MassIVE MSV000082389

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rawDiag

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Description

Data set for demonstration of rawDiag package functions. LC-MS data was recorded on a Q Exactive HF-X (Thermo Fisher Scientific) operated in line with an Acquity M-Class (Waters) UPLC. In short, peptides were loaded onto a nanoEase M/Z Symmetry C18 100A, 5 um, 180 um x 20 mm trap column (Waters, part# 186008821) and separated running a peace-wise linear gradient from 5% to 24% B in 50 min and 24% to 36% B in 10 min over the nanoEase M/Z C18 T3 Col 100A, 1.8 um, 75 um x 250 mm analytical column (Waters, part# 186008818) at a flow rate of 300 nl/min (buffer A: Water incl. 0.1% formic acid; buffer B: acetonitrile incl. 0.1% formic acid). Eluting peptides were ionized applying the principle of electro spray ionization on a Digital PicoView 550 (New Objective) nano source equipped with silica emitters (New Objective, part# FS360-20-10-N-20-C12 DOM). Data dependent analysis (DDA) was conducted by recording MS1 spectra at 60k R over the scan range of 350 to 1400 m/z. MS2 scans were acquired at 7500 R (AGC target: 1e5, maxIT: 11 ms) for the most abundant (topN: 36, 48 or 72) precursor signals using an isolation window of 1.3 Da and a NCE of 28 for peptide fragmentation. Dynamic exclusion was set to 10 s. Ions having a charge below 2 and above 6, as well as isotopes were excluded from further analysis. [dataset license: CC0 1.0 Universal (CC0 1.0)]

Keywords: LC-MS method optimization

Contact

Principal Investigators:
(in alphabetical order) 		Ralph Schlapbach, Functional Genomics Center Zurich, Switzerland
Submitting User: tobiasko

Publications

Christian Trachsel, Christian Panse, Tobias Kockmann, Witold Eryk Wolski, Jonas Grossmann, Ralph Schlapbach.
rawDiag - an R package supporting rational LC-MS method optimization for bottom-up proteomics.
rawDiag - an R package supporting rational LC-MS method optimization for bottom-up proteomics Christian Trachsel, Christian Panse, Tobias Kockmann, Witold Eryk Wolski, Jonas Grossmann, Ralph Schlapbach bioRxiv 304485; doi: https://doi.org/10.1101/304485.

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Experimental Design
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Identification Results
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Quantification Results
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Number of distinct conditions across all analyses (original submission and reanalyses) associated with this dataset.

Distinct condition labels are counted across all files submitted in the "Metadata" category having a "Condition" column in this dataset.

"N/A" means no results of this type were submitted.
Number of distinct biological replicates across all analyses (original submission and reanalyses) associated with this dataset.

Distinct replicate labels are counted across all files submitted in the "Metadata" category having a "BioReplicate" or "Replicate" column in this dataset.

"N/A" means no results of this type were submitted.
Number of distinct technical replicates across all analyses (original submission and reanalyses) associated with this dataset.

The technical replicate count is defined as the maximum number of times any one distinct combination of condition and biological replicate was analyzed across all files submitted in the "Metadata" category. In the case of fractionated experiments, only the first fraction is considered.

"N/A" means no results of this type were submitted.
Originally identified proteins that were automatically remapped by MassIVE to proteins in the SwissProt human reference database.

"N/A" means no results of this type were submitted.
Number of distinct protein accessions reported across all analyses (original submission and reanalyses) associated with this dataset.

"N/A" means no results of this type were submitted.
Number of distinct unmodified peptide sequences reported across all analyses (original submission and reanalyses) associated with this dataset.

"N/A" means no results of this type were submitted.
Number of distinct peptide sequences (including modified variants or peptidoforms) reported across all analyses (original submission and reanalyses) associated with this dataset.

"N/A" means no results of this type were submitted.
Total number of peptide-spectrum matches (i.e. spectrum identifications) reported across all analyses (original submission and reanalyses) associated with this dataset.

"N/A" means no results of this type were submitted.
Number of distinct proteins quantified across all analyses (original submission and reanalyses) associated with this dataset.

Distinct protein accessions are counted across all files submitted in the "Statistical Analysis of Quantified Analytes" category having a "Protein" column in this dataset.

"N/A" means no results of this type were submitted.
Number of distinct proteins found to be differentially abundant in at least one comparison across all analyses (original submission and reanalyses) associated with this dataset.

A protein is differentially abundant if its change in abundance across conditions is found to be statistically significant with an adjusted p-value <= 0.05 and lists no issues associated with statistical tests for differential abundance.

Distinct protein accessions are counted across all files submitted in the "Statistical Analysis of Quantified Analytes" category having a "Protein" column in this dataset.

"N/A" means no results of this type were submitted.
This dataset may not contain all raw spectra data as originally deposited in PRIDE. It has been imported to MassIVE for reanalysis purposes, so its spectra data here may consist solely of processed peak lists suitable for reanalysis with most software.