MS/MS spectra were searched using MaxQuant (v1.5.2.8) and Andromeda as search engine. Acquired data were searched against an in-house generated database containing all the spiked-in proteins (Supplementary Table 2), and the E. coli Swissprot protein database (November 2015 version). Precur- sor 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. Match between runs was activated with a matching time window of 0.7 min and an alignment time window of 20 min. False discovery rate (FDR) in peptide identification was evaluated by using a decoy database and it was set to a maximum of 1%. PSM areas were extracted with the intensity extraction algorithm of MaxQuant. The differential abundance analysis was performed by MSstats R package. Quantification result is the same as in RMSV000000261.2. Top 5 features were used for statistical analysis in MSstats R package for this reanalysis.
**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/C5ZF0P]
[See
results attachment job
for details]
Keywords: MassIVE.quant reviewed - Platinum
Number of Files: | |
Total Size: | |
Experimental Design | |
Conditions:
|
|
Biological Replicates:
|
|
Technical Replicates:
|
|
Identification Results | |
Proteins (Human, Remapped):
|
|
Proteins (Reported):
|
|
Peptides:
|
|
Variant Peptides:
|
|
PSMs:
|
|
Quantification Results | |
Differential Proteins:
|
|
Quantified Proteins:
|
|
Browse Reanalysis Files | |
Browse Quantification Results | Browse Metadata |
FTP Download Link (click to copy):
|