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

ABSTRACT: 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.

INSTRUMENT(S): LTQ Orbitrap Velos

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

SUBMITTER: Daniel C. Liebler

PROVIDER: MSV000078521 | MassIVE | Fri Jan 10 11:24:00 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: narrow-range, defined mixtures for quantitative proteomics (PubMed ID: 23879310)

Project description: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.

2014-01-10 | MSV000078522 | MassIVE

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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

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

Disturbed intramitochondrial phosphatidic acid transport impairs cellular stress signaling

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MaxLFQ label-free quantification algorithm benchmark datasets

Project description:We developed a set of algorithms for label-free quantification, termed MaxLFQ, embedded into MaxQuant. This contains two datasets to benchmark MaxLFQ: The proteome benchmark dataset consists of of HeLa and E. coli lysates mixed at defined ratios. The dynamic range benchmark dataset consists of UPS1/UPS2 standards (Sigma) spiked into E. coli lysates and quantified against each other.

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