7 research outputs found
Screening Method Using Selected Reaction Monitoring for Targeted Proteomics Studies of Nasal Lavage Fluid
Proteomic-based studies of nasal lavage fluid (NLF) may
identify
molecular pathways associated with disease pathology and new biomarker
candidates of upper airway diseases. However, most studies have used
rather tedious untargeted MS techniques. Selected reaction monitoring
(SRM) is a sensitive and specific technique that can be used with
high throughput. In this study, we developed a semiquantitative SRM-based
method targeting 244 NLF proteins. The protein set was identified
through a literature study in combination with untargeted LCāMS/MS
analyses of trypsin-digested NLF samples. The SRM assays were designed
using MS/MS data either downloaded from a proteomic data repository
or experimentally obtained. Each protein is represented by one to
five peptides, resulting in 708 SRM assays. Three to four transitions
per assay were used to ensure analyte specificity. The majority (69%)
of the assays showed good within-day precision (coefficient of variation
ā¤20%). The accuracy of the method was evaluated by analyzing
four samples prepared with varying amounts of four proteins. Peptide
and protein ratios were in good agreement with expected ratios. In
conclusion, a high throughput screening method for relative quantification
of 244 NLF proteins was developed. The method should be of general
use in any proteomic study of the upper airways
Aggregation of Calcium Silicate Hydrate Nanoplatelets
We study the aggregation of calcium
silicate hydrate nanoplatelets
on a surface by means of Monte Carlo and molecular dynamics simulations
at thermodynamic equilibrium. Calcium silicate hydrate (C-S-H) is
the main component formed in cement and is responsible for the strength
of the material. The hydrate is formed in early cement paste and grows
to form platelets on the nanoscale, which aggregate either on dissolving
cement particles or on auxiliary particles. The general result is
that the experimentally observed variations in these dynamic processes
generically called <i>growth</i> can be rationalized from
interaction free energies, that is, from pure thermodynamic arguments.
We further show that the surface charge density of the particles determines
the aggregate structures formed by C-S-H and thus their growth modes
Time-Dependent Proteomic iTRAQ Analysis of Nasal Lavage of Hairdressers Challenged by Persulfate
Feasibility Study on Measuring Selected Proteins in Malignant Melanoma Tissue by SRM Quantification
Currently there are no clinically
recognized molecular biomarkers
for malignant melanoma (MM) for either diagnosing disease stage or
measuring response to therapy. The aim of this feasibility study was
to develop targeted selected reaction monitoring (SRM) assays for
identifying candidate protein biomarkers in metastatic melanoma tissue
lysate. In a pilot study applying the SRM assay, the tissue expression
of nine selected proteins [complement 3 (C3), T-cell surface glycoprotein
CD3 epsilon chain E (CD3E), dermatopontin, minichromosome maintenance
complex component (MCM4), premelanosome protein (PMEL), S100 calcium
binding protein A8 (S100A8), S100 calcium binding protein A13 (S100A13),
transgelin-2 and S100B] was quantified in a small cohort of metastatic
malignant melanoma patients. The SRM assay was developed using a TSQ
Vantage triple quadrupole mass spectrometer that generated highly
accurate peptide quantification. Repeated injection of internal standards
spiked into matrix showed relative standard deviation (RSD) from 6%
to 15%. All nine target proteins were identified in tumor lysate digests
spiked with heavy peptide standards. The multiplex SRM peptide assay
panel was then measured and quantified on a set of frozen MM tissue
samples obtained from the Malignant Melanoma Biobank collected in
Lund, Sweden. All nine proteins could be accurately quantified using
the new SRM assay format. This study provides preliminary data on
the heterogeneity of biomarker expression within MM patients. The
S100B protein, which is clinically used as the pathology identifier
of MM, was identified in 9 out of 10 MM tissue lysates. The use of
the targeted SRM assay provides potential advancements in the diagnosis
of MM that can aid in future assessments of disease in melanoma patients