Oliver M. Bernhardt
@spectronaut.bsky.social
But one of the coolest things about Kuiper, I already teased in an earlier post. Kuiper is so powerful, that you can do an unspecific open modification search on a full 7-52 length cell-lysate search space with only a minor increase in search time compared to a closed search.
June 6, 2025 at 7:21 AM
But one of the coolest things about Kuiper, I already teased in an earlier post. Kuiper is so powerful, that you can do an unspecific open modification search on a full 7-52 length cell-lysate search space with only a minor increase in search time compared to a closed search.
We obviously spent a lot of time making sure that the results you get are trustworthy. Not only from a statistical point of view but also using biological result validation. e.g.: we could show that the overlapping peptides between individual patients correspond to their shared HLA allele.
June 6, 2025 at 7:21 AM
We obviously spent a lot of time making sure that the results you get are trustworthy. Not only from a statistical point of view but also using biological result validation. e.g.: we could show that the overlapping peptides between individual patients correspond to their shared HLA allele.
The runtime improvements are what is most impressive in my eyes. We can now do unspecific class-1 and class-2 in ~10 minutes per DIA raw file (library free, directDIA including all steps). That marks a 78% and 86% reduction in search time compared to SN19.
June 6, 2025 at 7:21 AM
The runtime improvements are what is most impressive in my eyes. We can now do unspecific class-1 and class-2 in ~10 minutes per DIA raw file (library free, directDIA including all steps). That marks a 78% and 86% reduction in search time compared to SN19.
Our focus was primarily on immunopeptidomics (class 1 and 2) which is where you will see the biggest total gains in terms of IDs (+75% on average for class-1 and +18% for class-2).
June 6, 2025 at 7:21 AM
Our focus was primarily on immunopeptidomics (class 1 and 2) which is where you will see the biggest total gains in terms of IDs (+75% on average for class-1 and +18% for class-2).
Kuiper is a novel search-engine unlike anything you have seen before. It uses a new approach for MS2 indexing that is incredibly light-weight (full unspecific MS2 index of a 7-52 peptide length search space only occupies about 5GB in memory). Together with Pulsar, it can process DIA as well as DDA.
June 6, 2025 at 7:21 AM
Kuiper is a novel search-engine unlike anything you have seen before. It uses a new approach for MS2 indexing that is incredibly light-weight (full unspecific MS2 index of a 7-52 peptide length search space only occupies about 5GB in memory). Together with Pulsar, it can process DIA as well as DDA.
Compared to a fully specific tryptic search-space, unspecific search-spaces (which produce every possible sub-sequence of the specified length-range), very quickly explode in search-space complexity. A fully unspecific search-space (length 7-52) is almost 900x larger then the tryptic equivalent.
June 6, 2025 at 7:21 AM
Compared to a fully specific tryptic search-space, unspecific search-spaces (which produce every possible sub-sequence of the specified length-range), very quickly explode in search-space complexity. A fully unspecific search-space (length 7-52) is almost 900x larger then the tryptic equivalent.
Really looking forward to Spectronaut 20 release at #ASMS2025. We will be showing our new search-engine Kuiper, purpose built for tackling unspecific search spaces.
It can do an unspecific (peptide length 7-52) open-search in ~30 minutes (2h gradient length Human cell Lysate).
It can do an unspecific (peptide length 7-52) open-search in ~30 minutes (2h gradient length Human cell Lysate).
May 30, 2025 at 12:47 PM
Really looking forward to Spectronaut 20 release at #ASMS2025. We will be showing our new search-engine Kuiper, purpose built for tackling unspecific search spaces.
It can do an unspecific (peptide length 7-52) open-search in ~30 minutes (2h gradient length Human cell Lysate).
It can do an unspecific (peptide length 7-52) open-search in ~30 minutes (2h gradient length Human cell Lysate).
But we have exactly that already for years. Okey, it does not ask you to "safe the changes", but it warns you that you have experiments open and anything that is not saved will be lost 😅
December 12, 2024 at 10:43 AM
But we have exactly that already for years. Okey, it does not ask you to "safe the changes", but it warns you that you have experiments open and anything that is not saved will be lost 😅