MS/MS spectra were searched using MaxQuant (v1.5.1.2) and Andromeda as search engine. Acquired data were searched against a concatenated database containing all the UPS human spike-in proteins and all reviewed E.coli K-12 (Taxonomy ID 83333) proteins in Unipro(downloaded November 2015). Precursor ion mass tolerance was set to 4.5 ppm at the MS1 level and to 0.5 Da at the fragment ion level. Up to three missed cleavages for trypsin were allowed. Oxidation of methionine and protein N-terminal acetylation were considered as variable modifications, whereas carbamidomethylation on cysteines was set as a fixed modification. False discovery rate (FDR) in peptide and protein identification was evaluated by using a decoy database and it was set to a maximum of 1%. All identified peptides were quantified with MaxQuant's LFQ algorithm, with the 'match between runs' option activated using a matching time window of 0.7 min and an alignment time window of 20 min. PSM areas were extracted with the intensity extraction algorithm of MaxQuant.The quantification result is the same as in RMSV000000249.2. The differential abundance analysis was performed by MSstats (v3.16.2) R package: Uninformative features and outliers were flagged by feature selection algorithm and removed for this reanalysis. Details for data processing and statistical analysis are available in description.pdf ('Methods' folder).
**Publication : Tsai TH, Choi M, Banfai B, Liu Y, MacLean BX, Dunkley T, Vitek O. (2020). Selection of features with consistent proles improves relative protein quantification in mass spectrometry experiments. Molecular & Cellular Proteomics. 2020 March 31, 19(6) 944-959, doi:10.1074/mcp.RA119.001792. PMID: 32234965.
[doi:10.25345/C57436]
[See
results attachment job
for details]
Keywords: MassIVE.quant reviewed - Platinum
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Identification Results | |
Proteins (Human, Remapped):
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Quantification Results | |
Differential Proteins:
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Browse Reanalysis Files | |
Browse Quantification Results | Browse Metadata |
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