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Reanalysis of spike-in samples

ABSTRACT: Two samples in submission PXD001091 were reanalysed 22 months later on the same instrument.

INSTRUMENT(S): LTQ Orbitrap XL ETD

ORGANISM(S): Streptoccous Pyogenes

SUBMITTER: Fredrik Levander

LAB HEAD: Fredrik Levander

PROVIDER: PXD002037 | Pride | 2015-04-20

REPOSITORIES: Pride

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Dataset's files

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			Action	DRS
	141126_AS_6_I_P_01.mgf	Mgf
	141126_AS_6_I_P_01.raw	Raw
	141126_AS_6_I_P_02.mgf	Mgf
	141126_AS_6_I_P_02.raw	Raw
	141126_AS_8_I_P_01.mgf	Mgf

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Publications

Is label-free LC-MS/MS ready for biomarker discovery?

Sandin Marianne M Chawade Aakash A Levander Fredrik F

Proteomics. Clinical applications 20150321 3-4

Label-free LC-MS methods are attractive for high-throughput quantitative proteomics, as the sample processing is straightforward and can be scaled to a large number of samples. Label-free methods therefore facilitate biomarker discovery in studies involving dozens of clinical samples. However, despite the increased popularity of label-free workflows, there is a hesitance in the research community to use it in clinical proteomics studies. Therefore, we here discuss pros and cons of label-free LC- ...[more]

PMID: 25656266

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Bull plasma proteomes at different seasons

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Bull seminal plasma proteomes follow-up

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Reanalysis of Chinese Treponema pallidum samples: all Chinese samples cluster with SS14-like group of syphilis-causing treponemes.

Project description:ObjectiveTreponema pallidum subsp. pallidum (TPA) is the causative agent of syphilis. Genetic analyses of TPA reference strains and human clinical isolates have revealed two genetically distinct groups of syphilis-causing treponemes, called Nichols-like and SS14-like groups. So far, no genetic intermediates, i.e. strains containing a mixed pattern of Nichols-like and SS14-like genomic sequences, have been identified. Recently, Sun et al. (Oncotarget 2016. https://doi.org/10.18632/oncotarget.10154 ) described a new "phylogenetic group" (called Lineage 2) among Chinese TPA strains. This lineage exhibited a "mosaic genomic structure" of Nichols-like and SS14-like lineages.ResultsWe reanalyzed the primary sequencing data (Project Number PRJNA305961) from the Sun et al. publication with respect to the molecular basis of Lineage 2. While Sun et al. based the analysis on several selected genomic single nucleotide variants (SNVs) and a subset of highly variable but phylogenetically poorly informative genes, which may confound the phylogenetic analysis, our reanalysis primarily focused on a complete set of whole genomic SNVs. Based on our reanalysis, only two separate TPA clusters were identified: one consisted of Nichols-like TPA strains, the other was formed by the SS14-like TPA strains, including all Chinese strains.

| S-EPMC5765698 | biostudies-literature

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