Peak scanner software

Manufactured by Thermo Fisher Scientific

Sourced in United States, United Kingdom

Peak Scanner software is a data analysis tool designed for scientists and researchers working in the field of chromatography. The software provides an intuitive interface for visualizing, analyzing, and reporting data from chromatographic experiments. It offers automated peak detection, integration, and quantification capabilities to assist users in the interpretation of their chromatographic results.

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Peak Scanner software v1.0 (63 citations) Peak Scanner (41 citations) Peak Scanner Software version 1.0 (14 citations) Peak Scanner Software 2 (13 citations) Peak Scanner Software 1.0 (4 citations) Peak Scanner software v 2.0 (3 citations)

72 protocols using peak scanner software

Capillary Electrophoresis Data Analysis

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The CE data analysis workflow is outlined in Figure 1. Peak Scanner software (Applied Biosystems) displays CE peak fluorescence intensity and generates an .fsa file of raw data including peak dye, size, height, area, as well as information about peak start and end points. The .fsa file data can be exported as a comma-separated values (.csv) file and manually analyzed with spreadsheet software such as Microsoft Excel or Apple Numbers. Relevant data peaks are identified and peak areas are extracted (Figure 1). The fraction of substrate or products is calculated as described in Figure 1. If necessary, the product concentration can then be calculated by multiplying (starting substrate concentration)*(%product). Relative peak areas from each capillary should be analyzed independently since the amount of injected DNA varies between capillaries due to differences in loading efficiencies and buffer conditions. Manual analysis of substrates and products using Microsoft Excel or other spreadsheet software is straightforward, yet analysis of large data sets is time consuming (>1 h analysis per 96 reactions). To speed analysis, custom software tools or macros can be designed to rapidly extract and analyze large data sets (<10 s analysis per 96 reactions) and increase throughput. For final data analysis, data are plotted and curves fit using standard statistical or graphical software.

Greenough L., Schermerhorn K.M., Mazzola L., Bybee J., Rivizzigno D., Cantin E., Slatko B.E, & Gardner A.F. (2015). Adapting capillary gel electrophoresis as a sensitive, high-throughput method to accelerate characterization of nucleic acid metabolic enzymes. Nucleic Acids Research, 44(2), e15.

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Quantifying modA2 Expression in Chinchilla Otitis Media

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Fluid samples were taken from the left and right middle ears on days 0, 2, 4, 7, 10, 14, 18 and 22 from each cohort of 10 chinchillas that had been challenged with either strain 723 modA2(22)ON or strain 723 modA2(24)OFF. The ratio of modA2ON and modA2OFF from the starting inoculum (day 0) compared with days 4, 7, 10, 14, 18 and 22 was verified via fragment analysis for each of the chinchillas. Samples were thawed briefly on ice, with 1 μl serving as the template in a 25 μl GoTaq PCR reaction (Promega) using primers Him1F and Him3 (Supplementary Table 5) as described previously^{6 (link)}. Samples were run using GeneScan fluorescent-PCR fragment-length analysis by GUDSF, and analysed using Peak Scanner software (Applied Biosystems).

Atack J.M., Srikhanta Y.N., Fox K.L., Jurcisek J.A., Brockman K.L., Clark T.A., Boitano M., Power P.M., Jen F.E., McEwan A.G., Grimmond S.M., Smith A.L., Barenkamp S.J., Korlach J., Bakaletz L.O, & Jennings M.P. (2015). A biphasic epigenetic switch controls immunoevasion, virulence and niche adaptation in non-typeable Haemophilus influenzae. Nature Communications, 6, 7828.

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Differential Diagnosis of Ovine Footrot

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The four D. nodosus tandem repeat (DNTR) loci were amplified individually as described previously (Russell et al., 2014 (link)) (Table 1) from the DNA isolated from the feet of all ewes and lambs. Primer specificity was tested against genomic DNA isolated from 11 bacterial species and from a range of diverse environmental samples (Supplementary Table 2). D. nodosus strain VCS1703A was included as a positive control for all PCR reactions. The amplified products from the community DNA were pooled in the ratio of 1:1:1:1 and submitted for fragment analysis to the University of Dundee (DNA Sequencing & Services, Dundee, Scotland). GeneScan 1200 LIZ dye (Applied Biosystems, Warrington, UK) was used as a size standard in fragment analysis. The data obtained were processed using Peak Scanner Software (Applied Biosystems, Warrington, UK) and analysed using T-REX (Culman et al., 2009 (link)) with a minimum fragment length cut off values of 300 bp and 500 bp for DNTR10 and DNTR19 respectively, peak height baseline threshold of 40 and bin range of 4 bp.

Muzafar M., Calvo-Bado L.A., Green L.E., Smith E.M., Russell C.L., Grogono-Thomas R, & Wellington E.M. (2015). The role of the environment in transmission of Dichelobacter nodosus between ewes and their lambs. Veterinary Microbiology, 179(1-2), 53-59.

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Spatial and Temporal Genetic Structure of Crab

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To study the spatial genetic structure, 291 adult crabs were sampled from six localities: Concepción (CO), Los Molinos (LM), Ancud (AN), Calbuco (CA), Dalcahue (DA) and Quellón (QU) (Fig 1). Samples were obtained by Scuba diving during 2011 to 2014. To study the temporal genetic variability a total of 157 megalopa larvae were collected from Los Molinos (LM) during four years (2009 to 2012) using a passive larva collector, described by Pardo et al. 2010 [42 ]. Each megalopa was identified using the description of Pardo et al. (2009b) [41 ] and stored in 95% ethanol until analysis. Sample size and year of sampling are shown in Table 1. All collections and analyses were conducted in Chile and complied with its existing laws (Resolución Exenta No. 3088 Subsecretaría de Pesca).
Genomic DNA was extracted from adult crabs using the salt method described by Aljanabi and Martinez (1997) [43 (link)]. DNA was extracted from megalopae using the QIAamp DNA Mini Kit (QIAGEN) and purified with sodium acetate (3M, pH 5.2). Eight polymorphic microsatellite loci were amplified following the procedure of Rojas-Hernández et al. (2014) [44 ]. Fragment analysis was performed using an Applied Biosystems 3100 sequencer at the Pontificia Universidad Católica de Chile. The allelic data matrix was built using the Peak Scanner software (Applied Biosystems).

Rojas-Hernandez N., Veliz D., Riveros M.P., Fuentes J.P, & Pardo L.M. (2016). Highly Connected Populations and Temporal Stability in Allelic Frequencies of a Harvested Crab from the Southern Pacific Coast. PLoS ONE, 11(11), e0166029.

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DNA Footprinting Analysis Protocol

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Footprinting was performed according to a previously described method (42 (link)). DNA fragments were generated by PCR with TaKaRa LA Taq (TaKaRa Bio Inc., Shiga, Japan). PCR products were purified and ligated with pGEM-T Easy (Promega) using Ligation High ver. 2 (Toyobo, Osaka, Japan). The resulting plasmids were then used as a template for the amplification of DNA probes using the primer pair Fp-M13-F and Fp-M13-R (5′ 6-carboxyfluorescein [FAM] labeled). DNA fragments (0.45 pmol) were mixed with purified proteins in 50 μl of a reaction mixture containing the same buffer used for gel shift assays. After a 20-min incubation at room temperature, the reaction mixtures were treated with 0.3 U of DNase I (Promega, Madison, WI) for 1 min and then purified by phenol-chloroform-isoamyl alcohol (CIAA) extraction and ethanol precipitation. After purification, the samples were analyzed using an ABI 3130xl Genetic Analyzer equipped with the Peak Scanner software (Applied Biosystems).

Yu L., Hisatsune J., Hayashi I., Tatsukawa N., Sato’o Y., Mizumachi E., Kato F., Hirakawa H., Pier G.B, & Sugai M. (2017). A Novel Repressor of the ica Locus Discovered in Clinically Isolated Super-Biofilm-Elaborating Staphylococcus aureus. mBio, 8(1), e02282-16.

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Genetic Analysis of HSAN Cases

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All undiagnosed HSAN cases through NGS were processed through (GGC)exp analysis in the NOTCH2NLC gene. Primer design, RP-PCR, and fluorescence amplicon length analysis were carried out according to our previous study (14 (link)).
All PCR products of RFC1 and NOTCH2NLC were subjected to capillary electrophoresis using the ABI PRISM 3130xL Genetic Analyzer (Applied Biosystems, Foster City, CA, USA), and results were visualized using the Peakscanner software (Applied Biosystems).

Yuan J.H., Higuchi Y., Ando M., Matsuura E., Hashiguchi A., Yoshimura A., Nakamura T., Sakiyama Y., Mitsui J., Ishiura H., Tsuji S, & Takashima H. (2022). Multi-type RFC1 repeat expansions as the most common cause of hereditary sensory and autonomic neuropathy. Frontiers in Neurology, 13, 986504.

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Characterization of C. difficile Isolates

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The C. difficile isolates used in this study include those from our laboratory collection and those kindly provided by Richard Stabler (London School of Hygiene and Tropical Medicine, London, United Kingdom), Trevor Lawley (Wellcome Trust Sanger Institute, Cambridge, United Kingdom), and Mark Wilcox (University of Leeds, Leeds, United Kingdom), who also donated the U.S. strains. The Australian strains were a kind gift from Dena Lyras (Monash University, Australia) and Tom Borody (Center for Digestive Diseases, Australia). C. difficile strains were subcultured on brain heart infusion (BHI) agar (Oxoid, Ltd., United Kingdom) supplemented with 7% defibrinated horse blood (TCS Biosciences, Ltd., United Kingdom). The strains were preserved in Protect bacterial preservers (Abtek Biologicals Ltd., Liverpool, United Kingdom) and stored at −80°C. Strains were characterized using the primers 5′-TTGAGCGATTTACTTCGGTAAAGA-3′ and 5′-CCATCCTGTACTGGCTCACCT-3′ targeting the C. difficile 16S rRNA gene (38 (link)) and capillary gel electrophoresis-based PCR ribotyping with primers 5′-GTGCGGCTGGATCACCTCCT-3′ and 5′-CCCTGCACCCTTAATAACTTGACC-3′ to amplify the 16S-23S rRNA genes (39 (link)). Data analysis was performed using Peak Scanner software (Applied Biosystems, United Kingdom) and the Multivariate statistical package (version 3.1).

Nale J.Y., Spencer J., Hargreaves K.R., Buckley A.M., Trzepiński P., Douce G.R, & Clokie M.R. (2016). Bacteriophage Combinations Significantly Reduce Clostridium difficile Growth In Vitro and Proliferation In Vivo. Antimicrobial Agents and Chemotherapy, 60(2), 968-981.

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Capillary Electrophoresis Protocol for Kinetic Analysis

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Samples of 20 μL, containing 0.4 nM (incorporation of free nucleotides) or 2 nM (incorporation of conjugated nucleotides) 5′-FAM-labelled oligonucleotides and ~0.3 μL GeneScan 600 LIZ dye size standard in 75% Hi-Di formamide, were submitted to the UC Berkeley Sequencing Facility for capillary electrophoresis (CE). CE samples were run on an Applied Biosystems 3730xl DNA Analyzer with a 50 cm capillary array, containing POP-7 Polymer, with 15-s injection at 1.5 kV and a 41-min run at 15 kV, oven temperature of 68 °C, and buffer temperature of 35 °C. Electropherogram data files were processed using custom software written in R (r-project.org) with comparable functionality to the Peak Scanner software from Applied Biosystems. Substrate and product peak heights were measured to calculate relative yields at each time point of a time course. Each time course was fit to a monoexponential form in R (Formula: 1-y ~ exp(-k*x), where y = relative yield, x = time, and k = rate constant) and data are reported as the mean and standard deviation of the fitted rates for each set of replicates.

Barthel S., Palluk S., Hillson N.J., Keasling J.D, & Arlow D.H. (2020). Enhancing Terminal Deoxynucleotidyl Transferase Activity on Substrates with 3′ Terminal Structures for Enzymatic De Novo DNA Synthesis. Genes, 11(1), 102.

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Microsatellite Genotyping of Plasmodium falciparum

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The length of PCR products was determined with reference to an internal size standard (LIZ 600) using the GeneMapper software v5 (Applied Biosystems, USA). Alleles were scored manually using Peak Scanner Software (Applied Biosystems, USA) a height of 100 relative fluorescence units (rfu) used as the minimal peak threshold, any allele with a peak value of at least 100 rfu was scored. The size range of the alleles and the average number of alleles per loci for each population were calculated [31 (link)]. The allele sizes obtained from the control P. falciparum strain, 3D7 were used to correct run-to-run variation among capillary electrophoresis runs.

Amoah L.E., Abukari Z., Dawson-Amoah M.E., Dieng C.C., Lo E, & Afrane Y.A. (2021). Population structure and diversity of Plasmodium falciparum in children with asymptomatic malaria living in different ecological zones of Ghana. BMC Infectious Diseases, 21, 439.

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Quantifying TNNT3 Splice Forms in Rat Muscle

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The methods used for RNA isolation, reverse transcription, and PCR analysis as well as the sequence of the primers used to quantify TNNT3 splice forms has been previously published (Schilder et al. 2011 (link)). Briefly, the frozen gastrocnemius muscle was pulverized under liquid nitrogen and total RNA was isolated using Trizol reagent as per the manufacturer’s protocol (Invitrogen). cDNA was prepared using a High Capacity cDNA Reverse Transcription kit (Applied Biosystems), and PCR was carried out using GoTaq DNA polymerase (Promega) with a fluorescein-labeled forward primer and two reverse primers as previously described (Schilder et al. 2011 (link)). The fluorescein-labeled PCR amplicons were analyzed by capillary electrophoresis (3730XL DNA Analyzer, Applied Biosystems) and the fragment size of the PCR amplicons was determined using the 1200 LIZ internal size standard (Applied Biosystems). The peak height value for each PCR amplicon was obtained by analysis using Peak Scanner software (Applied Biosystems). This method (Schilder et al. 2011 (link)) was previously used to identify PCR amplicons corresponding to all 12 TNNT3 splice forms in rat gastrocnemius muscle based on fragment size (Supplementary Figure S1). The relative abundance of each TNNT3 splice form was calculated as the ratio of its detected peak height to the total of all peak heights.

Ravi S., Schilder R.J., Berg A.S, & Kimball S.R. (2015). Effects of Age and Hindlimb Immobilization and Remobilization on Fast Troponin T Precursor mRNA Alternative Splicing in Rat Gastrocnemius Muscle. Applied physiology, nutrition, and metabolism = Physiologie appliquee, nutrition et metabolisme, 41(2), 142-149.

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