GNPS - salvia officinalis samples format mzML LCMS
Ontology highlight
ABSTRACT:
INSTRUMENT(S): LCMS-8045
ORGANISM(S): Salvia Officinalis (ncbitaxon:38868)
SUBMITTER: 
Natalia Pachura
PROVIDER: MSV000090117 | GNPS | Fri Aug 12 03:31:00 BST 2022
REPOSITORIES: GNPS
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Project description:Salvia officinalis- extracts obtain from herb subjected to convective drying at 40 degrees. Exctract obtained by maceration in eighty percent of methanol.
2022-08-12 | MSV000090117 | MassIVE
Project description:This is a study to characterize gene expression profiles in stored Russet Burbank potato tubers. Tubers were harvested from commercial fields in the central sands region of Wisconsin in the fall of 2006. The tubers were put into storage at 55 degrees F for preconditioning and wound healing. Shortly after the temperature of the storage bin began to decrease, uniform, healthy tubers were selected for use in this microarray analysis. Tubers were at 53.6 degrees F at this time, and pieces of starch-storing tissue were collected for use as the reference sample. Other tubers were moved to temperature-controlled lockers and these were cooled gradually to either 48 or 40 degrees F following industry standard procedures. The expectation was that tubers held at 48 degrees would not have a significant accumulation of glucose and fructose, but that tubers cooled to 40 degrees would undergo low temperature sweetening and accumulate glucose and fructose to a degree that is unsuitable for processing. Three weeks later, when the locker temperatures were 48 degrees F and 41.5 degrees F, tissue samples were collected for RNA analysis. After another three weeks, samples were collected from tubers at 48 degrees F and 40 degrees F. At that time some tubers were moved from the 48 degree locker to the 40 degree locker in order to see if gene expression changes observed as a result of gradual cooling are similar to those that occur following a sudden decrease in temperature. Three weeks later, samples were collected from tubers held at 48 degrees F, tubers held at 40 degrees F, and from the tubers that were moved from 48 to 40 degrees F. At this time another set of tubers was transferred from 48 degrees to 40 degrees. Three weeks later the last samples were harvested from tubers held at 48 degrees F, from tubers held at 48 degrees F and from tubers that were transferred three weeks prior from 48 to 40 degrees. RNA was isolated from tissue extracted from three tubers. Keywords: Reference design
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2010-06-02 | GSE16535 | GEO
Project description:In this data set we investigate dynamic differences in the transcriptome between 37 and 40 degrees C after treatment with TNFalpha. In the continuous temperature experiments, cells were grown at 37 degrees C and were then left at 37 degrees C, or transferred to 40 degrees C, for 1hour after which they (at time 0) were stimulated with 10 ng/ml of TNFα . Measurements were taken at 0, 30, 130, 230 and 430 minutes. In the 'switch' experiment, cells were grown the same way but the temperature of the incubator was turned up to 40 degrees C after 200 minutes. Measurements were taken at 230 and 430 minutes.
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Project description:The LC-MS study was carried out to identify the proteins in urine samples of clinical cases of diabetic nephropathy (Healthy control, Diabetic group, Microalbuminuria, Overt albuminuria group).
Study design
The urine samples (10 ml) of patients with HbA1c greater than 6.5 percent were collected in a sterile container from the endocrinology OPD, PGIMER, Chandigarh, India, after obtaining informed consent. The study was carried out following the Helsinki Declaration. The Institute Ethics Committee approved the study protocol via (IEC) vide No INT/IEC/2020/SPL-1031.
The spot dipstick method was used to screen urine samples for the presence of blood (haematuria) and pus cells (leucocytes). Samples showing the presence of both blood and leucocytes were further excluded from the study. After screening, 90 patient samples (30 diabetic controls, 30 microalbuminuria, and 30 overt albuminuria) were included in the study. For control, urine samples of 30 healthy controls were also included in the study.
The albumin excretion rate parameters (Albumin to creatinine ratio (ACR)) was measured in Alere Afinion TM AS100 Analyser with ACR test kits. The ACR was expressed in mg per gram. Based on the obtained ACR, the patient groups were categorized following criteria as detailed under inclusion criteria. The inclusion and exclusion criteria are mentioned below.
Inclusion criteria
Microalbuminuria (meant as diabetic microalbuminuria)- Established case of Diabetes Mellitus with glycated hemoglobin more than or equal to 6.5 percent and urinary albumin excretion rate 30 to 300 mg per gram of creatinine in a spot urine sample.
Overt albuminuria (meant as diabetic overt albuminuria): Established case of Diabetes Mellitus with glycated hemoglobin more than or equal to 6.5 percent and urinary albumin concentration more than or equal to 300 mg per gram of creatinine in a spot urine sample.
Diabetic Control- Established case of diabetes mellitus with glycated hemoglobin more than or equal to 6.5 percent and urinary albumin excretion rate of less than 30 mg per gram of creatinine in a spot urine.
Exclusion criteria
Patients with any evidence of urine tract infection or haematuria by dipstick test.
Separation of urinary proteins
The urinary proteins are separated from the urine matrix through centrifugation (15000 g for 1 hour at 4 degrees Celsius. The pellet obtained was expected to contain the proteins. For this, a 2 ml urine sample was subjected to centrifugation for each participant. After centrifugation (1ml in different aliquots), 2 pellets from the same sample were obtained. The pellets were suspended in PB (200 microlitres, pH 7.38, 0.1 M) and mixed well with a vortex. The pellets obtained from the same group were pooled. A similar treatment was provided to all the samples to obtain pellets. Protein quantification was done using the BCA method.
LC-MS protocol: For this, 100 micrograms of urinary protein in 10 mM Tris HCl buffer, pH 7.38 was denatured by boiling with 10 mM dithiothreitol for 10 mins followed by the addition of Iodoacetamide (90 mM, SIGMA) and incubation for 30 mins in the dark at 37 degrees Celsius. These were then subjected to trypsin digestion (2 micrograms, Promega, MS grade, prepared in acetic acid) and kept overnight at 37 degrees Celsius. The reaction was stopped by the addition of 1 percent trifluoroacetic acid (TCI, LC-MS grade). The sample clean-up with C18 resins column was performed and the aliquots were then sent for data acquisition (PMID 39216816).
The different raw files obtained are named as follows and uploaded.
1- Healthy Control
2- Diabetic Controls
3- Microalbuminuria
4- Overt albuminuria
Prof Dibyajyoti Banerjee, Dr. Rajasri Bhattacharyya, Dr. Sheemona Chowdhary, Dr. Deepak Kumar, and Ms Monu Kumari acknowledge ICMR, New Delhi, India, sanctioned project titled Pseudoesterase activity of albumin as a determinant for serum cholesterol in rabbits for financial support.
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Project description:mzML and mzIdentML are commonly used, powerful tools for representing mass spectrometry data and derived identification information. These formats are complex, requiring non-trivial logic to translate data into the appropriate representation. Most published implementations are tightly coupled to data structures. The most complete implementations are written in compiled languages that cannot expose the complete flexibility of the implementation to external programs or bindings. To our knowledge, there are no complete implementations for mzML or mzIdentML available to scripting languages like Python or R. We present psims, a library written in Python for writing mzML and mzIdentML. The library allows writing either XML format using built-in Python data structures. It includes a controlled vocabulary resolution system to simplify the encoding process and an identity tracking system to manage entity relationships. The source code is available at https://github.com/mobiusklein/psims, and through the Python Package Index as psims, licensed under the Apache 2 common license.
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2015-03-23 | GSE67098 | GEO
Project description:Intervention1: Biopsy: The biopsy tissue will be processed to obtain the primary cell line. In the next stage of the study, the cultured primary cell line will be subjected to
various chemotherapeutic agents in different concentrations and studied using real
time cell analyzer for 5 days to obtain IC50 values. Both the primary cells and
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Control Intervention1: Nil: Nil
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