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Elucidating Proteoform Families from Proteoform Intact Mass and Lysine Count Measurements

ABSTRACT: Intact mass (66 files), top-down (18 files) and bottom-up (66 files) .raw files of GELFREE separated fractions of yeast.

INSTRUMENT(S): LTQ Velos

ORGANISM(S): Saccharomyces Cerevisiae (ncbitaxon:4932)

SUBMITTER: Lloyd Smith

PROVIDER: MSV000079456 | MassIVE | Thu Jan 14 08:04:00 GMT 2016

REPOSITORIES: MassIVE

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Elucidating Proteoform Families from Proteoform Intact-Mass and Lysine-Count Measurements.

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Project description:Intact mass analyses (HPLC-ESI-MS) of GELFREE separated fractions of yeast. A total of 66 raw files, representing two replicate analyses.

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Project description:This data set contains the following: 1) 66 raw files for NeuCode-labeled human proteoforms from the Jurkat cell line analyzed via "intact-mass" (i.e., LC-MS, with no precursor fragmentation). Three biological replicates were performed (files from the different replicates are labeled with 022317, 031617, or 031817, respectively). For each replicate, proteoforms were separated offline using a 12% Tris-acetate Gelfree cartridge and 11 fractions were collected. Two technical replicate LC-MS injections of each fraction were performed, yielding a total of 66 raw files (3 biological replicates x 11 fractions x 2 injections). 2) 22 raw files for label-free human proteoforms from the Jurkat cell line analyzed via "top-down" (i.e., LC-MS/MS, with precursor fragmentation). One biological replicate was performed (labeled 032017). Proteoforms were separated offline using a 12% Tris-acetate Gelfree cartridge and 11 fractions were collected. Two technical replicate LC-MS/MS injections of each fraction were performed, yielding a total of 22 raw files (1 biological replicate x 11 fractions x 2 injections). 3) Multi-protease and trypsin-only pruned G-PTM-D databases used for proteoform identification. Note that the bottom-up data used to generate these databases can be found elsewhere on MassIVE (MSV000083304).

2019-05-13 | MSV000083768 | MassIVE

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Project description:Intact mass analysis in high resolution for CN-GELFrEE fractions of HLD particles

2023-03-29 | MSV000091584 | MassIVE

Expanding Proteoform Identifications in Top-Down Proteomic Analyses by Constructing Proteoform Families

Project description:Raw top-down LC-MS/MS files from 12% GELFREE separated fractions of yeast. Raw files for 2 technical replicates of each fraction, in total 24 raw files.

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Identification and Quantification of Murine Mitochondrial Proteoforms Using an Integrated Top-Down and Intact-Mass Strategy

Project description:1) 144 intact-mass and top-down raw LC-MS and LC-MS/MS files (myoblast and myotube, 3 biological replicates, 6 fractions, 2 top-down MS/MS technical replicates and 2 MS1-only technical replicates) from 12% GELFrEE fractions of C2C12 mitochondrial extracts. 2) 12 intact-mass raw LC-MS files from unfractionated C2C12 mitochondrial extracts (myoblast and myotube, 3 biological replicates, 2 MS1-only technical replicates). 3) 12 bottom-up raw LC-MS/MS files from unfractionated C2C12 mitochondrial extracts digested with trypsin (myoblast and myotube, 3 biological replicates, 2 technical replicates).

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Proteoform Suite: Constructing, Quantifying, and Visualizing Proteoform Families

Project description:Proteoform Suite is a program for the analysis of intact proteoform MS data. The source code and a vignette containing all input files and settings can be found at https://smith-chem-wisc.github.io/ProteoformSuite. Proteoform identification files can be found in folders NoStress_BioRep1, NoStress_BioRep2, Stress_BioRep1, and Stress_BioRep2. For quantification: S-NS-Mixture_BioRepA, S-NS-Mixture_BioRepB, and S-NS-Mixture_BioRepC.

2017-11-13 | MSV000081711 | MassIVE

Proteoform Suite: Software for Constructing, Quantifying, and Visualizing Proteoform Families.

Project description: Not available

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E. coli Proteoform Families and G-PTM-D Database Expansion

Project description:E. coli (KL334) lysate data of a) intact-mass proteomics using NeuCode-labeled SILAC across 3 biological replicates, 10 molecular weight fractions, and 2 technical replicates, for elucidating proteoform families; b) bottom-up proteomics using label-free culture across 10 molecular weight fractions and 2 technical replicates, for constructing G-PTM-D augmented database.

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