Other Key Considerations
Other Key Considerations
Speed
Speed
We can deliver results to your inbox in record time, regardless of the number or size of your MS files, the size of your FASTA file, or the number of PTMs considered.
We can deliver results to your inbox in record time, regardless of the number or size of your MS files, the size of your FASTA file, or the number of PTMs considered.
Visualizations
Visualizations
For any requested peptide — identified or not — we can provide your lab with a visual audit report, even for projects with >>50 samples (e.g., 100s of samples). Most notably, the visualization is not limited to only those fragments that were used for quantitation or peptide identification: instead, one can see any/all MS1 or MS2 m/z fragments' XIC plots within seconds and can do so simultaneously for as many samples as one wishes. This allows scientists to look at diagnostic ions etc. In so doing, scientists can use their expertise to validate the informatics conclusions. (The client who insisted on this ability stated "If I can't visualize all the supporting data, I don't believe any of it [any software's claims]".) To see this in action, please schedule a free pilot and consultation.
For any requested peptide — identified or not — we can provide your lab with a visual audit report, even for projects with >>50 samples (e.g., 100s of samples). Most notably, the visualization is not limited to only those fragments that were used for quantitation or peptide identification: instead, one can see any/all MS1 or MS2 m/z fragments' XIC plots within seconds and can do so simultaneously for as many samples as one wishes. This allows scientists to look at diagnostic ions etc. In so doing, scientists can use their expertise to validate the informatics conclusions. (The client who insisted on this ability stated "If I can't visualize all the supporting data, I don't believe any of it [any software's claims]".) To see this in action, please schedule a free pilot and consultation.
Data Warehousing
Data Warehousing
All the data, including intermediary data, is stored in a relational-like database. So, should your future research involve a more complex question that spans even multiple projects simultaneously, we can likely answer your questions with ease. Also, the data is cleanly and consistently structured and catalogued (instead of having data files located on multiple computers and folders, and instead of having different tools for different MS vendor formats). Finally, the relational-like database is stored in a globally clustered manner (i.e., stored in USA, Europe, and Asia simultaneously) so data redundancy, even for these intermediary data results, is built-in.
All the data, including intermediary data, is stored in a relational-like database. So, should your future research involve a more complex question that spans even multiple projects simultaneously, we can likely answer your questions with ease. Also, the data is cleanly and consistently structured and catalogued (instead of having data files located on multiple computers and folders, and instead of having different tools for different MS vendor formats). Finally, the relational-like database is stored in a globally clustered manner (i.e., stored in USA, Europe, and Asia simultaneously) so data redundancy, even for these intermediary data results, is built-in.
Quality
Quality
Even though we focus on quantifying the dark proteome — the ~75-95% of peptides in your MS that are not in FASTA search spaces (the so-called dark proteome) — our accuracy for FASTA-only peptides even exceeds that of FASTA-only algorithms (Tables 2, 4, 5 & 6 in paper).
Even though we focus on quantifying the dark proteome — the ~75-95% of peptides in your MS that are not in FASTA search spaces (the so-called dark proteome) — our accuracy for FASTA-only peptides even exceeds that of FASTA-only algorithms (Tables 2, 4, 5 & 6 in paper).
Ease
Ease
We take care of all IT and bioinformatics concerns for DIA data processing. We transfer the risk, complexity, and the occasional IT or bioinformatics nightmares from your lab to ours.
We take care of all IT and bioinformatics concerns for DIA data processing. We transfer the risk, complexity, and the occasional IT or bioinformatics nightmares from your lab to ours.
Risk Level
Risk Level