Fengchao
@fcyucn.bsky.social
Research Investigator at U of M. Interested in proteomics, etc. Developer of FragPipe, MSFragger, IonQuant, etc.
Interesting idea. May I ask two questions?
1. Is the precursor detection performed before or after the database search?
2. If it is performed before the search, how can one identify the complementary fragment ions without knowing the precursor mass or peptide sequence?
Thanks
1. Is the precursor detection performed before or after the database search?
2. If it is performed before the search, how can one identify the complementary fragment ions without knowing the precursor mass or peptide sequence?
Thanks
August 14, 2025 at 11:52 AM
Interesting idea. May I ask two questions?
1. Is the precursor detection performed before or after the database search?
2. If it is performed before the search, how can one identify the complementary fragment ions without knowing the precursor mass or peptide sequence?
Thanks
1. Is the precursor detection performed before or after the database search?
2. If it is performed before the search, how can one identify the complementary fragment ions without knowing the precursor mass or peptide sequence?
Thanks
We didn’t cherry-pick the dataset for the benchmark—FragPipe also delivers excellent performance on another dataset (PXD028735).
Questions are always welcome! We're always happy to hear your feedback. (3/3)
Questions are always welcome! We're always happy to hear your feedback. (3/3)
May 8, 2025 at 1:22 AM
We didn’t cherry-pick the dataset for the benchmark—FragPipe also delivers excellent performance on another dataset (PXD028735).
Questions are always welcome! We're always happy to hear your feedback. (3/3)
Questions are always welcome! We're always happy to hear your feedback. (3/3)
Peptide-level LFQbench-style plot using the PXD003881 (IonStar) dataset. (2/3)
May 8, 2025 at 1:21 AM
Peptide-level LFQbench-style plot using the PXD003881 (IonStar) dataset. (2/3)
We also benchmarked LFQ precision and accuracy against the latest versions of other popular tools. Here's an protein-level LFQbench-style plot using the PXD003881 (IonStar) dataset. (1/3)
May 8, 2025 at 1:21 AM
We also benchmarked LFQ precision and accuracy against the latest versions of other popular tools. Here's an protein-level LFQbench-style plot using the PXD003881 (IonStar) dataset. (1/3)
Feature request well received🫡
March 4, 2025 at 8:05 PM
Feature request well received🫡
It doesn't "predict" the library. It perform the spectrum-centric search to get the IDs and build the experimental library.
And for the DIA without ion mobility, it is basically what DIA-Umpire is doing: www.nature.com/articles/nme...
And for the DIA without ion mobility, it is basically what DIA-Umpire is doing: www.nature.com/articles/nme...
DIA-Umpire: comprehensive computational framework for data-independent acquisition proteomics - Nature Methods
The computational workflow of DIA-Umpire allows untargeted peptide identificationdirectly from DIA (data-independent acquisition) proteomics data without dependence on a spectral library for data extr...
www.nature.com
January 4, 2025 at 4:24 PM
It doesn't "predict" the library. It perform the spectrum-centric search to get the IDs and build the experimental library.
And for the DIA without ion mobility, it is basically what DIA-Umpire is doing: www.nature.com/articles/nme...
And for the DIA without ion mobility, it is basically what DIA-Umpire is doing: www.nature.com/articles/nme...