Dataset Information

HPK-1 Citron Homology Domain interactions with Kinase Domain

ABSTRACT: The files uploaded here are converted into a standard mzxml format, and utilize processing procedures described in 10.1021/acs.analchem.9b01682 Briefly, HXMS data processing consists of 1. MSMS experiment to identify peptides and their associated retention times. These files have *MSMS* in the filename. They are searched using HPK.fasta. 2. Unlabeled peptide pool file is used to refine the exact RT range of the peptide in the experiment (MSMS experiment may be conducted at a different time). 3. Labeling experiments are then searched using ExMS2 (see manuscript linked above) to produce carried deuterium at each time point for peptides included in the pool. Comparing uptake patterns between "FullLength" files and "Kinase" files produces the map of differences on the kinase domain induced by the citron homology domain. There are two CSV files, these contain the peptides identified in each MSMS run. These are found in Search Engine Files. There are also finaltables produced by the ExMS program containing all raw and unfiltered results. There is a pdf file associated that shows the final peptides used for the analyses after discarding noisy peptides upon manual inspection. All protection factors extracted from this data along with a summary table can be found in "File_HX_TABLES.xlsx".

INSTRUMENT(S): Orbitrap Exploris 480

ORGANISM(S): Homo Sapiens (ncbitaxon:9606)

SUBMITTER: Benjamin Walters

PROVIDER: MSV000094133 | MassIVE | Tue Feb 20 11:32:00 GMT 2024

REPOSITORIES: MassIVE

ACCESS DATA

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Project description:Being inspired by metabolomic data processing, we have developed a bioinformatic pipeline that optimizes the processing of mass spectral data obtained from isobaric Tandem Mass Tag (TMT) experiments. Our method focuses on the tandem mass spectral level by first quantifying and then identifying (QtI), while preserving unidentified spectra for further investigations. The raw datasets were previously generated [1, 2]. Two-proteome model experiments were considered where identical pools of human CSF or plasma samples were mixed with E. coli samples at different concentrations. E. coli protein extract was spiked in 400 µL of CSF at amounts of 0, 2, 3, 5, 6.25, and 7.5 µg. Such sets of 6 spiked CSF samples were prepared in triplicate for comparison using sixplex isobaric tagging and analyzed in triplicates on two independent but identical LC MS/MS, for a total of 18 raw files [1]; this experiment is called “CSF-E.coli”. E. coli protein extract was spiked at 0, 2.5, 5, 6.25, 12.5, and 25 µg in 30 µL human plasma. Such sets of 6 spiked plasma samples were prepared in quadruplicate for comparison using sixplex isobaric tagging and analyzed in triplicates on one LC MS/MS, for a total of 12 raw files [2]; this experiment is referred as “Plasma-E.coli”.The so-called “96samples-CSF” experiment consists of 16 replicate TMT sixplex experiments measuring identical CSF samples from the pool described above [2], analyzed in triplicates on one LCMS/MS for a total of 48 raw files. The so-called “96samples-plasma” experiment consists of 16 replicate TMT sixplex experiments measuring identical plasma samples from the pool described before, analyzed in triplicates on one LC MS/MS for a total of 48 raw files [1]. References: [1] Dayon, L., Núñez Galindo, A., Corthésy, J., Cominetti, O. & Kussmann, M. Comprehensive and scalable highly automated MS-based proteomic workflow for clinical biomarker discovery in human plasma. J. Proteome Res. 13, 3837-3845 (2014). [2] Núñez Galindo, A., Kussmann, M. & Dayon, L. Proteomics of Cerebrospinal Fluid: Throughput and Robustness Using a Scalable Automated Analysis Pipeline for Biomarker Discovery. Anal. Chem. 87, 10755-10761 (2015).

Dataset Information

HPK-1 Citron Homology Domain interactions with Kinase Domain

Dataset's files

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets