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Orbitrap: narrow-range, defined mixtures for quantitative proteomics (PubMed ID: 23879310)

ABSTRACT: These six Orbi replicates of samples A and B represent 36 proteins from the Sigma UPS1 that have been mixed in defined concentrations that span a narrow dynamic range. These "NRD A" and "NRD B" mixtures have, in turn, been spiked into Agilent Pyrococcus furiosus lysate.

INSTRUMENT(S): LTQ Orbitrap

ORGANISM(S): Homo Sapiens (ncbitaxon:9606) Pyrococcus Furiosus (ncbitaxon:2261)

SUBMITTER: Daniel C. Liebler

PROVIDER: MSV000078522 | MassIVE | Fri Jan 10 11:25:00 GMT 2014

REPOSITORIES: MassIVE

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Publications

IDPQuantify: combining precursor intensity with spectral counts for protein and peptide quantification.

Chen Yao-Yi YY Chambers Matthew C MC Li Ming M Ham Amy-Joan L AJ Turner Jeffrey L JL Zhang Bing B Tabb David L DL

Journal of proteome research 20130812 9

Differentiating and quantifying protein differences in complex samples produces significant challenges in sensitivity and specificity. Label-free quantification can draw from two different information sources: precursor intensities and spectral counts. Intensities are accurate for calculating protein relative abundance, but values are often missing due to peptides that are identified sporadically. Spectral counting can reliably reproduce difference lists, but differentiating peptides or quantify ...[more]

PMID: 23879310

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Orbitrap Velos: narrow-range, defined mixtures for quantitative proteomics (PubMed ID: 23879310)

Project description:These five Orbi Velos replicates of samples A and B represent 36 proteins from the Sigma UPS1 that have been mixed in defined concentrations that span a narrow dynamic range. These "NRD A" and "NRD B" mixtures have, in turn, been spiked into Agilent Pyrococcus furiosus lysate.

2014-01-10 | MSV000078521 | MassIVE

Arabidopsis thaliana spiked UPS1 standard protein mixtures

Project description:This project aims at providing a quantitative dataset from LC-MS/MS injections of a calibrated UPS1 mixture spiked in an Arabidopsis thaliana background.

2022-07-31 | PXD027800 | Pride

Transcription profiling by array of oral squamous cell cancer (OSCC) surgical margins defined by narrow band imaging.

Project description:The purpose of this study was to provide molecular evidence that surgical margin definition using narrow band imaging (NBI) resulted in more complete OSCC excision that conventional while light (WL) imaging. Samples were taken prospectively from 18 patients undergoing surgical resection for intraoral SCC (excluding lip, pharynx and hypopharynx). Biopsies were taken from the tumour and from 5mm beyond each of the abnormal tissue margins defined by WL and NBI. Transcriptional profiling was performed by microarray.

2018-01-17 | E-MTAB-5933 | biostudies-arrayexpress

MicroRNA profiling by array of oral squamous cell cancer (OSCC) surgical margins defined by narrow band imaging.

2018-02-09 | E-MTAB-6470 | biostudies-arrayexpress

UPS1-yeast standard analysis - Technical Brief Calibration Plot for Proteomics (CP4P): A graphical tool to visually check the assumptions underlying FDR control in quantitative experiments

Project description:Label-free quantification of various concentrations of Universal Proteomic Standard (UPS1, Sigma-Aldrich) spiked in yeast extract.

2015-11-27 | PXD002370 | Pride

Expression data from mouse embryo (E5) cultured in the narrow and wide cavity

Project description:The mouse anterior-posterior (A-P) axis polarization is preceded by formation of the distal visceral endoderm (DVE). However, the mechanism of the emergence of DVE cells is not well understood. Here, we show by in vitro culturing of embryos immediately after implantation in micro-fabricated cavities (narrow; 90 micro-meter, wide; 180 miro-meter in diameter) that the external mechanical cues exerted on the embryo, i.e. cultured in the narrow cavity, are crucial for DVE formation as well as elongated egg cylinder shape. This implies that these developmental events immediately after implantation are not simply embryo-autonomous processes but require extrinsic mechanical factors. Further whole genome-wide gene expression profiles with DNA microarray revealed that no significant difference of transcripts were evident with or without mechanical cues except DVE-related markers. Thus, we propose that external mechanical cues rather than not specific molecular pathways can trigger the establishment of the A-P axis polarization, which is one of the fundamental proccesses of mammalian embryogenesis. To identify the differences between the embryos cultured with or without external mechanical cues, we collected mouse embryos at E5.0 and cultured in the narrow (90 micro-meter in diameter) or the wide (180 micro-meter in diameter) cavities for 8 hours for RNA extraction and hybridization on Affymetrix microarrays. Arrays were performed using Affymetrix mouse Gene 1.0 ST arrays. Analysis was performed on three biological replicates of the mouse embryos cultured in the narrow and wide cavities for 8 hours.

2013-09-27 | E-GEOD-51198 | biostudies-arrayexpress

Pan-genome of narrow leaf lupin

Project description:New genome assembly of narrow-leafed lupin (Lupinus angustifolius) and its pan-genome

| PRJEB38006 | ENA

TMT10 controlled mixtures - SILAC HeLa UPS1, acquired using SPS-MS3

Project description:The controlled mixtures were prepared to evaluate the ability of our proposed approach when dealing with the complicated design, e.g. multiple TMT mixtures with technical replicates. 500, 333, 250, and 62.5 fmol UPS1 peptides were spiked-into 50 g SILAC HeLa peptides in duplicate. It produced a dilution series corresponding to 1, 0.667, 0.5, and 0.125 of the highest UPS1 peptide amount (500 fmol). In addition, a reference sample was generated by pooling all four diluted UPS1 peptide samples (286.5 fmol) and combined with 50 g of SILAC HeLa in duplicate. These 10 replicates were labeled with TMT10-plex reagents and mixed together to pass LC-MS/MS analysis. The procedure was repeated to generate a total of five such controlled mixtures. To assess technical variability, three technical replicates were prepared for each mixture. Totally there are 15 MS runs from 5 TMT mixtures. LC-MS/MS was performed using an EASY-nLC 1200 ultrahigh pressure liquid chromatography (UHPLC) connected to an Orbitrap Fusion Lumos Tribrid and equipped with an EASY-spray source (Thermo Fisher Scientific, San Jose, CA). The data was acquired using an MS2/MS3 (also called multinotch MS3 or Synchronous Precursor Selection, SPS).

2019-08-30 | MSV000084264 | MassIVE

Tube-gel digestion: a fast and reproducible sample preparation protocol for label-free quantitative proteomics of complex biological samples

Project description:Comparison of tube-gel protocol to stacking gel and liquid digestion for label-free extracted ion-current quantification of complex biological samples Dataset with known fold-changes (UPS1 spiked in yeast background at 25-10-5-2.5-1-0.5 fmol)

2016-10-18 | PXD003841 | Pride

TMT10 controlled mixtures - SILAC HeLa UPS1, acquired using MS2-only strategy

Project description:The controlled mixtures were prepared to evaluate the ability of our proposed approach when dealing with the complicated design, e.g. multiple TMT mixtures with technical replicates. 500, 333, 250, and 62.5 fmol UPS1 peptides were spiked-into 50 g SILAC HeLa peptides in duplicate. It produced a dilution series corresponding to 1, 0.667, 0.5, and 0.125 of the highest UPS1 peptide amount (500 fmol). In addition, a reference sample was generated by pooling all four diluted UPS1 peptide samples (286.5 fmol) and combined with 50 g of SILAC HeLa in duplicate. These 10 replicates were labeled with TMT10-plex reagents and mixed together to pass LC-MS/MS analysis. The procedure was repeated to generate a total of five such controlled mixtures. To assess technical variability, three technical replicates were prepared for each mixture. Totally there are 15 MS runs from 5 TMT mixtures. LC-MS/MS was performed using an EASY-nLC 1200 ultrahigh pressure liquid chromatography (UHPLC) connected to an Orbitrap Fusion Lumos Tribrid and equipped with an EASY-spray source (Thermo Fisher Scientific, San Jose, CA). The same samples for MSV000084264 (or PXD0015258) are used. The data were acquired using MS2-only strategies.

2019-08-31 | MSV000084266 | MassIVE

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