How Existing DIA-MS Informatics Work
How Existing DIA-MS
Informatics Work
Current popular DIA-MS informatics algorithms:
* quantify what they identify, but
* only identify what is in the FASTA files.
However, between ~75% to ~95% of peptides in one's DIA-MS data files are not in the FASTA files*, despite their biological value.
The GoldenHaystack algorithm does not use the FASTA file for quantitation. It therefore is free to quantify all the peptides in one's DIA-MS data files (i.e., the dark proteome). This is a more transformational change than may be apparent at first glance.
*Please see summary Table 6 on page 20 or Mann lab reference on page 4 in preprint; or please see summary Table 6 in ASMS 2025 poster.
Current popular DIA-MS informatics algorithms:
* quantify what they identify, but
* only identify what is in the FASTA files.
However, between ~75% to ~95% of peptides in one's DIA-MS data files are not in the FASTA files*, despite their biological value.
The GoldenHaystack algorithm does not use the FASTA file for quantitation. It therefore is free to quantify all the peptides in one's DIA-MS data files (i.e., the dark proteome). This is a more transformational change than may be apparent at first glance.
*Please see summary Table 6 on page 20 or Mann lab reference on page 4 in preprint; or please see summary Table 6 in ASMS 2025 poster.