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Article ; Online: Identification and characterization of intact glycopeptides in human urine.

Garcia-Marques, Fernando / Fuller, Keely / Bermudez, Abel / Shamsher, Nikhiya / Zhao, Hongjuan / Brooks, James D / Flory, Mark R / Pitteri, Sharon J

Scientific reports

2024 Volume 14, Issue 1, Page(s) 3716

Abstract: Glycoproteins in urine have the potential to provide a rich class of informative molecules for studying human health and disease. Despite this promise, the urine glycoproteome has been largely uncharacterized. Here, we present the analysis of ... ...

Abstract	Glycoproteins in urine have the potential to provide a rich class of informative molecules for studying human health and disease. Despite this promise, the urine glycoproteome has been largely uncharacterized. Here, we present the analysis of glycoproteins in human urine using LC-MS/MS-based intact glycopeptide analysis, providing both the identification of protein glycosites and characterization of the glycan composition at specific glycosites. Gene enrichment analysis reveals differences in biological processes, cellular components, and molecular functions in the urine glycoproteome versus the urine proteome, as well as differences based on the major glycan class observed on proteins. Meta-heterogeneity of glycosylation is examined on proteins to determine the variation in glycosylation across multiple sites of a given protein with specific examples of individual sites differing from the glycosylation trends in the overall protein. Taken together, this dataset represents a potentially valuable resource as a baseline characterization of glycoproteins in human urine for future urine glycoproteomics studies.
MeSH term(s)	Humans ; Glycopeptides/chemistry ; Chromatography, Liquid ; Tandem Mass Spectrometry ; Glycoproteins/metabolism ; Proteome/chemistry ; Polysaccharides/chemistry
Chemical Substances	Glycopeptides ; Glycoproteins ; Proteome ; Polysaccharides
Language	English
Publishing date	2024-02-14
Publishing country	England
Document type	Journal Article
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-024-53299-3
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Article ; Online: Guanylate-binding protein 1 modulates proteasomal machinery in ovarian cancer.

Tailor, Dhanir / Garcia-Marques, Fernando Jose / Bermudez, Abel / Pitteri, Sharon J / Malhotra, Sanjay V

iScience

2023 Volume 26, Issue 11, Page(s) 108292

Abstract: Guanylate-binding protein 1 (GBP1) is known as an interferon-γ-induced GTPase. Here, we used genetically modified ovarian cancer (OC) cells to study the role of GBP1. The data generated show that GBP1 inhibition constrains the clonogenic potential of ... ...

Abstract	Guanylate-binding protein 1 (GBP1) is known as an interferon-γ-induced GTPase. Here, we used genetically modified ovarian cancer (OC) cells to study the role of GBP1. The data generated show that GBP1 inhibition constrains the clonogenic potential of cancer cells.
Language	English
Publishing date	2023-10-24
Publishing country	United States
Document type	Journal Article
ISSN	2589-0042
ISSN (online)	2589-0042
DOI	10.1016/j.isci.2023.108292
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Article: Proteomics analysis of urine and catheter-associated biofilms in spinal cord injury patients.

Garcia-Marques, Fernando J / Zakrasek, Elissa / Bermudez, Abel / Polasko, Alexandra L / Liu, Shiqin / Stoyanova, Tanya / Brooks, James D / Lavelle, John / Pitteri, Sharon J

American journal of clinical and experimental urology

2023 Volume 11, Issue 3, Page(s) 206–219

Abstract: After spinal cord injury (SCI), use chronic urinary catheters for bladder management is common, making these patients especially vulnerable to catheter-associated complications. Chronic catheterization is associated with bacterial colonization and ... ...

Abstract	After spinal cord injury (SCI), use chronic urinary catheters for bladder management is common, making these patients especially vulnerable to catheter-associated complications. Chronic catheterization is associated with bacterial colonization and frequent catheter-associated urinary tract infections (CAUTI). One determinant of infection success and treatment resistance is production of catheter-associated biofilms, composed of microorganisms and host- and microbial-derived components. To better understand the biofilm microenvironment, we performed proteomics analysis of catheter-associated biofilms and paired urine samples from four people with SCI with chronic indwelling urinary catheters. We developed a novel method for the removal of adhered cellular components on catheters that contained both human and microbial homologous proteins. Proteins from seven microbial species were identified including:
Language	English
Publishing date	2023-06-15
Publishing country	United States
Document type	Journal Article
ISSN	2330-1910
ISSN	2330-1910
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Article ; Online: The role of GCNT1 mediated O-glycosylation in aggressive prostate cancer.

Hodgson, Kirsty / Orozco-Moreno, Margarita / Scott, Emma / Garnham, Rebecca / Livermore, Karen / Thomas, Huw / Zhou, Yuhan / He, Jiepei / Bermudez, Abel / Garcia Marques, Fernando Jose / Bastian, Kayla / Hysenaj, Gerald / Archer Goode, Emily / Heer, Rakesh / Pitteri, Sharon / Wang, Ning / Elliott, David J / Munkley, Jennifer

Scientific reports

2023 Volume 13, Issue 1, Page(s) 17031

Abstract: Prostate cancer is the most common cancer in men and a major cause of cancer related deaths worldwide. Nearly all affected men develop resistance to current therapies and there is an urgent need to develop new treatments for advanced disease. Aberrant ... ...

Abstract	Prostate cancer is the most common cancer in men and a major cause of cancer related deaths worldwide. Nearly all affected men develop resistance to current therapies and there is an urgent need to develop new treatments for advanced disease. Aberrant glycosylation is a common feature of cancer cells implicated in all of the hallmarks of cancer. A major driver of aberrant glycosylation in cancer is the altered expression of glycosylation enzymes. Here, we show that GCNT1, an enzyme that plays an essential role in the formation of core 2 branched O-glycans and is crucial to the final definition of O-glycan structure, is upregulated in aggressive prostate cancer. Using in vitro and in vivo models, we show GCNT1 promotes the growth of prostate tumours and can modify the glycome of prostate cancer cells, including upregulation of core 2 O-glycans and modifying the O-glycosylation of secreted glycoproteins. Furthermore, using RNA sequencing, we find upregulation of GCNT1 in prostate cancer cells can alter oncogenic gene expression pathways important in tumour growth and metastasis. Our study highlights the important role of aberrant O-glycosylation in prostate cancer progression and provides novel insights regarding the mechanisms involved.
MeSH term(s)	Humans ; Male ; Glycosylation ; Polysaccharides/metabolism ; Prostate/pathology ; Prostatic Neoplasms/pathology
Chemical Substances	Polysaccharides ; beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,6-acetylglucosaminyl transferase (EC 2.4.1.102)
Language	English
Publishing date	2023-10-09
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-023-43019-8
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Article ; Online: Protein signatures to distinguish aggressive from indolent prostate cancer.

Garcia-Marques, Fernando / Liu, Shiqin / Totten, Sarah M / Bermudez, Abel / Tanimoto, Cheylene / Hsu, En-Chi / Nolley, Rosalie / Hembree, Amy / Stoyanova, Tanya / Brooks, James D / Pitteri, Sharon J

The Prostate

2022 Volume 82, Issue 5, Page(s) 605–616

Abstract: Background: Distinguishing men with aggressive from indolent prostate cancer is critical to decisions in the management of clinically localized prostate cancer. Molecular signatures of aggressive disease could help men overcome this major clinical ... ...

Abstract	Background: Distinguishing men with aggressive from indolent prostate cancer is critical to decisions in the management of clinically localized prostate cancer. Molecular signatures of aggressive disease could help men overcome this major clinical challenge by reducing unnecessary treatment and allowing more appropriate treatment of aggressive disease. Methods: We performed a mass spectrometry-based proteomic analysis of normal and malignant prostate tissues from 22 men who underwent surgery for prostate cancer. Prostate cancer samples included Grade Groups (3-5), with 8 patients experiencing recurrence and 14 without evidence of recurrence with a mean of 6.8 years of follow-up. To better understand the biological pathways underlying prostate cancer aggressiveness, we performed a systems biology analysis and gene enrichment analysis. Proteins that distinguished recurrent from nonrecurrent cancer were chosen for validation by immunohistochemical analysis on tissue microarrays containing samples from a larger cohort of patients with recurrent and nonrecurrent prostate cancer. Results: In all, 24,037 unique peptides (false discovery rate < 1%) corresponding to 3,313 distinct proteins were identified with absolute abundance ranges spanning seven orders of magnitude. Of these proteins, 115 showed significantly (p < 0.01) different levels in tissues from recurrent versus nonrecurrent cancers. Analysis of all differentially expressed proteins in recurrent and nonrecurrent cases identified several protein networks, most prominently one in which approximately 24% of the proteins in the network were regulated by the YY1 transcription factor (adjusted p < 0.001). Strong immunohistochemical staining levels of three differentially expressed proteins, POSTN, CALR, and CTSD, on a tissue microarray validated their association with shorter patient survival. Conclusions: The protein signatures identified could improve understanding of the molecular drivers of aggressive prostate cancer and be used as candidate prognostic biomarkers.
MeSH term(s)	Biomarkers, Tumor/metabolism ; Cohort Studies ; Humans ; Male ; Mass Spectrometry ; Prognosis ; Prostate/pathology ; Prostatic Neoplasms/metabolism ; Proteomics
Chemical Substances	Biomarkers, Tumor
Language	English
Publishing date	2022-01-31
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	604707-5
ISSN	1097-0045 ; 0270-4137
ISSN (online)	1097-0045
ISSN	0270-4137
DOI	10.1002/pros.24307
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Article ; Online: Interplay between the Chd4/NuRD Complex and the Transcription Factor Znf219 Controls Cardiac Cell Identity.

El Abdellaoui-Soussi, Fadoua / Yunes-Leites, Paula S / López-Maderuelo, Dolores / García-Marqués, Fernando / Vázquez, Jesús / Redondo, Juan Miguel / Gómez-Del Arco, Pablo

International journal of molecular sciences

2022 Volume 23, Issue 17

Abstract: The sarcomere regulates striated muscle contraction. This structure is composed of several myofibril proteins, isoforms of which are encoded by genes specific to either the heart or skeletal muscle. The chromatin remodeler complex Chd4/NuRD regulates the ...

Abstract	The sarcomere regulates striated muscle contraction. This structure is composed of several myofibril proteins, isoforms of which are encoded by genes specific to either the heart or skeletal muscle. The chromatin remodeler complex Chd4/NuRD regulates the transcriptional expression of these specific sarcomeric programs by repressing genes of the skeletal muscle sarcomere in the heart. Aberrant expression of skeletal muscle genes induced by the loss of Chd4 in the heart leads to sudden death due to defects in cardiomyocyte contraction that progress to arrhythmia and fibrosis. Identifying the transcription factors (TFs) that recruit Chd4/NuRD to repress skeletal muscle genes in the myocardium will provide important information for understanding numerous cardiac pathologies and, ultimately, pinpointing new therapeutic targets for arrhythmias and cardiomyopathies. Here, we sought to find Chd4 interactors and their function in cardiac homeostasis. We therefore describe a physical interaction between Chd4 and the TF Znf219 in cardiac tissue. Znf219 represses the skeletal-muscle sarcomeric program in cardiomyocytes in vitro and in vivo, similarly to Chd4. Aberrant expression of skeletal-muscle sarcomere proteins in mouse hearts with knocked down
MeSH term(s)	Animals ; DNA Helicases/metabolism ; DNA-Binding Proteins/metabolism ; Gene Expression Regulation ; Mi-2 Nucleosome Remodeling and Deacetylase Complex/metabolism ; Mice ; Muscle Proteins/genetics ; Muscle Proteins/metabolism ; Myocytes, Cardiac/cytology ; Myocytes, Cardiac/metabolism ; Nucleosomes ; Transcription Factors/genetics ; Transcription Factors/metabolism
Chemical Substances	DNA-Binding Proteins ; Muscle Proteins ; Nucleosomes ; Transcription Factors ; Mi-2 Nucleosome Remodeling and Deacetylase Complex (EC 3.5.1.98) ; Mi-2beta protein, mouse (EC 3.6.1.3) ; DNA Helicases (EC 3.6.4.-)
Language	English
Publishing date	2022-08-24
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2019364-6
ISSN	1422-0067 ; 1422-0067 ; 1661-6596
ISSN (online)	1422-0067
ISSN	1422-0067 ; 1661-6596
DOI	10.3390/ijms23179565
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Article ; Online: Integrated transcriptome-proteome analyses of human stem cells reveal source-dependent differences in their regenerative signature.

Ganguly, Abantika / Swaminathan, Ganesh / Garcia-Marques, Fernando / Regmi, Shobha / Yarani, Reza / Primavera, Rosita / Chetty, Shashank / Bermudez, Abel / Pitteri, Sharon J / Thakor, Avnesh S

Stem cell reports

2022 Volume 18, Issue 1, Page(s) 190–204

Abstract: Mesenchymal stem cells (MSCs) are gaining increasing prominence as an effective regenerative cellular therapy. However, ensuring consistent and reliable effects across clinical populations has proved to be challenging. In part, this can be attributed to ... ...

Abstract	Mesenchymal stem cells (MSCs) are gaining increasing prominence as an effective regenerative cellular therapy. However, ensuring consistent and reliable effects across clinical populations has proved to be challenging. In part, this can be attributed to heterogeneity in the intrinsic molecular and regenerative signature of MSCs, which is dependent on their source of origin. The present work uses integrated omics-based profiling, at different functional levels, to compare the anti-inflammatory, immunomodulatory, and angiogenic properties between MSCs from neonatal (umbilical cord MSC [UC-MSC]) and adult (adipose tissue MSC [AD-MSC], and bone marrow MSC [BM-MSC]) sources. Using multi-parametric analyses, we identified that UC-MSCs promote a more robust host innate immune response; in contrast, adult-MSCs appear to facilitate remodeling of the extracellular matrix (ECM) with stronger activation of angiogenic cascades. These data should help facilitate the standardization of source-specific MSCs, such that their regenerative signatures can be confidently used to target specific disease processes.
MeSH term(s)	Infant, Newborn ; Humans ; Proteome ; Transcriptome ; Mesenchymal Stem Cells ; Gene Expression Profiling ; Adult Stem Cells ; Bone Marrow Cells
Chemical Substances	Proteome
Language	English
Publishing date	2022-12-08
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
ZDB-ID	2720528-9
ISSN	2213-6711 ; 2213-6711
ISSN (online)	2213-6711
ISSN	2213-6711
DOI	10.1016/j.stemcr.2022.11.006
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Article ; Online: Multiomics Analysis of Spatially Distinct Stromal Cells Reveals Tumor-Induced O-Glycosylation of the CDK4-pRB Axis in Fibroblasts at the Invasive Tumor Edge.

Bouchard, Gina / Garcia-Marques, Fernando Jose / Karacosta, Loukia Georgiou / Zhang, Weiruo / Bermudez, Abel / Riley, Nicholas McIlvain / Varma, Sushama / Mehl, Lindsey Catherine / Benson, Jalen Anthony / Shrager, Joseph B / Bertozzi, Carolyn Ruth / Pitteri, Sharon J / Giaccia, Amato J / Plevritis, Sylvia Katina

Cancer research

2022 Volume 82, Issue 4, Page(s) 648–664

Abstract: The invasive leading edge represents a potential gateway for tumor metastasis. The role of fibroblasts from the tumor edge in promoting cancer invasion and metastasis has not been comprehensively elucidated. We hypothesize that cross-talk between tumor ... ...

Abstract	The invasive leading edge represents a potential gateway for tumor metastasis. The role of fibroblasts from the tumor edge in promoting cancer invasion and metastasis has not been comprehensively elucidated. We hypothesize that cross-talk between tumor and stromal cells within the tumor microenvironment results in activation of key biological pathways depending on their position in the tumor (edge vs. core). Here we highlight phenotypic differences between tumor-adjacent-fibroblasts (TAF) from the invasive edge and tumor core fibroblasts from the tumor core, established from human lung adenocarcinomas. A multiomics approach that includes genomics, proteomics, and O-glycoproteomics was used to characterize cross-talk between TAFs and cancer cells. These analyses showed that O-glycosylation, an essential posttranslational modification resulting from sugar metabolism, alters key biological pathways including the cyclin-dependent kinase 4 (CDK4) and phosphorylated retinoblastoma protein axis in the stroma and indirectly modulates proinvasive features of cancer cells. In summary, the O-glycoproteome represents a new consideration for important biological processes involved in tumor-stroma cross-talk and a potential avenue to improve the anticancer efficacy of CDK4 inhibitors. Significance: A multiomics analysis of spatially distinct fibroblasts establishes the importance of the stromal O-glycoproteome in tumor-stroma interactions at the leading edge and provides potential strategies to improve cancer treatment. See related commentary by De Wever, p. 537.
MeSH term(s)	A549 Cells ; Cancer-Associated Fibroblasts/metabolism ; Cell Line, Tumor ; Cyclin-Dependent Kinase 4/genetics ; Cyclin-Dependent Kinase 4/metabolism ; Genomics/methods ; Glycoproteins/genetics ; Glycoproteins/metabolism ; Glycosylation ; Humans ; Neoplasm Invasiveness ; Neoplasms/genetics ; Neoplasms/metabolism ; Neoplasms/pathology ; Phosphorylation ; Proteomics/methods ; Retinoblastoma Protein/genetics ; Retinoblastoma Protein/metabolism ; Signal Transduction/genetics ; Stromal Cells/metabolism ; Transcriptome/genetics
Chemical Substances	Glycoproteins ; Retinoblastoma Protein ; CDK4 protein, human (EC 2.7.11.22) ; Cyclin-Dependent Kinase 4 (EC 2.7.11.22)
Language	English
Publishing date	2022-07-07
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	1432-1
ISSN	1538-7445 ; 0008-5472
ISSN (online)	1538-7445
ISSN	0008-5472
DOI	10.1158/0008-5472.CAN-21-1705
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Article ; Online: UCHL1 is a potential molecular indicator and therapeutic target for neuroendocrine carcinomas.

Liu, Shiqin / Chai, Timothy / Garcia-Marques, Fernando / Yin, Qingqing / Hsu, En-Chi / Shen, Michelle / Shaw Toland, Angus Martin / Bermudez, Abel / Hartono, Alifiani B / Massey, Christopher F / Lee, Chung S / Zheng, Liwei / Baron, Maya / Denning, Caden J / Aslan, Merve / Nguyen, Holly M / Nolley, Rosalie / Zoubeidi, Amina / Das, Millie /

Kunder, Christian A / Howitt, Brooke E / Soh, H Tom / Weissman, Irving L / Liss, Michael A / Chin, Arnold I / Brooks, James D / Corey, Eva / Pitteri, Sharon J / Huang, Jiaoti / Stoyanova, Tanya

Cell reports. Medicine

2024 Volume 5, Issue 2, Page(s) 101381

Abstract: Neuroendocrine carcinomas, such as neuroendocrine prostate cancer and small-cell lung cancer, commonly have a poor prognosis and limited therapeutic options. We report that ubiquitin carboxy-terminal hydrolase L1 (UCHL1), a deubiquitinating enzyme, is ... ...

Abstract	Neuroendocrine carcinomas, such as neuroendocrine prostate cancer and small-cell lung cancer, commonly have a poor prognosis and limited therapeutic options. We report that ubiquitin carboxy-terminal hydrolase L1 (UCHL1), a deubiquitinating enzyme, is elevated in tissues and plasma from patients with neuroendocrine carcinomas. Loss of UCHL1 decreases tumor growth and inhibits metastasis of these malignancies. UCHL1 maintains neuroendocrine differentiation and promotes cancer progression by regulating nucleoporin, POM121, and p53. UCHL1 binds, deubiquitinates, and stabilizes POM121 to regulate POM121-associated nuclear transport of E2F1 and c-MYC. Treatment with the UCHL1 inhibitor LDN-57444 slows tumor growth and metastasis across neuroendocrine carcinomas. The combination of UCHL1 inhibitors with cisplatin, the standard of care used for neuroendocrine carcinomas, significantly delays tumor growth in pre-clinical settings. Our study reveals mechanisms of UCHL1 function in regulating the progression of neuroendocrine carcinomas and identifies UCHL1 as a therapeutic target and potential molecular indicator for diagnosing and monitoring treatment responses in these malignancies.
MeSH term(s)	Male ; Humans ; Ubiquitin Thiolesterase/genetics ; Ubiquitin Thiolesterase/metabolism ; Carcinoma, Neuroendocrine/drug therapy ; Carcinoma, Neuroendocrine/genetics ; Small Cell Lung Carcinoma ; Lung Neoplasms/diagnosis ; Lung Neoplasms/drug therapy ; Membrane Glycoproteins
Chemical Substances	Ubiquitin Thiolesterase (EC 3.4.19.12) ; POM121 protein, human ; Membrane Glycoproteins ; UCHL1 protein, human
Language	English
Publishing date	2024-01-19
Publishing country	United States
Document type	Journal Article
ISSN	2666-3791
ISSN (online)	2666-3791
DOI	10.1016/j.xcrm.2023.101381
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Article ; Online: SanXoT: a modular and versatile package for the quantitative analysis of high-throughput proteomics experiments.

Trevisan-Herraz, Marco / Bagwan, Navratan / García-Marqués, Fernando / Rodriguez, Jose Manuel / Jorge, Inmaculada / Ezkurdia, Iakes / Bonzon-Kulichenko, Elena / Vázquez, Jesús

Bioinformatics (Oxford, England)

2019 Volume 35, Issue 9, Page(s) 1594–1596

Abstract: Summary: Mass spectrometry-based proteomics has had a formidable development in recent years, increasing the amount of data handled and the complexity of the statistical resources needed. Here we present SanXoT, an open-source, standalone software ... ...

Abstract	Summary: Mass spectrometry-based proteomics has had a formidable development in recent years, increasing the amount of data handled and the complexity of the statistical resources needed. Here we present SanXoT, an open-source, standalone software package for the statistical analysis of high-throughput, quantitative proteomics experiments. SanXoT is based on our previously developed weighted spectrum, peptide and protein statistical model and has been specifically designed to be modular, scalable and user-configurable. SanXoT allows limitless workflows that adapt to most experimental setups, including quantitative protein analysis in multiple experiments, systems biology, quantification of post-translational modifications and comparison and merging of experimental data from technical or biological replicates. Availability and implementation: Download links for the SanXoT Software Package, source code and documentation are available at https://wikis.cnic.es/proteomica/index.php/SSP. Contact: jvazquez@cnic.es or ebonzon@cnic.es. Supplementary information: Supplementary information is available at Bioinformatics online.
MeSH term(s)	Mass Spectrometry ; Peptides ; Proteins ; Proteomics ; Software
Chemical Substances	Peptides ; Proteins
Language	English
Publishing date	2019-02-20
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1422668-6
ISSN	1367-4811 ; 1367-4803
ISSN (online)	1367-4811
ISSN	1367-4803
DOI	10.1093/bioinformatics/bty815
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