| 121 |
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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| 122 |
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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CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India |
Bottom-up |
2025-06-18 |
23692254
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| 123 |
IPD6181 |
Delineating pathogenesis of obese and lean PCOS phenotype using integrated transcriptomics and proteomics approach |
Dr. Pallavi Shukla |
This study explores the metabolic and hormonal impact of polycystic ovary syndrome
(PCOS) in women aged 18-39, incorporating plasma protein analysis to deepen
understanding of its biological mechanisms. Patients were recruited from the PCOS Clinic at
the National Institute for Research in Reproductive and Child Health (ICMR-NIRRCH) and
non-PCOS participants from general clinics and...
This study explores the metabolic and hormonal impact of polycystic ovary syndrome
(PCOS) in women aged 18-39, incorporating plasma protein analysis to deepen
understanding of its biological mechanisms. Patients were recruited from the PCOS Clinic at
the National Institute for Research in Reproductive and Child Health (ICMR-NIRRCH) and
non-PCOS participants from general clinics and communities. Blood and plasma samples
were collected for comprehensive biochemical and proteomic profiling. Participants were
categorized into four groups: Obese PCOS (N=33), Lean PCOS (N=11), Obese non-PCOS
(N=12), and Lean non-PCOS (N=25), with diagnoses based on the Rotterdam criteria.
Exclusion criteria ensured chronic diseases, medications, or interfering conditions did not
affect reproductive physiology. A total of 117 women were studied, with 57 diagnosed with
PCOS and 60 serving as controls.
PCOS patients demonstrated higher insulin resistance, as reflected in fasting insulin
levels and HOMA-IR scores. Testosterone levels were elevated across PCOS cases, with lean
PCOS participants exhibiting even higher androgen concentrations. Variations in LH and
FSH ratios further emphasized reproductive hormonal imbalances, while obese PCOS women
had lower sex hormone-binding globulin (SHBG) levels. Lipid profiles revealed elevated
very-low-density lipoprotein (VLDL) cholesterol in PCOS patients, reinforcing concerns
regarding cardiovascular risks. Though total cholesterol and triglyceride levels showed no
clear trend, HDL cholesterol was notably lower in obese PCOS participants.
To understand molecular variations in PCOS, plasma protein quantification and
depletion were performed. A total of 15 samples were pooled into four subgroups for
depletion, following strict protocols using the High Select Top 14 Abundant Protein
Depletion Resin. Plasma samples underwent two rounds of depletion to remove dominant
proteins, such as albumin and immunoglobulins, ensuring accuracy before being sent to IIT-
SAIF for liquid chromatography-mass spectrometry (LC-MS). After depletion, samples were
enzymatically digested and labeled using iTRAQ reagents for multiplex quantification. The
fractions were analyzed using an Orbitrap high-resolution mass spectrometer, generating
MS/MS spectra that mapped peptide identifications back to corresponding proteins. Using
stringent statistical criteria (False Discovery Rate <1%), a distinct list of differentially
expressed proteins (DEPs) was developed. Plasma proteome profiling revealed unique DEPs across four comparative groups:
Obese PCOS vs Obese Control (OP vs OC), Lean PCOS vs Lean Control (LP vs LC), Obese
Control vs Lean Control (OC vs LC), and Obese PCOS vs Lean Control (OP vs LC).
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National Institute for Research in Reproductive Health, Mumbai, Maharashtra, India |
Non targated proteomcis |
2028-12-23 |
|
| 124 |
IPD6123 |
Defining the Akt1 interactome and delineating alterations in its composition as a function of cell cycle progression. |
Dr. Kanury V.S. Rao |
Akt1 expressing Hek 293 cells were SILAC labeled to capture dynamic changes in Akt1 interactome as the cell cycle progresses from G0 to G1S and then G2 phase. This will help in understanding how Akt1 extends its regulatory effect upon cell cycle progression.
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THSTI - National Chair and Head, Drug Discovery Research Centre Translational Health Science and Technology Institute, Faridabad, INDIA |
Affinity purification coupled with mass spectrometry proteomics |
2025-08-06 |
28243621
|
| 125 |
IPD2550 |
Mycobacterial strain-specific temporal modulations of newly synthesized macrophage secretome |
Dr. Kanury V.S. Rao |
THP-1 macrophages were infected with four strains of Mycobacterium tuberculosis to study the temporal dynamics of newly synthesized proteins in the secretome. Temporal snapshots of secretome reflect the macrophage response to pathogenicity which in combination with intracellular events, completes the disease picture. However, such studies are compromised by limitations...
THP-1 macrophages were infected with four strains of Mycobacterium tuberculosis to study the temporal dynamics of newly synthesized proteins in the secretome. Temporal snapshots of secretome reflect the macrophage response to pathogenicity which in combination with intracellular events, completes the disease picture. However, such studies are compromised by limitations of quantitative proteomics. Metabolic labeling by SILAC allows a 3-plex experiment while isobaric chemical labeling by iTRAQ/TMT allows up to 8 to 10-plex respectively. This makes studying temporal proteome dynamics an intangible and elusive proposition. We have developed a new variant of hyperplexing method, combining triplex SILAC with 6-plex iTRAQ to achieve 18-plex quantitation in a single MS run. THP-1 macrophages were infected with H37Ra, H37Rv, BND433 and JAL2287 and the newly synthesized secreted host proteins were studied over six temporal frame still 30 hours post infection, at a difference of 4 hours each. For quantitation, the strains were encoded with two sets of triple SILAC- H37Ra & H37Rv in one and BND433 & JAL2287 in another with a control in each. These sets were then iTRAQ labeled to encode for temporal profiles across six time points in 6-plex iTRAQ. Effectively a 36-plex design with 4 replicates of each set, these experiments were completed within few days on the mass spectrometer. Using MaxQuant and in house developed tools and pipelines, we have analysed the data to map the temporal and strain specific dynamics of newly synthesized proteins in host. Hyperplexing enables large scale spatio-temporal systems biology studies where large number of samples can be processed simultaneously and in quantitative manner.
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THSTI - National Chair and Head, Drug Discovery Research Centre Translational Health Science and Technology Institute, Faridabad, INDIA |
Shotgun proteomics |
2025-08-06 |
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| 126 |
IPD6714 |
Delineating the Rb1 interactome data and its modulations during cell cycle progression. |
Dr. Kanury V.S. Rao |
The retinoblastoma (Rb) protein is a potent tumor suppressor which is known to negatively regulate the cell cycle as well as tumor progression. Phosphorylated Rb protein (pRb) has been demonstrated to be in-charge for the key G1 checkpoint, blocking entry into S-phase and thereby the cell growth. This study was...
The retinoblastoma (Rb) protein is a potent tumor suppressor which is known to negatively regulate the cell cycle as well as tumor progression. Phosphorylated Rb protein (pRb) has been demonstrated to be in-charge for the key G1 checkpoint, blocking entry into S-phase and thereby the cell growth. This study was designed to capture interacting protein partners of Rb1 as the cell cycle progresses. Rb1 expressing HEK-293 cells were cultured in light, medium and heavy SILAC labels to capture the changes in Rb1 interactome as the cell cycle progressed from G0 to G1S and then to G2 phase, respectively. This data might help in understanding the cell cycle regulatory effect of Rb1 protein and complement the available information on its interacting partners.
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THSTI - National Chair and Head, Drug Discovery Research Centre Translational Health Science and Technology Institute, Faridabad, INDIA |
Affinity purification coupled with mass spectrometry proteomics |
2025-08-07 |
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| 127 |
IPD4918 |
Identification of Potential Protein Biomarkers for Early Detection of Pregnancy in Cow Urine uses 2D DIGE and Label Free quantitation |
Dr. Ashok Kumar Mohanty |
Background: An early, reliable and noninvasive method of pregnancy diagnosis is a prerequisite for efficient reproductive management in dairy industry. The early detection of pregnancy also helps to reduce the calving interval and rebreeding time which is beneficial for farmers and dairy industries. The aim of this work to identify...
Background: An early, reliable and noninvasive method of pregnancy diagnosis is a prerequisite for efficient reproductive management in dairy industry. The early detection of pregnancy also helps to reduce the calving interval and rebreeding time which is beneficial for farmers and dairy industries. The aim of this work to identify potential biomarker for pregnancy detection at earlier stages (16-25 days). To achieve this goal, we performed differential in gel electrophoresis (DIGE) and label free quantitation (LFQ) for identification of protein which have significant differential expression during pregnancy. Results: DIGE experiment revealed eleven differentially expressed proteins out of which nine proteins were up regulated having fold change ≥1.5. The LFQ data analysis gave 202 differentially expressed protein out of 30 proteins were up-regulated and 40 down regulated having significant fold change ≥1.5 and ≤0.6 respectively. Further bioinformatic analysis showed that majority of proteins was involved in regulation of leukocyte immunity, endopeptidase inhibitor activity, regulation of peptidase activity and polysaccharide binding. Conclusion: To the best of our knowledge, this is first report on identification of differentially expressed proteins in urine of cows during various time points of pregnancy using DIGE and LFQ. In our investigation, we have discussed functional significance of few selected proteins such as A2HS, MBP, GRP, IGFBP-II, SERPIN, Vitamin D binding protein etc which were differentially expressed and actively involved in pregnancy associated events such as embryo implantation, establishment and maintenance of pregnancy. Thus, we have identified a set of potential protein biomarkers for early detection of pregnancy.
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Proteomics and Structural Biology Lab, Animal biotechnology Center, National Dairy Research Institute, Karnal, Haryana, India |
Shotgun proteomics, Gel-based experiment |
2025-08-15 |
27429603
|
| 128 |
IPD1891 |
Deep proteome analysis of more than 12000 proteins in buffalo mammary epithelial cells identifies protein signatures for active proliferation and lactation |
Dr. Ashok Kumar Mohanty |
Extensive branching morphogenesis takes place during pregnancy in the mammary gland. It is accompanied by the rapid proliferation of the Mammary Epithelial Cells (MECs). To gain insights into the proteomic changes that occur during the proliferation of MECs from buffalo (Bubalus bubalis) origin, we explored the deep proteome profile of...
Extensive branching morphogenesis takes place during pregnancy in the mammary gland. It is accompanied by the rapid proliferation of the Mammary Epithelial Cells (MECs). To gain insights into the proteomic changes that occur during the proliferation of MECs from buffalo (Bubalus bubalis) origin, we explored the deep proteome profile of buffalo mammary epithelial cells (BuMECs) using mass spectrometry (MS). To achieve this, we employed the sub-cellular fractionation approach and secretome analysis. Proteins were isolated separately from four subcellular fractions (SCFs) containing cytosolic (SCF-I), membranous and membranous organelle’s (SCF-II), nuclear (SCF-III) and cytoskeletal (SCF-IV). These sub-cellular specific protein fractions were processed using in-solution digestion and analyzed with nano-LCMS/MS. The MS analysis identified 8330, 5970, 5288 and 4818 non-redundant proteins in the fractions SCF I, II, III and IV respectively. To evaluate the secretory proteins in these cells, gel-based proteome approach was used which revealed a total of 792 non-redundant proteins. Altogether, combined analysis of all the five fractions including four sub-cellular fractions and secretome resulted in the identification of 12,609 non-redundant proteins. A total of 325 molecular pathways were identified after extensive analysis. The most enriched pathways associated with these proteins were metabolic, PI3-AKT, MAPK, mTOR, Insulin, estrogen and Oxytocin signaling. Our study demonstrated for the first time highest number of proteins identified by MS in any cell types including MECs.
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Proteomics and Structural Biology Lab, Animal biotechnology Center, National Dairy Research Institute, Karnal, Haryana, India |
Shotgun proteomics |
2025-08-15 |
32179766
|
| 129 |
IPD2682 |
Profiling of cow urinary proteins using various extraction methods reveals more than 1550 proteins |
Dr. Ashok Kumar Mohanty |
Urine can help in diagnosis of different diseases including cancer and other patho-physiological conditions. Urine proteome studies have been mainly human- centric. No information is available on urinary proteome from bovine till date. In the present study, we have used 3 protein extraction methods such as ammonium sulphate precipitation, ProteoSpin...
Urine can help in diagnosis of different diseases including cancer and other patho-physiological conditions. Urine proteome studies have been mainly human- centric. No information is available on urinary proteome from bovine till date. In the present study, we have used 3 protein extraction methods such as ammonium sulphate precipitation, ProteoSpin column and diafiltration method from bovine urine for identification of urinary proteome. The tryptic peptides generated after In-gel and In-solution method were identified using LC/MS/MS (ESI-qTOF) which resulted in identification of 1582 proteins. In-gel trypsin digestion method revealed more protein (1191) in comparison to in-solution digestion method (541). Maximum proteins were identified in ammonium sulphate precipitation method (938) followed by ProteoSpin (606) and diafiltration (444) methods respectively. The profile of the identified proteins were compared with human urinary proteome of which 311 bovine urinary proteins matched with human. An exclusive list of 38 bovine urinary proteins with high protein scores were listed which are absent in human urine. All identified proteins were analyzed according to Gene Ontology which were classified according to cellular component, biological processes and molecular functions. This study reports for the first time an exclusive evidence of more than 1550 proteins in urine of healthy cow donors.
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Proteomics and Structural Biology Lab, Animal biotechnology Center, National Dairy Research Institute, Karnal, Haryana, India |
Shotgun proteomics, Gel-based experiment |
2025-08-15 |
26021477
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