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Thermo proteome discoverer 1.4.1 platform

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The Thermo Proteome Discoverer 1.4.1 platform is a software solution designed for the analysis and identification of proteins from mass spectrometry data. It provides a comprehensive suite of tools for peptide and protein identification, quantification, and bioinformatics analysis.

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Proteome Discoverer (1141 citations) Proteome Discoverer 1.4 (655 citations) Thermo Proteome Discoverer (28 citations) Proteome Discoverer platform (16 citations) Thermo Proteome Discoverer 1.4 (5 citations)

5 protocols using thermo proteome discoverer 1.4.1 platform

1

Quantitative Proteome Analysis Pipeline

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The raw MS files were analyzed using the Thermo Proteome Discoverer™ 1.4.1 platform (Thermo Scientific; Bremen, Germany) for peptide identification and protein assembly. For each cell sample, 16 raw MS files obtained from 16 sequential LCMS analyses were grouped for a single database search against the Human UniProtKB/Swiss-Prot human protein sequence databases (20,608 entries, as of December 20, 2015) based on the SEQUEST and percolator algorithms through the Proteome Discoverer 1.4.1 platform. Carbamidomethylation of cysteines was set as a fixed modification. The minimum peptide length was specified to be five amino acids. The precursor mass tolerance was set to 15 ppm, whereas fragment mass tolerance was set to 0.05 Da. The maximum false peptide discovery rate was specified as 0.01 or 0.05. The resulting Proteome Discoverer Report contains all assembled proteins with peptide sequences and matched spectrum counts. Protein quantification used the normalized spectral abundance factor (NSAF) method37 (link),38 (link) to calculate the protein relative abundance.
Li R., Hao J., Fujiwara H., Xu M., Yang S., Dai S., Long Y., Swaroop M., Li C., Vu M., Marugan J.J., Ory D.S, & Zheng W. (2017). Analytical Characterization of Methyl-β-Cyclodextrin for Pharmacological Activity to Reduce Lysosomal Cholesterol Accumulation in Niemann-Pick Disease Type C1 Cells. Assay and Drug Development Technologies, 15(4), 154-166.
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2

Proteome Profiling of HDACI-Treated Cells

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The raw MS files were analyzed using the Thermo Proteome Discoverer 1.4.1 platform (Thermo Fisher Scientific, Bremen, GmbH) for peptide identification and protein assembly. For each cell sample, 16 raw MS files obtained from 16 sequential LC/MS analyses were grouped for a single database search against the Human UniProtKB/Swiss-Prot human protein sequence databases (20597 entries, 12/20/2013) based on the SEQUEST and percolator algorithms through the Proteome Discoverer 1.4.1 platform. Carbamidomethylation of cysteines was set as a fixed modification. The minimum peptide length was specified to be five amino acids. The precursor mass tolerance was set to 15 ppm, whereas fragment mass tolerance was set to 0.05 kDa. The maximum false peptide discovery rate was specified as 0.01. The resulting Proteome Discoverer Report contains all assembled proteins (a proteome profile) with peptides sequences and matched spectrum counts. Three proteome profiles were generated for the untreated control cells and two HDACI-treated cell samples.
LI Q.Q., HAO J.J., ZHANG Z., HSU I., LIU Y., TAO Z., LEWI K., METWALLI A.R, & AGARWAL P.K. (2016). Histone deacetylase inhibitor-induced cell death in bladder cancer is associated with chromatin modification and modifying protein expression: A proteomic approach. International Journal of Oncology, 48(6), 2591-2607.
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3

MS-based Proteomic Identification and Analysis

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The raw MS files were analyzed using the Thermo Proteome Discoverer 1.4.1 platform (Thermo Scientific, Bremen, Germany) for peptide identification and protein assembly. The raw data files were searched against the human protein sequence database obtained from the NCBI website (
https://www.ncbi.nlm.nih.gov) using the Proteome Discoverer software based on the SEQUEST algorithm. The carbamidomethylation of cysteines was set as a fixed modification, and Oxidation and Deamidation Q/N-deamidated (+0.98402 Da), and Pro>Glu (+31.990 Da) were set as dynamic modifications. The minimum peptide length was specified to be five amino acids. The precursor mass tolerance was set to 15 ppm, whereas fragment mass tolerance was set to 0.05 Da. The maximum false peptide discovery rate was specified as 0.01.
Suzuki Y.J, & Hao J.J. (2018). Results supporting the concept of the oxidant-mediated protein amino acid conversion, a naturally occurring protein engineering process, in human cells. F1000Research, 6, 594.
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4

Proteome Profiling with Proteome Discoverer

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The raw MS files were analyzed using the Thermo Proteome Discoverer 1.4.1 platform (Thermo Scientific, Bremen, Germany) for peptide identification and protein assembly. For each specimen sample, 16 raw MS files obtained from 16 sequential LC-MS analyses were grouped for a single database search against the Human UniProtKB human protein sequence databases (20,597 entries, 12/20/2013) based on the SEQUEST and percolator algorithms through the Proteome Discoverer 1.4.1 platform. The carbamido methylation of cysteines was set as a fixed modification. The minimum peptide length was specified as 5 amino acids. The precursor mass tolerance was set to 15 ppm, whereas the fragment mass tolerance was set to 0.05 Da. The maximum false peptide discovery rate was specified as 0.01. The resulting Proteome Discoverer Report contains all assembled proteins (a proteome profile) with peptide sequences and matched spectrum counts.
Hao J.J., Zhi X., Wang Y., Zhang Z., Hao Z., Ye R., Tang Z., Qian F., Wang Q, & Zhu J. (2017). Comprehensive Proteomic Characterization of the Human Colorectal Carcinoma Reveals Signature Proteins and Perturbed Pathways. Scientific Reports, 7, 42436.
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5

Proteomic Analysis of HSP90 Inhibition

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The raw MS files were analyzed using the Thermo Proteome Discoverer 1.4.1 platform (Thermo Scientific; Bremen, Germany) for peptide identification and protein assembly. For each cell sample, 16 raw MS files obtained from 16 sequential LC-MS analyses were grouped for a single database search against the Human UniProtKB/Swiss-Prot human protein sequence databases (20597 entries, 12/20/2013) based on the SEQUEST and percolator algorithms through the Proteome Discoverer 1.4.1 platform. Carbamidomethylation of cysteines was set as a fixed modification. The minimum peptide length was specified to be five amino acids. The precursor mass tolerance was set to 15 ppm, whereas fragment mass tolerance was set to 0.05 kDa. The maximum false peptide discovery rate was specified as 0.01. The resulting Proteome Discoverer Report contains all assembled proteins (a proteome profile) with peptides sequences and matched spectrum counts. Three proteome profiles were generated for the untreated control cells and two HSP90 inhibitor-treated cell samples.
Li Q.Q., Hao J.J., Zhang Z., Krane L.S., Hammerich K.H., Sanford T., Trepel J.B., Neckers L, & Agarwal P.K. (2017). Proteomic analysis of proteome and histone post-translational modifications in heat shock protein 90 inhibition-mediated bladder cancer therapeutics. Scientific Reports, 7, 201.
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