Computational protocol: Comparative proteomic profiling of refractory/relapsed multiple myeloma reveals biomarkers involved in resistance to bortezomib-based therapy

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Protocol publication

[…] The raw files that were positively evaluated by PD were quantitatively analyzed by MQ/Perseus [, ] version 1.5.1.2, as previously described []. A protein was considered to be differentially expressed if the difference was statistically significant (p < 0.05), the minimum fold change was +/− 1.5, and it was identified with a minimum of 2 peptides with >99% confidence. Multivariate analyses were conducted by untargeted principal component analysis (PCA). All statistical analyses were performed using Statistica v. 10.0 software (StatSoft, Inc., www.statsoft.com) and Perseus 1.4.1.3, which is freely available from the MQ web site. [...] Only the proteins that were quantified as unique and non-redundant were used in the subsequent analyses. Proteins with a fold change of at least 1.5 that were identified as differential by both LF- and iTRAQ-based approaches were considered to be differentially expressed and were subsequently analyzed. The dysregulated proteins were chosen based on the criterion that the protein must be quantified by a minimum of two peptides with >99% confidence. Uncharacterized proteins were excluded from the analysis. The differential proteins were analyzed using the DAVID (http://david.abcc.ncifcrf.gov/) [] and PANTHER (http://pantherdb.org/) [] analysis tools to identify enriched functions, biological process and pathways categories []. Benjamini-corrected P-values less than 0.05 were considered significant. Pathway analysis using the DAVID tool was based on the REACTOME, KEGG pathway and PANTHER databases. […]

Pipeline specifications

Software tools Perseus, Statistica, DAVID, PANTHER
Applications Miscellaneous, MS-based targeted proteomics, Protein sequence analysis
Organisms Homo sapiens
Diseases Multiple Myeloma, Fatigue Syndrome, Chronic
Chemicals Dexamethasone, Doxorubicin