Origin of "GoldenHaystack" Name

Origin of "GoldenHaystack" Name

Genesis of Name

Genesis of Name

Years ago, when talking to a European scientist, we unintentionally ended with an impromptu and emphatic "…we've been searching [all these years] the wrong haystack!".

For the other scientist, the words "wrong haystack" stuck. He repeated it back to us.

Years ago, when talking to a European scientist, we unintentionally ended with an impromptu and emphatic "…we've been searching [all these years] the wrong haystack!".

For the other scientist, the words "wrong haystack" stuck. He repeated it back to us.

What We Meant by "Wrong Haystack"

What We Meant by "Wrong Haystack"

For the last >20 years, MS discovery proteomics has produced few real-world benefits. One potential reason for this paucity may be that the other, existing informatics solutions focus exclusively on quantifying only those peptides identified from FASTA search spaces.

However, the peptides which separate conditions are — almost by definition — rarely present in generic (i.e., rarely disease or cohort specific), genomics-derived (i.e., known to be incomplete) FASTA search spaces with typically no more than two PTMs considered ( instead of hundreds ). (Please see preprint or posters.)

Thus, even if future LC-MS instruments were magically to be simultaneously ~10x more sensitive, ~10x better resolution, ~10x better dynamic range, and ~1/10th the pricing, if we continue to use existing DIA-MS algorithms to quantify only those peptides identified in the FASTA search space, we would still be "looking in the wrong haystack."

For the last >20 years, MS discovery proteomics has produced few real-world benefits. One potential reason for this paucity may be that the other, existing informatics solutions focus exclusively on quantifying only those peptides identified from FASTA search spaces.

However, the peptides which separate conditions are — almost by definition — rarely present in generic (i.e., rarely disease or cohort specific), genomics-derived (i.e., known to be incomplete) FASTA search spaces with typically no more than two PTMs considered ( instead of hundreds ). (Please see preprint or posters.)

Thus, even if future LC-MS instruments were magically to be simultaneously ~10x more sensitive, ~10x better resolution, ~10x better dynamic range, and ~1/10th the pricing, if we continue to use existing DIA-MS algorithms to quantify only those peptides identified in the FASTA search space, we would still be "looking in the wrong haystack."

Different Naming Ideas

Different Naming Ideas

Our initial name for the algorithm was "Not Wrong Haystack", but it was discarded for obvious reasons. We then thought of "RightHaystack," but the homonym "right" vs "write" vs "rite" worried us. We eventually settled on "GoldenHaystack," which connoted the immense scientific, biological, and even financial value of quantifying the ~75-95% of data in DIA-MS datasets that were not previously being quantified, i.e., quantifying the dark proteome.

Our initial name for the algorithm was "Not Wrong Haystack", but it was discarded for obvious reasons. We then thought of "RightHaystack," but the homonym "right" vs "write" vs "rite" worried us. We eventually settled on "GoldenHaystack," which connoted the immense scientific, biological, and even financial value of quantifying the ~75-95% of data in DIA-MS datasets that were not previously being quantified, i.e., quantifying the dark proteome.

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