| 111 |
IPD6138 |
Analysis of Conus monile venom duct. |
Prof. P. Balaram |
Mass Spectrometric Characterisation of Linear Conotoxins.
|
Molecular Biophysics Unit, Indian Institute of Science, Bangalore, Karnataka, India |
Top-down |
2025-05-25 |
38009400
|
| 112 |
IPD7154 |
Analysis of Conus monile venom duct |
Dr. P. Balaram |
Mass Spectrometric Characterisation of Linear Conotoxins.
|
Molecular Biophysics Unit, Indian Institute of Science, Bangalore, Karnataka, India |
Top-down |
2025-05-25 |
38009400
|
| 113 |
IPD8610 |
Contryphan sequence diversity: Messy N-terminus processing, effects on chromatographic behaviour and mass spectrometric fragmentation. |
Prof. P. Balaram |
Mass Spectrometric Characterisation of contryphans.
|
Molecular Biophysics Unit, Indian Institute of Science, Bangalore, Karnataka, India |
Top-down |
2025-05-25 |
36587728
|
| 114 |
IPD8895 |
Analysis of Conus venom peptides |
Prof. P. Balaram |
Mass Spectrometric Characterisation of Pyroglutamyl Conotoxins.
|
Molecular Biophysics Unit, Indian Institute of Science, Bangalore, Karnataka, India |
Top-down |
2025-05-25 |
29947227
|
| 115 |
IPD9056 |
Contryphan sequence diversity:Conus frigidus |
Prof. P. Balaram |
Mass Spectrometric Characterisation of contryphans.
|
Molecular Biophysics Unit, Indian Institute of Science, Bangalore, Karnataka, India |
Top-down |
2025-05-25 |
36587728
|
| 116 |
IPD9367 |
Contryphan sequence diversity:Conus amadis |
Prof. P. Balaram |
Mass Spectrometric Characterisation of contryphans.
|
Molecular Biophysics Unit, Indian Institute of Science, Bangalore, Karnataka, India |
Top-down |
2025-05-25 |
36587728
|
| 117 |
IPD2486 |
Mass spectral Analysis of Synthetic Peptides: Implications in Proteomics |
Dr. Medicharla Venkata Jagannadham |
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.
|
Centre for Cellular and Molecular Biology, Hyderabad, Telangana, India |
Shotgun proteomics |
2025-06-18 |
33953644
|
| 118 |
IPD5120 |
Characterization of the novel broad-spectrum kinase inhibitor CTx-0294885 as an affinity reagent for mass spectrometry-based kinome profiling |
Dr. Medicharla Venkata Jagannadham |
Kinome profiling of human basal breast cancer cell line MDA-MB-231 using CTx-0294885 or mixture of 4 broad-spectrum kinase inhibitor (Purvalanol B, SU6668, VI16832 and CTx-0294885). Kinase enrichment utilizing broad-spectrum kinase inhibitors enables the identification of large proportions of the expressed kinome by mass spectrometry. However, the existing inhibitors are still...
Kinome profiling of human basal breast cancer cell line MDA-MB-231 using CTx-0294885 or mixture of 4 broad-spectrum kinase inhibitor (Purvalanol B, SU6668, VI16832 and CTx-0294885). Kinase enrichment utilizing broad-spectrum kinase inhibitors enables the identification of large proportions of the expressed kinome by mass spectrometry. However, the existing inhibitors are still inadequate in covering the entire kinome. Here, we identified a novel bis-anilino pyrimidine, CTx-0294885, exhibiting inhibitory activity against a broad range of kinases in vitro, and further developed it into a Sepharose supported kinase capture reagent. Use of a quantitative proteomics approach confirmed the selectivity of CTx-0294885-bound beads for kinase enrichment. Large-scale CTx-0294885-based affinity purification followed by LC-MS/MS led to the identification of 235 protein kinases from MDA-MB-231 cells, including all members of the AKT family that had not been previously detected by other broad spectrum kinase inhibitors. Addition of CTx-0294885 to a mixture of three kinase inhibitors commonly used for kinase-enrichment increased the number of kinase identifications to 261, representing the largest kinome coverage from a single cell line reported to date. Coupling phosphopeptide enrichment with affinity purification using the four inhibitors enabled the identification of 799 high confidence phosphosites on 183 kinases, approximately 10 % of which were localized to the activation loop, and included previously unreported phosphosites on BMP2K, MELK, HIPK2 and PRKDC. Therefore, CTx 0294885 represents a powerful new reagent for analysis of kinome signalling networks that may facilitate development of targeted therapeutic strategies. Data processing and bioinformatics: Raw files were processed with MaxQuant (version 1.1.1.25) for feature detection, protein identification and quantification, using the Andromeda search engine integrated into the MaxQuant environment for database searching. Extracted peak lists were searched against the UniProtKB/Swiss-Prot Homo sapiens database (Uniprot_human_2010_10) containing 35052 entries and a separate reverse decoy database for controlling the false discovery rate (FDR). The following search parameters were selected; fixed cysteine carbamidomethylation modification; variable methionine oxidation modification, variable protein N-acetylation, variable phosphorylation of serine, threonine and tyrosine; minimum peptide length of 6 amino acids and up to 2 missed cleavages were allowed. In addition, for SILAC experiments, the SILAC labels Arg10 and Lys8 were selected as modifications, and minimum peptide count for protein quantification was set to 1. The initial first search mass tolerance was 20 ppm for precursor ions and 0.5 Da for fragment ions, with individualized peptide mass tolerances used for the subsequent searches. The ‘match between runs’ option in MaxQuant was used to transfer identifications between runs based on matching of precursors with high mass accuracy. The FDR was limited to 1 % for both protein and peptide identifications. Peptides with posterior error probability greater than 10 % were removed and protein identification required a minimum of 1 unique peptide. For phosphopeptides, those exhibiting a phosphosite localization probability (LP) > 0.75 were included in further analyses.
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Centre for Cellular and Molecular Biology, Hyderabad, Telangana, India |
Bottom-up |
2025-06-18 |
23692254
|
| 119 |
IPD7455 |
Phosphoproteomic Analysis of Lethal Castration Resistant Prostate Cancer Reveals Patient but not Metastatic Site Heterogeneity of Tyrosine Kinase Activation |
Dr. Medicharla Venkata Jagannadham |
Tissue lysis was performed as previously described (Drake, J.M., et al. Oncogene-specific activation of tyrosine kinase networks during prostate cancer progression. Proc Natl Acad Sci U S A 109, 1643-1648 (2012)) Briefly, greater than 300 mg of frozen tumor mass was homogenized and sonicated in urea lysis buffer (20 mM...
Tissue lysis was performed as previously described (Drake, J.M., et al. Oncogene-specific activation of tyrosine kinase networks during prostate cancer progression. Proc Natl Acad Sci U S A 109, 1643-1648 (2012)) Briefly, greater than 300 mg of frozen tumor mass was homogenized and sonicated in urea lysis buffer (20 mM HEPES pH 8.0, 9 M urea, 2.5 mM sodium pyrophosphate, 1.0 mM beta-glycerophosphate, 1% N-octyl glycoside, 2 mM sodium orthovanadate). Total protein was measured using the BCA Protein Assay Kit (Thermo Scientific/Pierce) and 25 mg of total protein was used for phospho-proteomic analysis. Phospho-tyrosine peptide enrichment and liquid chromatography tandem mass spectrometry (LC-MS/MS) analysis was performed as previously described (Drake, J.M., et al. Oncogene-specific activation of tyrosine kinase networks during prostate cancer progression. Proc Natl Acad Sci U S A 109, 1643-1648 (2012); Rubbi, L., et al. Global phosphoproteomics reveals crosstalk between Bcr-Abl and negative feedback mechanisms controlling Src signaling. Sci Signal 4, ra18 (2011); Graham, N.A., et al. Glucose deprivation activates a metabolic and signaling amplification loop leading to cell death. Molecular systems biology 8, 589 (2012)) Phospho-peptides were identified using the Proteome Discoverer software (version 1.3.0.339, Thermo Fisher Scientific). MS/MS fragmentation spectra were searched using SEQUEST against the Uniprot human reference proteome database with canonical and isoform sequences (downloaded January 2012 from uniprot.org). Search parameters included carbamidomethyl cysteine (*C) as a static modification. Dynamic modifications included phosphorylated tyrosine, serine, or threonine (pY, pS, pT, respectively) and oxidized methionine (*M). The Percolator node of Protein Discoverer was used to calculate false-discovery rate (FDR) thresholds and the FDR for the datasets was adjusted to 1% (version 1.17, Thermo Scientific). The Percolator algorithm uses a target-decoy database search strategy and discriminates true and false identifications with a support vector machine. The PhosphoRS 2.0 node was used to more accurately localize the phosphate on the peptide44. Only phospho-peptides with at least one phospho-tyrosine assignment with a reported probability above 20% were considered. MS2 spectra for all reported phosphopeptides are available under the PRIDE accession numbers.
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Centre for Cellular and Molecular Biology, Hyderabad, Telangana, India |
Bottom-up |
2025-06-18 |
24248375
|
| 120 |
IPD8488 |
LC-MS analysis of human tumour cell lines |
Dr. Medicharla Venkata Jagannadham |
Main aim of this study was to identify and characterize human hypothetical proteins. These are the protein sequences for which there is no experimental evidence at translation level and are functionally unknown. First part of the project deals with identification and characterization of hypothetical proteins using label-free lc-ms/ms approaches. Second...
Main aim of this study was to identify and characterize human hypothetical proteins. These are the protein sequences for which there is no experimental evidence at translation level and are functionally unknown. First part of the project deals with identification and characterization of hypothetical proteins using label-free lc-ms/ms approaches. Second part deals with providing functional clues to those identified proteins thus connecting the missing links in biological mechanisms.
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Centre for Cellular and Molecular Biology, Hyderabad, Telangana, India |
Gel-based experiment |
2025-06-18 |
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