DPHL v.2: An updated and comprehensive DIA pan-human assay library for quantifying more than 14,000 proteins

被引：8

作者：

Xue, Zhangzhi ^{[1
,2
,3
]}

Zhu, Tiansheng ^{[1
,2
,3
]}

Zhang, Fangfei ^{[1
,2
,3
]}

Zhang, Cheng ^{[1
,2
,3
]}

Xiang, Nan ^{[4
]}

Qian, Liujia ^{[1
,2
,3
]}

Yi, Xiao ^{[4
]}

Sun, Yaoting ^{[1
,2
,3
]}

Liu, Wei ^{[4
]}

Cai, Xue ^{[1
,2
,3
]}

Wang, Linyan ^{[5
]}

Dai, Xizhe ^{[5
]}

Yue, Liang ^{[1
,2
,3
]}

Li, Lu ^{[1
,2
,3
]}

Pham, Thang, V ^{[6
]}

Piersma, Sander R. ^{[6
]}

Xiao, Qi ^{[1
,2
,3
]}

Luo, Meng ^{[7
,8
]}

Lu, Cong ^{[9
]}

Zhu, Jiang ^{[9
]}

Zhao, Yongfu ^{[10
]}

Wang, Guangzhi ^{[10
]}

Xiao, Junhong ^{[10
]}

Liu, Tong ^{[11
]}

Liu, Zhiyu

He, Yi

Wu, Qijun

Gong, Tingting

Zhu, Jianqin

Zheng, Zhiguo

Ye, Juan ^{[5
]}

Li, Yan ^{[7
,8
]}

Jimenez, Connie R. ^{[6
]}

Jun, A. ^{[1
,2
,3
]}

Guo, Tiannan ^{[1
,2
,3
]}

机构：

[1] Westlake Univ, Sch Life Sci, Westlake Lab Life Sci & Biomed, Key Lab Struct Biol Zhejiang Prov,iMarker Lab, Hangzhou 310024, Zhejiang, Peoples R China

[2] Westlake Inst Adv Study, Inst Basic Med Sci, Hangzhou 310024, Zhejiang, Peoples R China

[3] Westlake Univ, Res Ctr Ind Future, 600 Dunyu Rd, Hangzhou 310030, Zhejiang, Peoples R China

[4] Westlake Om Hangzhou Biotechnol Co Ltd, Hangzhou 310024, Peoples R China

[5] Zhejiang Univ, Affiliated Hosp 2, Sch Med, Dept Ophthalmol, Hangzhou 310000, Zhejiang, Peoples R China

[6] Vrije Univ Amsterdam, VU Univ Med Ctr, Dept Med Oncol, OncoProte Lab, NL-1011 Amsterdam, Netherlands

[7] Shanghai Jiao Tong Univ, Songjiang Hosp, Coll Basic Med Sci, Sch Med,Dept Anat & Physiol, Shanghai 201600, Peoples R China

[8] Shanghai Jiao Tong Univ, Songjiang Res Inst, Sch Med, Shanghai 201600, Peoples R China

[9] Huazhong Univ Sci & Technol, Union Hosp, Tongji Med Coll, Ctr Stem Cell Res & Applicat, Wuhan 430074, Hubei, Peoples R China

[10] Dalian Med Univ, Hosp 2, Dept Gen Surg, Dalian 116044, Liaoning, Peoples R China

[11] Harbin Med Univ, Canc Hosp, Harbin 150081, Heilongjiang, Peoples R China

来源：

PATTERNS | 2023年 / 4卷 / 07期

关键词：

BETA-II SPECTRIN; MASS-SPECTROMETRY; BLOOD MARKERS; CANCER; IDENTIFICATION; VALIDATION; EXPRESSION; CEACAM6; LGALS4; TSPAN8;

D O I：

10.1016/j.patter.2023.100792

中图分类号：

TP18 [人工智能理论];

学科分类号：

081104 ; 0812 ; 0835 ; 1405 ;

摘要：

A comprehensive pan-human spectral library is critical for biomarker discovery using mass spectrometry (MS) -based proteomics. DPHL v.1, a previous pan-human library built from 1,096 data-dependent acquisition (DDA) MS data of 16 human tissue types, allows quantifying of 10,943 proteins. Here, we generated DPHL v.2 from 1,608 DDA-MS data. The data included 586 DDA-MS data acquired from 18 tissue types, while 1,022 files were derived from DPHL v.1. DPHL v.2 thus comprises data from 24 sample types, including several cancer types (lung, breast, kidney, and prostate cancer, among others). We generated four variants of DPHL v.2 to include semi-tryptic peptides and protein isoforms. DPHL v.2 was then applied to two colorectal cancer cohorts. The numbers of identified and significantly dysregulated proteins increased by at least 21.7% and 14.2%, respectively, compared with DPHL v.1. Our findings show that the increased human proteome coverage of DPHL v.2 provides larger pools of potential protein biomarkers.

引用

页数：12

共 61 条

[1] A high-stringency blueprint of the human proteome [J].

Adhikari, Subash ;

Nice, Edouard C. ;

Deutsch, Eric W. ;

Lane, Lydie ;

Omenn, Gilbert S. ;

Pennington, Stephen R. ;

Paik, Young-Ki ;

Overall, Christopher M. ;

Corrales, Fernando J. ;

Cristea, Ileana M. ;

Van Eyk, Jennifer E. ;

Uhlen, Mathias ;

Lindskog, Cecilia ;

Chan, Daniel W. ;

Bairoch, Amos ;

Waddington, James C. ;

Justice, Joshua L. ;

LaBaer, Joshua ;

Rodriguez, Henry ;

He, Fuchu ;

Kostrzewa, Markus ;

Ping, Peipei ;

Gundry, Rebekah L. ;

Stewart, Peter ;

Srivastava, Sanjeeva ;

Srivastava, Sudhir ;

Nogueira, Fabio C. S. ;

Domont, Gilberto B. ;

Vandenbrouck, Yves ;

Lam, Maggie P. Y. ;

Wennersten, Sara ;

Vizcaino, Juan Antonio ;

Wilkins, Marc ;

Schwenk, Jochen M. ;

Lundberg, Emma ;

Bandeira, Nuno ;

Marko-Varga, Gyorgy ;

Weintraub, Susan T. ;

Pineau, Charles ;

Kusebauch, Ulrike ;

Moritz, Robert L. ;

Ahn, Seong Beom ;

Palmblad, Magnus ;

Snyder, Michael P. ;

Aebersold, Ruedi ;

Baker, Mark S. .

NATURE COMMUNICATIONS, 2020, 11 (01)

[2] Mass-spectrometric exploration of proteome structure and function [J].

Aebersold, Ruedi ;

Mann, Matthias .

NATURE, 2016, 537 (7620) :347-355

[3] Generation of a zebrafish SWATH-MS spectral library to quantify 10,000 proteins [J].

Blattmann, Peter ;

Stutz, Vivienne ;

Lizzo, Giulia ;

Richard, Joy ;

Gut, Philipp ;

Aebersold, Ruedi .

SCIENTIFIC DATA, 2019, 6 (1)

[4] A cross-platform toolkit for mass spectrometry and proteomics [J].

Chambers, Matthew C. ;

Maclean, Brendan ;

Burke, Robert ;

Amodei, Dario ;

Ruderman, Daniel L. ;

Neumann, Steffen ;

Gatto, Laurent ;

Fischer, Bernd ;

Pratt, Brian ;

Egertson, Jarrett ;

Hoff, Katherine ;

Kessner, Darren ;

Tasman, Natalie ;

Shulman, Nicholas ;

Frewen, Barbara ;

Baker, Tahmina A. ;

Brusniak, Mi-Youn ;

Paulse, Christopher ;

Creasy, David ;

Flashner, Lisa ;

Kani, Kian ;

Moulding, Chris ;

Seymour, Sean L. ;

Nuwaysir, Lydia M. ;

Lefebvre, Brent ;

Kuhlmann, Frank ;

Roark, Joe ;

Rainer, Paape ;

Detlev, Suckau ;

Hemenway, Tina ;

Huhmer, Andreas ;

Langridge, James ;

Connolly, Brian ;

Chadick, Trey ;

Holly, Krisztina ;

Eckels, Josh ;

Deutsch, Eric W. ;

Moritz, Robert L. ;

Katz, Jonathan E. ;

Agus, David B. ;

MacCoss, Michael ;

Tabb, David L. ;

Mallick, Parag .

NATURE BIOTECHNOLOGY, 2012, 30 (10) :918-920

[5] ADAM22/LGI1 complex as a new actionable target for breast cancer brain metastasis [J].

Charmsaz, Sara ;

Doherty, Ben ;

Cocchiglia, Sinead ;

Vareslija, Damir ;

Marino, Attilio ;

Cosgrove, Nicola ;

Marques, Ricardo ;

Priedigkeit, Nolan ;

Purcell, Siobhan ;

Bane, Fiona ;

Bolger, Jarlath ;

Byrne, Christopher ;

O'Halloran, Philip J. ;

Brett, Francesca ;

Sheehan, Katherine ;

Brennan, Kieran ;

Hopkins, Ann M. ;

Keelan, Stephen ;

Jagust, Petra ;

Madden, Stephen ;

Martinelli, Chiara ;

Battaglini, Matteo ;

Oesterreich, Steffi ;

Lee, Adrian V. ;

Ciofani, Gianni ;

Hill, Arnold D. K. ;

Young, Leonie S. .

BMC MEDICINE, 2020, 18 (01)

[6] Pan-cancer molecular subtypes revealed by mass-spectrometry-based proteomic characterization of more than 500 human cancers [J].

Chen, Fengju ;

Chandrashekar, Darshan S. ;

Varambally, Sooryanarayana ;

Creighton, Chad J. .

NATURE COMMUNICATIONS, 2019, 10 (1)

[7] ASPM promotes glioblastoma growth by regulating G1 restriction point progression and Wnt-β-catenin signaling [J].

Chen, Xin ;

Huang, Lijie ;

Yang, Yang ;

Chen, Suhua ;

Sun, Jianjun ;

Ma, Changcheng ;

Xie, Jingcheng ;

Song, Yongmei ;

Yang, Jun .

AGING-US, 2020, 12 (01) :224-241

[8] Philosopher: a versatile toolkit for shotgun proteomics data analysis [J].

da Veiga Leprevost, Felipe ;

Haynes, Sarah E. ;

Avtonomov, Dmitry M. ;

Chang, Hui-Yin ;

Shanmugam, Avinash K. ;

Mellacheruvu, Dattatreya ;

Kong, Andy T. ;

Nesvizhskii, Alexey I. .

NATURE METHODS, 2020, 17 (09) :869-870

[9] DIA-NN: neural networks and interference correction enable deep proteome coverage in high throughput [J].

Demichev, Vadim ;

Messner, Christoph B. ;

Vernardis, Spyros I. ;

Lilley, Kathryn S. ;

Ralser, Markus .

NATURE METHODS, 2020, 17 (01) :41-+

[10] Colorectal cancer screening: Assessment of CEACAM6, LGALS4, TSPAN8 and COL1A2 as blood markers in faecal immunochemical test negative subjects [J].

Ferlizza, Enea ;

Solmi, Rossella ;

Miglio, Rossella ;

Nardi, Elena ;

Mattei, Gabriella ;

Sgarzi, Michela ;

Lauriola, Mattia .

JOURNAL OF ADVANCED RESEARCH, 2020, 24 :99-107

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