公开(公告)号：US11694769B2

公开(公告)日：2023-07-04

申请号：US16226575

申请日：2018-12-19

申请人： BIOINFORMATICS SOLUTIONS INC.

发明人： Baozhen Shan ,  Ngoc Hieu Tran ,  Ming Li ,  Lei Xin ,  Rui Qiao ,  Xin Chen ,  Chuyi Liu

IPC分类号： G01N33/48 ,  G01N33/50 ,  G16B40/10 ,  H01J49/00 ,  G01N33/68 ,  G16B30/20 ,  G16B40/20 ,  G06N3/02

CPC分类号： G16B40/10 ,  G01N33/6818 ,  G01N33/6848 ,  G06N3/02 ,  G16B30/20 ,  G16B40/20 ,  H01J49/0036

摘要： The present systems and methods introduce deep learning to de novo peptide sequencing from tandem mass spectrometry data, and in particular mass spectrometry data obtained by data-independent acquisition. The systems and methods achieve improvements in sequencing accuracy over existing systems and methods and enables complete assembly of novel protein sequences without assisting databases. To sequence peptides from mass spectrometry data obtained by data-independent acquisition, precursor profiles representing intensities of one or more precursor ion signals associated with a precursor retention time and fragment ion spectra representing signals from fragment ions and fragment retention times are fed into a neural network.

公开(公告)号：US11644470B2

公开(公告)日：2023-05-09

申请号：US16846817

申请日：2020-04-13

申请人： BIOINFORMATICS SOLUTIONS INC.

发明人： Rui Qiao ,  Ngoc Hieu Tran ,  Lei Xin ,  Xin Chen ,  Baozhen Shan ,  Ali Ghodsi ,  Ming Li

IPC分类号： G01N33/00 ,  G01N33/68 ,  G16B40/00 ,  G16B20/00 ,  G16B30/00

CPC分类号： G01N33/6848 ,  G16B20/00 ,  G16B30/00 ,  G16B40/00

摘要： The present systems and methods are directed to de novo identification of peptide sequences from tandem mass spectrometry data. The systems and methods uses unconverted mass spectrometry data from which features are extracted. Using unconverted mass spectrometry data reduces the loss of information and provides more accurate sequencing of peptides. The systems and methods combine deep learning and neural networks to sequencing of peptides.

公开(公告)号：US20200243164A1

公开(公告)日：2020-07-30

申请号：US16775947

申请日：2020-01-29

申请人： BIOINFORMATICS SOLUTIONS INC.

发明人： Rui Qiao ,  Ngoc Hieu Tran ,  Lei Xin ,  Xin Chen ,  Baozhen Shan ,  Ming Li

IPC分类号： G16B40/10 ,  G16B30/00 ,  G16B25/10 ,  G16B50/30 ,  G01N33/68

摘要： The present systems and workflows identify neoantigens for cancer immunotherapy by introducing deep learning to de novo peptide sequencing from tandem mass spectrometry data. The systems and workflow allows for patient specific identification of neoantigens for personalized immunotherapy.

公开(公告)号：US20190147983A1

公开(公告)日：2019-05-16

申请号：US16226575

申请日：2018-12-19

申请人： BIOINFORMATICS SOLUTIONS INC.

发明人： Baozhen Shan ,  Ngoc Hieu Tran ,  Ming Li ,  Lei Xin ,  Rui Qiao ,  Xin Chen ,  Chuyi Liu

IPC分类号： G16B40/10 ,  H01J49/00

摘要： The present systems and methods introduce deep learning to de novo peptide sequencing from tandem mass spectrometry data, and in particular mass spectrometry data obtained by data-independent acquisition. The systems and methods achieve improvements in sequencing accuracy over existing systems and methods and enables complete assembly of novel protein sequences without assisting databases. To sequence peptides from mass spectrometry data obtained by data-independent acquisition, precursor profiles representing intensities of one or more precursor ion signals associated with a precursor retention time and fragment ion spectra representing signals from fragment ions and fragment retention times are fed into a neural network.