Comprehensive Overview of Bottom-Up Proteomics Using Mass Spectrometry

Autores
Jiang, Yuming; Rex, Devasahayam Arokia Balaya; Schuster, Dina; Neely, Benjamin A.; Rosano, German Leandro; Volkmar, Norbert; Momenzadeh, Amanda; Peters Clarke, Trenton M.; Egbert, Susan B.; Kreimer, Simion; Doud, Emma H.; Crook, Oliver M.; Yadav, Amit Kumar; Vanuopadath, Muralidharan; Hegeman, Adrian D.; Mayta, Martín Leonardo; Duboff, Anna G.; Riley, Nicholas M.; Moritz, Robert L.; Meyer, Jesse G.
Año de publicación
2024
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
Proteomics is the large scale study of protein structure and function from biological systems through protein identification and quantification. “Shotgun proteomics” or “bottom-up proteomics” is the prevailing strategy, in which proteins are hydrolyzed into peptides that are analyzed by mass spectrometry. Proteomics studies can be applied to diverse studies ranging from simple protein identification to studies of proteoforms, protein-protein interactions, protein structural alterations, absolute and relative protein quantification, post-translational modifications, and protein stability. To enable this range of different experiments, there are diverse strategies for proteome analysis. The nuances of how proteomic workflows differ may be challenging to understand for new practitioners. Here, we provide a comprehensive overview of different proteomics methods. We cover from biochemistry basics and protein extraction to biological interpretation and orthogonal validation. We expect this Review will serve as a handbook for researchers who are new to the field of bottom-up proteomics.
Fil: Jiang, Yuming. Cedars Sinai Medical Center; Estados Unidos
Fil: Rex, Devasahayam Arokia Balaya. Yenepoya Research Centre; India
Fil: Schuster, Dina. Departament Of Biology ; Eidgenossische Technische Hochschule zurich;
Fil: Neely, Benjamin A.. No especifíca;
Fil: Rosano, German Leandro. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Rosario. Instituto de Biología Molecular y Celular de Rosario. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas. Instituto de Biología Molecular y Celular de Rosario; Argentina
Fil: Volkmar, Norbert. Departament Of Biology ; Eidgenossische Technische Hochschule zurich;
Fil: Momenzadeh, Amanda. Cedars Sinai Medical Center; Estados Unidos
Fil: Peters Clarke, Trenton M.. University of California; Estados Unidos
Fil: Egbert, Susan B.. University of Manitoba; Canadá
Fil: Kreimer, Simion. Cedars Sinai Medical Center; Estados Unidos
Fil: Doud, Emma H.. Indiana University. School Of Medicine.; Estados Unidos
Fil: Crook, Oliver M.. University of Oxford; Reino Unido
Fil: Yadav, Amit Kumar. No especifíca;
Fil: Vanuopadath, Muralidharan. Universidad Adventista del Plata. Facultad de Ciencias de la Salud; Argentina
Fil: Hegeman, Adrian D.. Universidad Adventista del Plata. Facultad de Ciencias de la Salud; Argentina
Fil: Mayta, Martín Leonardo. Universidad Adventista del Plata. Facultad de Ciencias de la Salud; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Rosario. Instituto de Biología Molecular y Celular de Rosario. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas. Instituto de Biología Molecular y Celular de Rosario; Argentina
Fil: Duboff, Anna G.. University of Washington; Estados Unidos
Fil: Riley, Nicholas M.. University of Washington; Estados Unidos
Fil: Moritz, Robert L.. University of Washington; Estados Unidos
Fil: Meyer, Jesse G.. Cedars Sinai Medical Center; Estados Unidos
Materia
Proteomics
liquid chromatography
review
mass spectrometry
tutorial
proteins
peptides
LC-MS
Nivel de accesibilidad
acceso abierto
Condiciones de uso
https://creativecommons.org/licenses/by-nc-nd/2.5/ar/
Repositorio
CONICET Digital (CONICET)
Institución
Consejo Nacional de Investigaciones Científicas y Técnicas
OAI Identificador
oai:ri.conicet.gov.ar:11336/266733
Acceder
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oai_identifier_str oai:ri.conicet.gov.ar:11336/266733
network_acronym_str CONICETDig
repository_id_str 3498
network_name_str CONICET Digital (CONICET)
spelling Comprehensive Overview of Bottom-Up Proteomics Using Mass SpectrometryJiang, YumingRex, Devasahayam Arokia BalayaSchuster, DinaNeely, Benjamin A.Rosano, German LeandroVolkmar, NorbertMomenzadeh, AmandaPeters Clarke, Trenton M.Egbert, Susan B.Kreimer, SimionDoud, Emma H.Crook, Oliver M.Yadav, Amit KumarVanuopadath, MuralidharanHegeman, Adrian D.Mayta, Martín LeonardoDuboff, Anna G.Riley, Nicholas M.Moritz, Robert L.Meyer, Jesse G.Proteomicsliquid chromatographyreviewmass spectrometrytutorialproteinspeptidesLC-MShttps://purl.org/becyt/ford/1.6https://purl.org/becyt/ford/1Proteomics is the large scale study of protein structure and function from biological systems through protein identification and quantification. “Shotgun proteomics” or “bottom-up proteomics” is the prevailing strategy, in which proteins are hydrolyzed into peptides that are analyzed by mass spectrometry. Proteomics studies can be applied to diverse studies ranging from simple protein identification to studies of proteoforms, protein-protein interactions, protein structural alterations, absolute and relative protein quantification, post-translational modifications, and protein stability. To enable this range of different experiments, there are diverse strategies for proteome analysis. The nuances of how proteomic workflows differ may be challenging to understand for new practitioners. Here, we provide a comprehensive overview of different proteomics methods. We cover from biochemistry basics and protein extraction to biological interpretation and orthogonal validation. We expect this Review will serve as a handbook for researchers who are new to the field of bottom-up proteomics.Fil: Jiang, Yuming. Cedars Sinai Medical Center; Estados UnidosFil: Rex, Devasahayam Arokia Balaya. Yenepoya Research Centre; IndiaFil: Schuster, Dina. Departament Of Biology ; Eidgenossische Technische Hochschule zurich;Fil: Neely, Benjamin A.. No especifíca;Fil: Rosano, German Leandro. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Rosario. Instituto de Biología Molecular y Celular de Rosario. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas. Instituto de Biología Molecular y Celular de Rosario; ArgentinaFil: Volkmar, Norbert. Departament Of Biology ; Eidgenossische Technische Hochschule zurich;Fil: Momenzadeh, Amanda. Cedars Sinai Medical Center; Estados UnidosFil: Peters Clarke, Trenton M.. University of California; Estados UnidosFil: Egbert, Susan B.. University of Manitoba; CanadáFil: Kreimer, Simion. Cedars Sinai Medical Center; Estados UnidosFil: Doud, Emma H.. Indiana University. School Of Medicine.; Estados UnidosFil: Crook, Oliver M.. University of Oxford; Reino UnidoFil: Yadav, Amit Kumar. No especifíca;Fil: Vanuopadath, Muralidharan. Universidad Adventista del Plata. Facultad de Ciencias de la Salud; ArgentinaFil: Hegeman, Adrian D.. Universidad Adventista del Plata. Facultad de Ciencias de la Salud; ArgentinaFil: Mayta, Martín Leonardo. Universidad Adventista del Plata. Facultad de Ciencias de la Salud; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Rosario. Instituto de Biología Molecular y Celular de Rosario. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas. Instituto de Biología Molecular y Celular de Rosario; ArgentinaFil: Duboff, Anna G.. University of Washington; Estados UnidosFil: Riley, Nicholas M.. University of Washington; Estados UnidosFil: Moritz, Robert L.. University of Washington; Estados UnidosFil: Meyer, Jesse G.. Cedars Sinai Medical Center; Estados UnidosAmerican Chemical Society2024-06info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/266733Jiang, Yuming; Rex, Devasahayam Arokia Balaya; Schuster, Dina; Neely, Benjamin A.; Rosano, German Leandro; et al.; Comprehensive Overview of Bottom-Up Proteomics Using Mass Spectrometry; American Chemical Society; ACS Measurement Science Au; 4; 4; 6-2024; 338-4172694-250XCONICET DigitalCONICETenginfo:eu-repo/semantics/altIdentifier/url/https://pubs.acs.org/doi/10.1021/acsmeasuresciau.3c00068info:eu-repo/semantics/altIdentifier/doi/10.1021/acsmeasuresciau.3c00068info:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by-nc-nd/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-09-29T09:33:57Zoai:ri.conicet.gov.ar:11336/266733instacron:CONICETInstitucionalhttp://ri.conicet.gov.ar/Organismo científico-tecnológicoNo correspondehttp://ri.conicet.gov.ar/oai/requestdasensio@conicet.gov.ar; lcarlino@conicet.gov.arArgentinaNo correspondeNo correspondeNo correspondeopendoar:34982025-09-29 09:33:58.155CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse
dc.title.none.fl_str_mv Comprehensive Overview of Bottom-Up Proteomics Using Mass Spectrometry
title Comprehensive Overview of Bottom-Up Proteomics Using Mass Spectrometry
spellingShingle Comprehensive Overview of Bottom-Up Proteomics Using Mass Spectrometry
Jiang, Yuming
Proteomics
liquid chromatography
review
mass spectrometry
tutorial
proteins
peptides
LC-MS
title_short Comprehensive Overview of Bottom-Up Proteomics Using Mass Spectrometry
title_full Comprehensive Overview of Bottom-Up Proteomics Using Mass Spectrometry
title_fullStr Comprehensive Overview of Bottom-Up Proteomics Using Mass Spectrometry
title_full_unstemmed Comprehensive Overview of Bottom-Up Proteomics Using Mass Spectrometry
title_sort Comprehensive Overview of Bottom-Up Proteomics Using Mass Spectrometry
dc.creator.none.fl_str_mv Jiang, Yuming
Rex, Devasahayam Arokia Balaya
Schuster, Dina
Neely, Benjamin A.
Rosano, German Leandro
Volkmar, Norbert
Momenzadeh, Amanda
Peters Clarke, Trenton M.
Egbert, Susan B.
Kreimer, Simion
Doud, Emma H.
Crook, Oliver M.
Yadav, Amit Kumar
Vanuopadath, Muralidharan
Hegeman, Adrian D.
Mayta, Martín Leonardo
Duboff, Anna G.
Riley, Nicholas M.
Moritz, Robert L.
Meyer, Jesse G.
author Jiang, Yuming
author_facet Jiang, Yuming
Rex, Devasahayam Arokia Balaya
Schuster, Dina
Neely, Benjamin A.
Rosano, German Leandro
Volkmar, Norbert
Momenzadeh, Amanda
Peters Clarke, Trenton M.
Egbert, Susan B.
Kreimer, Simion
Doud, Emma H.
Crook, Oliver M.
Yadav, Amit Kumar
Vanuopadath, Muralidharan
Hegeman, Adrian D.
Mayta, Martín Leonardo
Duboff, Anna G.
Riley, Nicholas M.
Moritz, Robert L.
Meyer, Jesse G.
author_role author
author2 Rex, Devasahayam Arokia Balaya
Schuster, Dina
Neely, Benjamin A.
Rosano, German Leandro
Volkmar, Norbert
Momenzadeh, Amanda
Peters Clarke, Trenton M.
Egbert, Susan B.
Kreimer, Simion
Doud, Emma H.
Crook, Oliver M.
Yadav, Amit Kumar
Vanuopadath, Muralidharan
Hegeman, Adrian D.
Mayta, Martín Leonardo
Duboff, Anna G.
Riley, Nicholas M.
Moritz, Robert L.
Meyer, Jesse G.
author2_role author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
dc.subject.none.fl_str_mv Proteomics
liquid chromatography
review
mass spectrometry
tutorial
proteins
peptides
LC-MS
topic Proteomics
liquid chromatography
review
mass spectrometry
tutorial
proteins
peptides
LC-MS
purl_subject.fl_str_mv https://purl.org/becyt/ford/1.6
https://purl.org/becyt/ford/1
dc.description.none.fl_txt_mv Proteomics is the large scale study of protein structure and function from biological systems through protein identification and quantification. “Shotgun proteomics” or “bottom-up proteomics” is the prevailing strategy, in which proteins are hydrolyzed into peptides that are analyzed by mass spectrometry. Proteomics studies can be applied to diverse studies ranging from simple protein identification to studies of proteoforms, protein-protein interactions, protein structural alterations, absolute and relative protein quantification, post-translational modifications, and protein stability. To enable this range of different experiments, there are diverse strategies for proteome analysis. The nuances of how proteomic workflows differ may be challenging to understand for new practitioners. Here, we provide a comprehensive overview of different proteomics methods. We cover from biochemistry basics and protein extraction to biological interpretation and orthogonal validation. We expect this Review will serve as a handbook for researchers who are new to the field of bottom-up proteomics.
Fil: Jiang, Yuming. Cedars Sinai Medical Center; Estados Unidos
Fil: Rex, Devasahayam Arokia Balaya. Yenepoya Research Centre; India
Fil: Schuster, Dina. Departament Of Biology ; Eidgenossische Technische Hochschule zurich;
Fil: Neely, Benjamin A.. No especifíca;
Fil: Rosano, German Leandro. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Rosario. Instituto de Biología Molecular y Celular de Rosario. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas. Instituto de Biología Molecular y Celular de Rosario; Argentina
Fil: Volkmar, Norbert. Departament Of Biology ; Eidgenossische Technische Hochschule zurich;
Fil: Momenzadeh, Amanda. Cedars Sinai Medical Center; Estados Unidos
Fil: Peters Clarke, Trenton M.. University of California; Estados Unidos
Fil: Egbert, Susan B.. University of Manitoba; Canadá
Fil: Kreimer, Simion. Cedars Sinai Medical Center; Estados Unidos
Fil: Doud, Emma H.. Indiana University. School Of Medicine.; Estados Unidos
Fil: Crook, Oliver M.. University of Oxford; Reino Unido
Fil: Yadav, Amit Kumar. No especifíca;
Fil: Vanuopadath, Muralidharan. Universidad Adventista del Plata. Facultad de Ciencias de la Salud; Argentina
Fil: Hegeman, Adrian D.. Universidad Adventista del Plata. Facultad de Ciencias de la Salud; Argentina
Fil: Mayta, Martín Leonardo. Universidad Adventista del Plata. Facultad de Ciencias de la Salud; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Rosario. Instituto de Biología Molecular y Celular de Rosario. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas. Instituto de Biología Molecular y Celular de Rosario; Argentina
Fil: Duboff, Anna G.. University of Washington; Estados Unidos
Fil: Riley, Nicholas M.. University of Washington; Estados Unidos
Fil: Moritz, Robert L.. University of Washington; Estados Unidos
Fil: Meyer, Jesse G.. Cedars Sinai Medical Center; Estados Unidos
description Proteomics is the large scale study of protein structure and function from biological systems through protein identification and quantification. “Shotgun proteomics” or “bottom-up proteomics” is the prevailing strategy, in which proteins are hydrolyzed into peptides that are analyzed by mass spectrometry. Proteomics studies can be applied to diverse studies ranging from simple protein identification to studies of proteoforms, protein-protein interactions, protein structural alterations, absolute and relative protein quantification, post-translational modifications, and protein stability. To enable this range of different experiments, there are diverse strategies for proteome analysis. The nuances of how proteomic workflows differ may be challenging to understand for new practitioners. Here, we provide a comprehensive overview of different proteomics methods. We cover from biochemistry basics and protein extraction to biological interpretation and orthogonal validation. We expect this Review will serve as a handbook for researchers who are new to the field of bottom-up proteomics.
publishDate 2024
dc.date.none.fl_str_mv 2024-06
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
http://purl.org/coar/resource_type/c_6501
info:ar-repo/semantics/articulo
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/11336/266733
Jiang, Yuming; Rex, Devasahayam Arokia Balaya; Schuster, Dina; Neely, Benjamin A.; Rosano, German Leandro; et al.; Comprehensive Overview of Bottom-Up Proteomics Using Mass Spectrometry; American Chemical Society; ACS Measurement Science Au; 4; 4; 6-2024; 338-417
2694-250X
CONICET Digital
CONICET
url http://hdl.handle.net/11336/266733
identifier_str_mv Jiang, Yuming; Rex, Devasahayam Arokia Balaya; Schuster, Dina; Neely, Benjamin A.; Rosano, German Leandro; et al.; Comprehensive Overview of Bottom-Up Proteomics Using Mass Spectrometry; American Chemical Society; ACS Measurement Science Au; 4; 4; 6-2024; 338-417
2694-250X
CONICET Digital
CONICET
dc.language.none.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv info:eu-repo/semantics/altIdentifier/url/https://pubs.acs.org/doi/10.1021/acsmeasuresciau.3c00068
info:eu-repo/semantics/altIdentifier/doi/10.1021/acsmeasuresciau.3c00068
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
https://creativecommons.org/licenses/by-nc-nd/2.5/ar/
eu_rights_str_mv openAccess
rights_invalid_str_mv https://creativecommons.org/licenses/by-nc-nd/2.5/ar/
dc.format.none.fl_str_mv application/pdf
application/pdf
dc.publisher.none.fl_str_mv American Chemical Society
publisher.none.fl_str_mv American Chemical Society
dc.source.none.fl_str_mv reponame:CONICET Digital (CONICET)
instname:Consejo Nacional de Investigaciones Científicas y Técnicas
reponame_str CONICET Digital (CONICET)
collection CONICET Digital (CONICET)
instname_str Consejo Nacional de Investigaciones Científicas y Técnicas
repository.name.fl_str_mv CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicas
repository.mail.fl_str_mv dasensio@conicet.gov.ar; lcarlino@conicet.gov.ar
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score 13.070432

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