| 111 |
IPD2008 |
Contryphan sequence diversity:Conus inscriptus |
Prof. P. Balaram |
Mass Spectrometric Characterisation of contryphans.
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Molecular Biophysics Unit, Indian Institute of Science, Bangalore, Karnataka, India |
Top-down |
2025-05-25 |
36587728
|
| 112 |
IPD3563 |
Contryphan sequence diversity:Conus virgo |
Prof. P. Balaram |
Mass Spectrometric Characterisation of contryphans.
|
Molecular Biophysics Unit, Indian Institute of Science, Bangalore, Karnataka, India |
Top-down |
2025-05-25 |
36587728
|
| 113 |
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
|
| 114 |
IPD2840 |
Analysis of venom peptide from Conus betulinus |
Prof. P. Balaram |
Characterization of venom peptides from Conus betulinus using mass spectrometry
|
Molecular Biophysics Unit, Indian Institute of Science, Bangalore, Karnataka, India |
Shotgun proteomics |
2025-05-25 |
38009400
|
| 115 |
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
|
| 116 |
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
|
| 117 |
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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CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India |
Gel-based experiment |
2025-06-18 |
|
| 118 |
IPD9282 |
Proteins from Outer Membrane Vesicules of Pseudomonas syringae Lz4W |
Dr. Medicharla Venkata Jagannadham |
The proteins from Outer Membrane Vesicles (OMVs) were extracted by chilled acetone method. The proteins were separated on 1D SDS-PAGE (12%). From the gel, total 10 fractions were made and all of them were subjected to in gel digestion using trypsin. The MS/MS spectra of the resulting tryptic peptides were...
The proteins from Outer Membrane Vesicles (OMVs) were extracted by chilled acetone method. The proteins were separated on 1D SDS-PAGE (12%). From the gel, total 10 fractions were made and all of them were subjected to in gel digestion using trypsin. The MS/MS spectra of the resulting tryptic peptides were recordedby using LC coupled ESI-MS/MS (Thermo Orbitrap Velos). The mass spectral data thus obtained was analysed by using Proteome Discoverer 1.3. Since the genome sequence of P. syringae Lz4W is not available, the data was searched against a database prepared from 20 related Pseudomonas species whose genome sequence is available on Uniprot (Updated upto Jan 2013). The search was observed by using nodes Sequest and Mascot both, the enzyme selected was trypsin with maximum 2 missed cleavages, the precursor tolerance set at 10 ppm, fragment tolerance at 0.8 Da, carbamidomethylated cystein (57.02 Da) as fixed modification, oxidised methionine (15.99 Da) as variable modification. After the search is over, the results were refined applying result filters as Peptide confidence (High) and Differentiable Proteins (including distinct proteins), which makes sure that each protein entry in the list is identified with at least one unique peptide.
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CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India |
Bottom-up |
2025-06-18 |
24437924
|
| 119 |
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.
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CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India |
Shotgun proteomics |
2025-06-18 |
33953644
|
| 120 |
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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CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India |
Bottom-up |
2025-06-18 |
24248375
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