Project ID: IPD2486

Project Title: Mass spectral Analysis of Synthetic Peptides: Implications in Proteomics

Principal Investigator: Dr. Medicharla Venkata Jagannadham

PI Affiliation: Chief Scientist, CSIR-Centre for Cellular and Molecular Biology, Hyderabad-500007, India

Description: Tryptic synthetic peptides generated in silico from human proteome are used as standards to evaluate the performance of MS and algorithm used to identify the proteins.

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Sample Preparation: Sample preparation steps: 599 synthetic peptides were dissolved in suitable solvents (Acetonitrile and water with different ratios) and mixed (equimolar and different concentrations).

Peptide Separation: Trypsin digestion was carried out in silico with 1 or 2 missed cleavages, and peptides were selected from a mass range of 616–3169 Da. Solvent A: 5% ACN in water containing 0.1% formic acid, Solvent B: 95% ACN in water containing 0.1% formic acid LC runs were carried out using pepmapRSLC C18 column, 3 μm, 100A0, 75μm X 15cms with different time gradient and the mass spectral data was combined in the final analysis.

Protein Characterization: Proteins and peptides were identified using SEQUEST algorithm supplied by the manufacturer. Using no enzyme provided maximum results by setting precursor ion mass tolerance to 5ppm and MS/MS mass tolerance at 0.02Da. Human proteome database from Uniprot was used to analyse the results: UniProt human curated fasta.

Experiment Type: Shotgun proteomics

PubMed-ID: 33953644

Species: Homo sapiens-9606

Tissue: Unknown

Cell Type: Unknown

Disease: Disease free

Instrument Details: Q Exactive HF (MS:1002523)

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