Additional file 1 of Quantitative proteomics identified circulating biomarkers in lung adenocarcinoma diagnosis

Hongyu Chen (105612)
Xiaoqin Lai (14148899)
Yihan Zhu (1333899)
Hong Huang (119275)
Lingyan Zeng (1414378)
Li Zhang (8200)

Open link

Publication date

November 2022

DOI

10.6084/m9.figshare.21593948.v1

Abstract

Additional file 1: Table S1. Differentially expressed proteins identified in plasma samples

Extracted data

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Data Protection

Additional file 1 of Quantitative proteomics identified circulating biomarkers in lung adenocarcinoma diagnosis

Hongyu Chen (105612)
Xiaoqin Lai (14148899)
Yihan Zhu (1333899)
Hong Huang (119275)
Lingyan Zeng (1414378)
Li Zhang (8200)

Open link

Publication date

November 2022

DOI

10.6084/m9.figshare.21593948.v1

Abstract

Additional file 1: Table S1. Differentially expressed proteins identified in plasma samples

Extracted data

Robert Quinn (453809)
Sandeep Adem (6332756)
Robert Mills (6005816)
William Comstock (6332759)
Lindsay DeRight Goldasich (4900375)
Gregory Humphrey (4900273)
Alexander Aksenov (2146969)
Alexei Melnik (6332762)
Ricardo Silva (4739820)
Gail Ackermann (618902)
Nuno Bandeira (801994)
David Gonzalez (1399030)
Doug Conrad (6332765)
Anthony OâDonoghue (6332768)
Rob Knight (11635)
Pieter Dorrestein (3463673)

February 2019

Table S3. Peptidomics data on human proteome as produced using PEAKS software. (XLSX 87 kb

Additional file 1: Table S1. of The prognostic value of serum CA 19-9 for patients with advanced lung adenocarcinoma

Yuki Sato (243074)
Daichi Fujimoto (3400052)
Keiichiro Uehara (3400055)
Ryoko Shimizu (27094)
Jiro Ito (3400037)
Mariko Kogo (3400046)
Shunsuke Teraoka (3400043)
Ryoji Kato (3400049)
Kazuma Nagata (3400058)
Atsushi Nakagawa (482199)
Kojiro Otsuka (2626141)
Hiroshi Hamakawa (290064)
Yutaka Takahashi (600869)
Yukihiro Imai (2157358)
Keisuke Tomii (3400040)

November 2016

Characteristics and differences by serum CYFRA 21-1 levels in patients with advanced-stage lung aden...

Additional file 1: Table S1. of Blood-based lung cancer biomarkers identified through proteomic discovery in cancer tissues, cell lines and conditioned medium

Charles Birse (3420953)
Robert Lagier (3420938)
William FitzHugh (484022)
Harvey Pass (202310)
William Rom (2400067)
Eric Edell (3420962)
Aaron Bungum (3420959)
Fabien Maldonado (544207)
James Jett (3420956)
Mehdi Mesri (484015)
Erin Sult (3420947)
Elizabeth Joseloff (1342536)
Aiqun Li (289891)
Jenny Heidbrink (484017)
Gulshan Dhariwal (3420941)
Chad Danis (3420950)
Jennifer Tomic (3420965)
Robert Bruce (2019028)
Paul Moore (469661)
Tao He (23919)
Marcia Lewis (3420944)
Steve Ruben (484023)

July 2015

Demographics and clinical profiles for subjects selected for fresh tissue discovery study

Additional file 3: Table S3. of Blood-based lung cancer biomarkers identified through proteomic discovery in cancer tissues, cell lines and conditioned medium

Charles Birse (3420953)
Robert Lagier (3420938)
William FitzHugh (484022)
Harvey Pass (202310)
William Rom (2400067)
Eric Edell (3420962)
Aaron Bungum (3420959)
Fabien Maldonado (544207)
James Jett (3420956)
Mehdi Mesri (484015)
Erin Sult (3420947)
Elizabeth Joseloff (1342536)
Aiqun Li (289891)
Jenny Heidbrink (484017)
Gulshan Dhariwal (3420941)
Chad Danis (3420950)
Jennifer Tomic (3420965)
Robert Bruce (2019028)
Paul Moore (469661)
Tao He (23919)
Marcia Lewis (3420944)
Steve Ruben (484023)

July 2015

Candidate lung cancer biomarkers (nâ=â179) identified through LC/MS analysis

Additional file 4: Figure S1. of Blood-based lung cancer biomarkers identified through proteomic discovery in cancer tissues, cell lines and conditioned medium

Charles Birse (3420953)
Robert Lagier (3420938)
William FitzHugh (484022)
Harvey Pass (202310)
William Rom (2400067)
Eric Edell (3420962)
Aaron Bungum (3420959)
Fabien Maldonado (544207)
James Jett (3420956)
Mehdi Mesri (484015)
Erin Sult (3420947)
Elizabeth Joseloff (1342536)
Aiqun Li (289891)
Jenny Heidbrink (484017)
Gulshan Dhariwal (3420941)
Chad Danis (3420950)
Jennifer Tomic (3420965)
Robert Bruce (2019028)
Paul Moore (469661)
Tao He (23919)
Marcia Lewis (3420944)
Steve Ruben (484023)

July 2015

Panther-based classification of protein class for candidate lung cancer markers (nâ=â179)

Additional file 1: of Levels and prognostic impact of circulating markers of inflammation, endothelial activation and extracellular matrix remodelling in patients with lung cancer and chronic obstructive pulmonary disease

Janna Berg (5515091)
Ann Halvorsen (3415001)
May-Bente Bengtson (5515097)
Kristin TaskĂŠn (5515100)
Gunhild MĂŚlandsmo (5515103)
Arne Yndestad (224387)
Bente Halvorsen (151367)
Odd Brustugun (3415010)
PĂĽl Aukrust (3567137)
Thor Ueland (307058)
Ăslaug Helland (5049539)

July 2018

Table S1. Serum protein levels. All data from the serum analyses are presented. This includes result...

Additional file 5: Figure S2. of Blood-based lung cancer biomarkers identified through proteomic discovery in cancer tissues, cell lines and conditioned medium

Charles Birse (3420953)
Robert Lagier (3420938)
William FitzHugh (484022)
Harvey Pass (202310)
William Rom (2400067)
Eric Edell (3420962)
Aaron Bungum (3420959)
Fabien Maldonado (544207)
James Jett (3420956)
Mehdi Mesri (484015)
Erin Sult (3420947)
Elizabeth Joseloff (1342536)
Aiqun Li (289891)
Jenny Heidbrink (484017)
Gulshan Dhariwal (3420941)
Chad Danis (3420950)
Jennifer Tomic (3420965)
Robert Bruce (2019028)
Paul Moore (469661)
Tao He (23919)
Marcia Lewis (3420944)
Steve Ruben (484023)

July 2015

Panther-based classification of protein class comparing lung cancer markers identified in tissues an...

Additional file 6: Figure S3. of Blood-based lung cancer biomarkers identified through proteomic discovery in cancer tissues, cell lines and conditioned medium

Charles Birse (3420953)
Robert Lagier (3420938)
William FitzHugh (484022)
Harvey Pass (202310)
William Rom (2400067)
Eric Edell (3420962)
Aaron Bungum (3420959)
Fabien Maldonado (544207)
James Jett (3420956)
Mehdi Mesri (484015)
Erin Sult (3420947)
Elizabeth Joseloff (1342536)
Aiqun Li (289891)
Jenny Heidbrink (484017)
Gulshan Dhariwal (3420941)
Chad Danis (3420950)
Jennifer Tomic (3420965)
Robert Bruce (2019028)
Paul Moore (469661)
Tao He (23919)
Marcia Lewis (3420944)
Steve Ruben (484023)

July 2015

Panther-based classification of protein pathways comparing lung cancer markers identified in tissues...

Additional file 7: Figure S4. of Blood-based lung cancer biomarkers identified through proteomic discovery in cancer tissues, cell lines and conditioned medium

Charles Birse (3420953)
Robert Lagier (3420938)
William FitzHugh (484022)
Harvey Pass (202310)
William Rom (2400067)
Eric Edell (3420962)
Aaron Bungum (3420959)
Fabien Maldonado (544207)
James Jett (3420956)
Mehdi Mesri (484015)
Erin Sult (3420947)
Elizabeth Joseloff (1342536)
Aiqun Li (289891)
Jenny Heidbrink (484017)
Gulshan Dhariwal (3420941)
Chad Danis (3420950)
Jennifer Tomic (3420965)
Robert Bruce (2019028)
Paul Moore (469661)
Tao He (23919)
Marcia Lewis (3420944)
Steve Ruben (484023)

July 2015

Expression levels of biomarker candidates in serum collected from patients with NSCLC (nâ=â94) a...

Additional file 1 of Plasma proteomics-based biomarkers for predicting response to mesenchymal stem cell therapy in severe COVID-19

Tian-Tian Li (451683)
Wei-Qi Yao (17612434)
Hai-Bo Dong (17612437)
Ze-Rui Wang (17612440)
Zi-Ying Zhang (17612443)
Meng-Qi Yuan (17612446)
Lei Shi (8144)
Fu-Sheng Wang (17612449)

December 2023

Additional file 1. Fig. S1: Distribution and quality control of the total proteins detected

Additional file 1: of Diagnostic role of circulating extracellular matrix-related proteins in non-small cell lung cancer

Francesca Andriani (4987880)
Elena Landoni (3399467)
Mavis Mensah (4987874)
Federica Facchinetti (4987877)
Rosalba Miceli (545436)
Elda Tagliabue (222687)
Marta Giussani (5767259)
Maurizio Callari (107071)
Loris De Cecco (107073)
Mario Colombo (5767262)
Luca Roz (4987883)
Ugo Pastorino (440075)
Gabriella Sozzi (371979)

September 2018

Table S1. Quantile regression multivariable analysis of association between COL11A1 and COL10A1 leve...

Additional file 3 of Proteomic analysis identifies a signature of disease severity in the plasma of COVID-19 pneumonia patients associated to neutrophil, platelet and complement activation

Fabiola Ciccosanti (2118151)
Manuela Antonioli (6561800)
Alessandra Sacchi (322123)
Stefania Notari (10699017)
Anna Farina (119664)
Alessia Beccacece (14081113)
Marisa Fusto (14081116)
Alessandra Vergori (4540474)
Gianpiero D’Offizi (322128)
Fabrizio Taglietti (10684545)
Andrea Antinori (103654)
Emanuele Nicastri (310235)
Luisa Marchioni (9775049)
Fabrizio Palmieri (2830802)
Giuseppe Ippolito (7056)
Mauro Piacentini (377487)
Chiara Agrati (322137)
Gian Maria Fimia (431159)

November 2022

Additional file 3: Table S3: MaxQuant software identification of proteins from plasma of COVID-19 pa...

Additional file 2 of Proteomic analysis identifies a signature of disease severity in the plasma of COVID-19 pneumonia patients associated to neutrophil, platelet and complement activation

Fabiola Ciccosanti (2118151)
Manuela Antonioli (6561800)
Alessandra Sacchi (322123)
Stefania Notari (10699017)
Anna Farina (119664)
Alessia Beccacece (14081113)
Marisa Fusto (14081116)
Alessandra Vergori (4540474)
Gianpiero D’Offizi (322128)
Fabrizio Taglietti (10684545)
Andrea Antinori (103654)
Emanuele Nicastri (310235)
Luisa Marchioni (9775049)
Fabrizio Palmieri (2830802)
Giuseppe Ippolito (7056)
Mauro Piacentini (377487)
Chiara Agrati (322137)
Gian Maria Fimia (431159)

November 2022

Additional file 2: Tables S2: MaxQuant software analysis of peptides detected by mass spectrometry f...

Additional file 6: of Neutrophilic proteolysis in the cystic fibrosis lung correlates with a pathogenic microbiome

Robert Quinn (453809)
Sandeep Adem (6332756)
Robert Mills (6005816)
William Comstock (6332759)
Lindsay DeRight Goldasich (4900375)
Gregory Humphrey (4900273)
Alexander Aksenov (2146969)
Alexei Melnik (6332762)
Ricardo Silva (4739820)
Gail Ackermann (618902)
Nuno Bandeira (801994)
David Gonzalez (1399030)
Doug Conrad (6332765)
Anthony OâDonoghue (6332768)
Rob Knight (11635)
Pieter Dorrestein (3463673)

February 2019

Table S3. Peptidomics data on human proteome as produced using PEAKS software. (XLSX 87 kb

Additional file 1: Table S1. of The prognostic value of serum CA 19-9 for patients with advanced lung adenocarcinoma

Yuki Sato (243074)
Daichi Fujimoto (3400052)
Keiichiro Uehara (3400055)
Ryoko Shimizu (27094)
Jiro Ito (3400037)
Mariko Kogo (3400046)
Shunsuke Teraoka (3400043)
Ryoji Kato (3400049)
Kazuma Nagata (3400058)
Atsushi Nakagawa (482199)
Kojiro Otsuka (2626141)
Hiroshi Hamakawa (290064)
Yutaka Takahashi (600869)
Yukihiro Imai (2157358)
Keisuke Tomii (3400040)

November 2016

Characteristics and differences by serum CYFRA 21-1 levels in patients with advanced-stage lung aden...

Additional file 1: Table S1. of Blood-based lung cancer biomarkers identified through proteomic discovery in cancer tissues, cell lines and conditioned medium

Charles Birse (3420953)
Robert Lagier (3420938)
William FitzHugh (484022)
Harvey Pass (202310)
William Rom (2400067)
Eric Edell (3420962)
Aaron Bungum (3420959)
Fabien Maldonado (544207)
James Jett (3420956)
Mehdi Mesri (484015)
Erin Sult (3420947)
Elizabeth Joseloff (1342536)
Aiqun Li (289891)
Jenny Heidbrink (484017)
Gulshan Dhariwal (3420941)
Chad Danis (3420950)
Jennifer Tomic (3420965)
Robert Bruce (2019028)
Paul Moore (469661)
Tao He (23919)
Marcia Lewis (3420944)
Steve Ruben (484023)

July 2015

Demographics and clinical profiles for subjects selected for fresh tissue discovery study

Additional file 3: Table S3. of Blood-based lung cancer biomarkers identified through proteomic discovery in cancer tissues, cell lines and conditioned medium

Charles Birse (3420953)
Robert Lagier (3420938)
William FitzHugh (484022)
Harvey Pass (202310)
William Rom (2400067)
Eric Edell (3420962)
Aaron Bungum (3420959)
Fabien Maldonado (544207)
James Jett (3420956)
Mehdi Mesri (484015)
Erin Sult (3420947)
Elizabeth Joseloff (1342536)
Aiqun Li (289891)
Jenny Heidbrink (484017)
Gulshan Dhariwal (3420941)
Chad Danis (3420950)
Jennifer Tomic (3420965)
Robert Bruce (2019028)
Paul Moore (469661)
Tao He (23919)
Marcia Lewis (3420944)
Steve Ruben (484023)

July 2015

Candidate lung cancer biomarkers (nâ=â179) identified through LC/MS analysis

Additional file 4: Figure S1. of Blood-based lung cancer biomarkers identified through proteomic discovery in cancer tissues, cell lines and conditioned medium

Charles Birse (3420953)
Robert Lagier (3420938)
William FitzHugh (484022)
Harvey Pass (202310)
William Rom (2400067)
Eric Edell (3420962)
Aaron Bungum (3420959)
Fabien Maldonado (544207)
James Jett (3420956)
Mehdi Mesri (484015)
Erin Sult (3420947)
Elizabeth Joseloff (1342536)
Aiqun Li (289891)
Jenny Heidbrink (484017)
Gulshan Dhariwal (3420941)
Chad Danis (3420950)
Jennifer Tomic (3420965)
Robert Bruce (2019028)
Paul Moore (469661)
Tao He (23919)
Marcia Lewis (3420944)
Steve Ruben (484023)

July 2015

Panther-based classification of protein class for candidate lung cancer markers (nâ=â179)

Janna Berg (5515091)
Ann Halvorsen (3415001)
May-Bente Bengtson (5515097)
Kristin TaskĂŠn (5515100)
Gunhild MĂŚlandsmo (5515103)
Arne Yndestad (224387)
Bente Halvorsen (151367)
Odd Brustugun (3415010)
PĂĽl Aukrust (3567137)
Thor Ueland (307058)
Ăslaug Helland (5049539)

July 2018

Table S1. Serum protein levels. All data from the serum analyses are presented. This includes result...

Additional file 5: Figure S2. of Blood-based lung cancer biomarkers identified through proteomic discovery in cancer tissues, cell lines and conditioned medium

Charles Birse (3420953)
Robert Lagier (3420938)
William FitzHugh (484022)
Harvey Pass (202310)
William Rom (2400067)
Eric Edell (3420962)
Aaron Bungum (3420959)
Fabien Maldonado (544207)
James Jett (3420956)
Mehdi Mesri (484015)
Erin Sult (3420947)
Elizabeth Joseloff (1342536)
Aiqun Li (289891)
Jenny Heidbrink (484017)
Gulshan Dhariwal (3420941)
Chad Danis (3420950)
Jennifer Tomic (3420965)
Robert Bruce (2019028)
Paul Moore (469661)
Tao He (23919)
Marcia Lewis (3420944)
Steve Ruben (484023)

July 2015

Panther-based classification of protein class comparing lung cancer markers identified in tissues an...

Additional file 6: Figure S3. of Blood-based lung cancer biomarkers identified through proteomic discovery in cancer tissues, cell lines and conditioned medium

Charles Birse (3420953)
Robert Lagier (3420938)
William FitzHugh (484022)
Harvey Pass (202310)
William Rom (2400067)
Eric Edell (3420962)
Aaron Bungum (3420959)
Fabien Maldonado (544207)
James Jett (3420956)
Mehdi Mesri (484015)
Erin Sult (3420947)
Elizabeth Joseloff (1342536)
Aiqun Li (289891)
Jenny Heidbrink (484017)
Gulshan Dhariwal (3420941)
Chad Danis (3420950)
Jennifer Tomic (3420965)
Robert Bruce (2019028)
Paul Moore (469661)
Tao He (23919)
Marcia Lewis (3420944)
Steve Ruben (484023)

July 2015

Panther-based classification of protein pathways comparing lung cancer markers identified in tissues...

Additional file 7: Figure S4. of Blood-based lung cancer biomarkers identified through proteomic discovery in cancer tissues, cell lines and conditioned medium

Charles Birse (3420953)
Robert Lagier (3420938)
William FitzHugh (484022)
Harvey Pass (202310)
William Rom (2400067)
Eric Edell (3420962)
Aaron Bungum (3420959)
Fabien Maldonado (544207)
James Jett (3420956)
Mehdi Mesri (484015)
Erin Sult (3420947)
Elizabeth Joseloff (1342536)
Aiqun Li (289891)
Jenny Heidbrink (484017)
Gulshan Dhariwal (3420941)
Chad Danis (3420950)
Jennifer Tomic (3420965)
Robert Bruce (2019028)
Paul Moore (469661)
Tao He (23919)
Marcia Lewis (3420944)
Steve Ruben (484023)

July 2015

Expression levels of biomarker candidates in serum collected from patients with NSCLC (nâ=â94) a...

Additional file 1 of Plasma proteomics-based biomarkers for predicting response to mesenchymal stem cell therapy in severe COVID-19

Tian-Tian Li (451683)
Wei-Qi Yao (17612434)
Hai-Bo Dong (17612437)
Ze-Rui Wang (17612440)
Zi-Ying Zhang (17612443)
Meng-Qi Yuan (17612446)
Lei Shi (8144)
Fu-Sheng Wang (17612449)

December 2023

Additional file 1. Fig. S1: Distribution and quality control of the total proteins detected

Additional file 1: of Diagnostic role of circulating extracellular matrix-related proteins in non-small cell lung cancer

Francesca Andriani (4987880)
Elena Landoni (3399467)
Mavis Mensah (4987874)
Federica Facchinetti (4987877)
Rosalba Miceli (545436)
Elda Tagliabue (222687)
Marta Giussani (5767259)
Maurizio Callari (107071)
Loris De Cecco (107073)
Mario Colombo (5767262)
Luca Roz (4987883)
Ugo Pastorino (440075)
Gabriella Sozzi (371979)

September 2018

Table S1. Quantile regression multivariable analysis of association between COL11A1 and COL10A1 leve...

Additional file 3 of Proteomic analysis identifies a signature of disease severity in the plasma of COVID-19 pneumonia patients associated to neutrophil, platelet and complement activation

Fabiola Ciccosanti (2118151)
Manuela Antonioli (6561800)
Alessandra Sacchi (322123)
Stefania Notari (10699017)
Anna Farina (119664)
Alessia Beccacece (14081113)
Marisa Fusto (14081116)
Alessandra Vergori (4540474)
Gianpiero D’Offizi (322128)
Fabrizio Taglietti (10684545)
Andrea Antinori (103654)
Emanuele Nicastri (310235)
Luisa Marchioni (9775049)
Fabrizio Palmieri (2830802)
Giuseppe Ippolito (7056)
Mauro Piacentini (377487)
Chiara Agrati (322137)
Gian Maria Fimia (431159)

November 2022

Additional file 3: Table S3: MaxQuant software identification of proteins from plasma of COVID-19 pa...

Additional file 2 of Proteomic analysis identifies a signature of disease severity in the plasma of COVID-19 pneumonia patients associated to neutrophil, platelet and complement activation

Fabiola Ciccosanti (2118151)
Manuela Antonioli (6561800)
Alessandra Sacchi (322123)
Stefania Notari (10699017)
Anna Farina (119664)
Alessia Beccacece (14081113)
Marisa Fusto (14081116)
Alessandra Vergori (4540474)
Gianpiero D’Offizi (322128)
Fabrizio Taglietti (10684545)
Andrea Antinori (103654)
Emanuele Nicastri (310235)
Luisa Marchioni (9775049)
Fabrizio Palmieri (2830802)
Giuseppe Ippolito (7056)
Mauro Piacentini (377487)
Chiara Agrati (322137)
Gian Maria Fimia (431159)

November 2022

Additional file 2: Tables S2: MaxQuant software analysis of peptides detected by mass spectrometry f...

Additional file 6: of Neutrophilic proteolysis in the cystic fibrosis lung correlates with a pathogenic microbiome

Robert Quinn (453809)
Sandeep Adem (6332756)
Robert Mills (6005816)
William Comstock (6332759)
Lindsay DeRight Goldasich (4900375)
Gregory Humphrey (4900273)
Alexander Aksenov (2146969)
Alexei Melnik (6332762)
Ricardo Silva (4739820)
Gail Ackermann (618902)
Nuno Bandeira (801994)
David Gonzalez (1399030)
Doug Conrad (6332765)
Anthony OâDonoghue (6332768)
Rob Knight (11635)
Pieter Dorrestein (3463673)

February 2019

Table S3. Peptidomics data on human proteome as produced using PEAKS software. (XLSX 87 kb

Additional file 1: Table S1. of The prognostic value of serum CA 19-9 for patients with advanced lung adenocarcinoma

Yuki Sato (243074)
Daichi Fujimoto (3400052)
Keiichiro Uehara (3400055)
Ryoko Shimizu (27094)
Jiro Ito (3400037)
Mariko Kogo (3400046)
Shunsuke Teraoka (3400043)
Ryoji Kato (3400049)
Kazuma Nagata (3400058)
Atsushi Nakagawa (482199)
Kojiro Otsuka (2626141)
Hiroshi Hamakawa (290064)
Yutaka Takahashi (600869)
Yukihiro Imai (2157358)
Keisuke Tomii (3400040)

November 2016

Characteristics and differences by serum CYFRA 21-1 levels in patients with advanced-stage lung aden...

Additional file 1 of Quantitative proteomics identified circulating biomarkers in lung adenocarcinoma diagnosis

Abstract

Extracted data

Additional file 1 of Quantitative proteomics identified circulating biomarkers in lung adenocarcinoma diagnosis

Abstract

Extracted data

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