Hi Ash,
Could you please be more specific about the review article?. I think Mzmine
does not have such feature.
In rode to do spectral counting in proteomic experiments, first you need to get
the identification of the spectrum (peptide sequence - Protein ID) and Mzmine
does not have that feature. That is performed using a software like Mascot or
Sequest. And using this id's, you can perform semi-absolute quantification
outside of Mzmine, just using excel.
Previously Mzmine had an option to create a mgf (Mascot Generic Format) file
from a peak list. Then you can send this file to a Mascot server. After
retrieving the identification from Mascot, Mzmine assigns the id to the
corresponding peak. But this is not for quantification, it's more like
confirmation of the true identity of the peaks on your data.
However, due the last improvements in Mzmine data model and modules management,
this option is currently unavailable. We have plans to implement this feature
again in the short future.
I hope this can help you,
Alex Villar
On Jun 29, 2012, at 8:11 AM, Ashkan Tafti wrote:
Hi,
I read in a review article "Mass Spectrometry-Based Label-Free Quantitative
Proteomics" that Mzmine is able to do label-free quantification or "spectral
counting". Is this true? If so, can someone tell me how to do it?
Thank you,
Ash
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