Surface functionalization of silica microparticles for capillary electrochromatography (CEC)

We derivatized small (0.5 -3 {mu}m) silica particles by silating their surfaces with long-chain alkyl substituted silanes. These functionalized particles were packed into 100 {mu}m capillaries and used as stationary phases for capillary electrochromatography. The particles supported electroosmotic flow in mixtures of acetonitrile and aqueous buffer (4 mM sodium tetraborate or 2mM TRIS). The columns were used to separate mixtures of organic analytes demonstrating the effectiveness of the functionalized stationary phase

Demonstration of Protein-Based Human Identification Using the Hair Shaft Proteome

YesHuman identification from biological material is largely dependent on the ability to characterize genetic polymorphisms in DNA. Unfortunately, DNA can degrade in the environment, sometimes below the level at which it can be amplified by PCR. Protein however is chemically more robust than DNA and can persist for longer periods. Protein also contains genetic variation in the form of single amino acid polymorphisms. These can be used to infer the status of non-synonymous single nucleotide polymorphism alleles. To demonstrate this, we used mass spectrometry-based shotgun proteomics to characterize hair shaft proteins in 66 European-American subjects. A total of 596 single nucleotide polymorphism alleles were correctly imputed in 32 loci from 22 genes of subjects’ DNA and directly validated using Sanger sequencing. Estimates of the probability of resulting individual non-synonymous single nucleotide polymorphism allelic profiles in the European population, using the product rule, resulted in a maximum power of discrimination of 1 in 12,500. Imputed non-synonymous single nucleotide polymorphism profiles from European–American subjects were considerably less frequent in the African population (maximum likelihood ratio = 11,000). The converse was true for hair shafts collected from an additional 10 subjects with African ancestry, where some profiles were more frequent in the African population. Genetically variant peptides were also identified in hair shaft datasets from six archaeological skeletal remains (up to 260 years old). This study demonstrates that quantifiable measures of identity discrimination and biogeographic background can be obtained from detecting genetically variant peptides in hair shaft protein, including hair from bioarchaeological contexts.The Technology Commercialization Innovation Program (Contracts #121668, #132043) of the Utah Governors Office of Commercial Development, the Scholarship Activitie

RefSeq_Protein_Variant_Database

<p>The RefSeq Protein Variant Database is a unique protein sequence database, developed for the express purpose of defining variant peptides that can then be detected for use in the identification of individuals. This database is in Mascot compatible FASTA format and can be used in conjunction with proteomic mass spectrometry analytical tools such as X!tandem, Sequest, PEAKs and Mascot.</p

Direct validation of imputed non-synonymous SNP alleles.

<p><b>A</b>) Genetically variant peptides (GVPs) that contained single amino-acid polymorphisms (SAPs) were identified in both European-American cohorts (EA1 and EA2) and collated for each subject. Imputed nsSNP alleles (Gene Name = GN, SNP accession number = rs#, allele nucleotide = nuc) were directly compared to the genotype resulting from direct Sanger sequencing (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0160653#pone.0160653.s011" target="_blank">S1 Methods</a>). Correctly imputed nsSNP alleles (TP, true positives) are indicated by a blue square. Imputed alleles that were incorrectly predicted (FP, false positive) are indicated by red squares. Alleles that were identified using Sanger sequencing, but did not contain a resulting GVP in the matching proteomic dataset (FN, false negative) are indicated by light green squares. Alleles absent in both subjects DNA and in resulting proteomic datasets (TN, true negatives) are indicated by white squares[<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0160653#pone.0160653.ref049" target="_blank">49</a>]. Failed Sanger sequencing determination of nsSNP allelic status is indicated by grey. <b>B</b>) The effectiveness of each SAP-containing peptide to impute nsSNP alleles was also quantified. The sensitivity of each genetically variant peptide, measured as the proportion of nsSNP-alleles that are correctly detected and imputed (TP/(TP+FN)), was calculated as a percentage (log₁₀(%). The positive predictive value (PPV) of genetically variant peptide-based SNP imputations was calculated as the percentage of correct validated SNP imputations of all imputations (TP/(TP + FP); log₁₀(%))[<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0160653#pone.0160653.ref049" target="_blank">49</a>]. <b>C</b>)</p