description:Comprehensive study of the human brain-insoluble proteome in AD by mass spectrometry. Mass spectrometry analysis of detergent insoluble fractions was processed based on our optimized LC-MS/MS protocol. Protein concentration was determined by bicinchoninic acid (BCA) assay (Thermo Scientific) using bovine serum albumin as standard, and further verified by Coomassie staining on a short SDS gel. Approximately 50 ug of protein per sample were resolved on a 9% SDS gel and stained with Coomassie blue. Each gel lane was excised into 20 bands followed by in-gel trypsin digestion. The resulting peptides were analyzed by LC-MS/MS (2 h) on an LTQ-Orbitrap mass spectrometer (Thermo). MS/MS spectra were searched against a human reference database from the National Center for Biotechnology Information using the SEQUEST algorithm (version 28). Identifications in Sequest .out files were converted into pepXML format using out2xml program of the Trans-Proteomic Pipeline (Institute of Systems Biology,Seattle, WA). Searching parameters included mass tolerance of precursor ions (+- 20 ppm) and product ion (+- 0.5 Da), partial tryptic restriction, fixed mass shift for modification of carboxyamidomethylated Cys (+ 57.0215 Da), dynamic mass shifts for oxidized Met (+ 15.9949 Da), three maximal modification sites and three maximal missed cleavages. Only b and y ions were considered during the database match. To evaluate false discovery rate during the spectrum-peptide matching, all original protein sequences were reversed to generate a decoy database that was concatenated to the original database. Related RNA-seq files have been deposited in the Sequence Read Archive database with accession SRA060572.

2013-08-28 | PXD000067 | Pride

Archael ubiquitin-like SAMP3 is isopeptide-linked to Proteins by an UbaA-dependent mechanism

Project description:FLAG-SAMP3ylated proteins were immunoprecipitated from Haloferax volcanii using anti-FLAG affinity agarose and separated using SDS-PAGE. The Coomassie-stained IP-bands represented FLAG-SAMP3ylated proteins harvested from the wild type and also from the ubaA mutant as negative control. The Coomassie-lanes from the IP samples were cut into 10 fractions and in-gel tryptic digested and the tryptic peptides measured using Orbitrap Velos LC-MS/MS.

2020-07-02 | PXD000202 | Pride

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