Hello, I received a dataset (from proteome discoverer) containing the below information for both protein and peptide levels:
Protein level:
Accession
Description
Exp. q-value
Sum PEP Score
Coverage
Peptides
PSMs
Unique Peptides
AAs
MW [kDa]
calc. pI
Score Sequest HT
Peptides Sequest HT
Peptide level:
Annotated Sequence
Master Protein Accessions
Missed Cleavages
Charge
DeltaScore
DeltaCn Rank
Search Engine Rank
m/z [Da]
MH+ [Da]
DeltaM [ppm]
Deltam/z [Da]
Activation Type MS Order
Isolation Interference [%]
Ion Inject Time [ms]
RT [min]
First Scan
Spectrum File
Ions Matched
XCorr
Percolator q-Value
Percolator PEP
However, there is no quantitative values of proteins that enables me to do deferentially expression analysis, and …. May I ask whether it is possible to perform protein quantitation from this dataset by MSnbase package? If the quantification of protein values is possible from my dataset, may I ask which of the above features can be used for calculation of protein values?
I would highly appreciate great help in this regard.
Yes, you could do quantitation in
MSnbase
, depending on your MS quantitation methodology employed. However, from you mail above, it doesn't seem that you have the raw data anyway. Also, it is unclear what quantitation methodology was used - it could be spectral counting, or may be the quantitation values are stored in the Sequest variables? I would be useful to clarify what kind of quantitative data you have received.