First community-wide, comparative cross-linking mass spectrometry study

Claudio Iacobucci; Christine Piotrowski; Ruedi Aebersold; Bruno C. Amaral; Philip Andrews; Katja Bernfur; Christoph Borchers; Nicolas I. Brodie; James E. Bruce; Yong Cao; Stéphane Chaignepain; Juan D. Chavez; Stéphane Claverol; Jürgen Cox; Trisha Davis; Gianluca Degliesposti; Meng Qiu Dong; Nufar Edinger; Cecilia Emanuelsson; Marina Gay; Michael Götze; Francisco Gomes-Neto; Fabio C. Gozzo; Craig Gutierrez; Caroline Haupt; Albert J.R. Heck; Franz Herzog; Lan Huang; Michael R. Hoopmann; Nir Kalisman; Oleg Klykov; Zdeněk Kukačka; Fan Liu; Michael J. Maccoss; Karl Mechtler; Ravit Mesika; Robert L. Moritz; Nagarjuna Nagaraj; Victor Nesati; Ana G.C. Neves-Ferreira; Robert Ninnis; Petr Novák; Francis J. O'Reilly; Matthias Pelzing; Evgeniy Petrotchenko; Lolita Piersimoni; Manolo Plasencia; Tara Pukala; Kasper D. Rand; Juri Rappsilber; Dana Reichmann; Carolin Sailer; Chris P. Sarnowski; Richard A. Scheltema; Carla Schmidt; David C. Schriemer; Yi Shi; J. Mark Skehel; Moriya Slavin; Frank Sobott; Victor Solis-Mezarino; Heike Stephanowitz; Florian Stengel; Christian E. Stieger; Esben Trabjerg; Michael Trnka; Marta Vilaseca; Rosa Viner; Yufei Xiang; Sule Yilmaz; Alex Zelter; Daniel Ziemianowicz; Alexander Leitner; Andrea Sinz

doi:10.1021/acs.analchem.9b00658

First community-wide, comparative cross-linking mass spectrometry study

Claudio Iacobucci, Christine Piotrowski, Ruedi Aebersold, Bruno C. Amaral, Philip Andrews, Katja Bernfur, Christoph Borchers, Nicolas I. Brodie, James E. Bruce, Yong Cao, Stéphane Chaignepain, Juan D. Chavez, Stéphane Claverol, Jürgen Cox, Trisha Davis, Gianluca Degliesposti, Meng Qiu Dong, Nufar Edinger, Cecilia Emanuelsson, Marina GayMichael Götze, Francisco Gomes-Neto, Fabio C. Gozzo, Craig Gutierrez, Caroline Haupt, Albert J.R. Heck, Franz Herzog, Lan Huang, Michael R. Hoopmann, Nir Kalisman, Oleg Klykov, Zdeněk Kukačka, Fan Liu, Michael J. Maccoss, Karl Mechtler, Ravit Mesika, Robert L. Moritz, Nagarjuna Nagaraj, Victor Nesati, Ana G.C. Neves-Ferreira, Robert Ninnis, Petr Novák, Francis J. O'Reilly, Matthias Pelzing, Evgeniy Petrotchenko, Lolita Piersimoni, Manolo Plasencia, Tara Pukala, Kasper D. Rand, Juri Rappsilber, Dana Reichmann, Carolin Sailer, Chris P. Sarnowski, Richard A. Scheltema, Carla Schmidt, David C. Schriemer, Yi Shi, J. Mark Skehel, Moriya Slavin, Frank Sobott, Victor Solis-Mezarino, Heike Stephanowitz, Florian Stengel, Christian E. Stieger, Esben Trabjerg, Michael Trnka, Marta Vilaseca, Rosa Viner, Yufei Xiang, Sule Yilmaz, Alex Zelter, Daniel Ziemianowicz, Alexander Leitner^*, Andrea Sinz

^*Corresponding author for this work

Research output: Contribution to journal › Review article › peer-review

Abstract

The number of publications in the field of chemical cross-linking combined with mass spectrometry (XL-MS) to derive constraints for protein three-dimensional structure modeling and to probe protein-protein interactions has increased during the last years. As the technique is now becoming routine for in vitro and in vivo applications in proteomics and structural biology there is a pressing need to define protocols as well as data analysis and reporting formats. Such consensus formats should become accepted in the field and be shown to lead to reproducible results. This first, community-based harmonization study on XL-MS is based on the results of 32 groups participating worldwide. The aim of this paper is to summarize the status quo of XL-MS and to compare and evaluate existing cross-linking strategies. Our study therefore builds the framework for establishing best practice guidelines to conduct cross-linking experiments, perform data analysis, and define reporting formats with the ultimate goal of assisting scientists to generate accurate and reproducible XL-MS results.

Original language	English
Pages (from-to)	6953-6961
Number of pages	9
Journal	Analytical Chemistry
Volume	91
Issue number	11
Early online date	2 May 2019
DOIs	https://doi.org/10.1021/acs.analchem.9b00658
Publication status	Published - 4 Jun 2019

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Iacobucci, C., Piotrowski, C., Aebersold, R., Amaral, B. C., Andrews, P., Bernfur, K., Borchers, C., Brodie, N. I., Bruce, J. E., Cao, Y., Chaignepain, S., Chavez, J. D., Claverol, S., Cox, J., Davis, T., Degliesposti, G., Dong, M. Q., Edinger, N., Emanuelsson, C., ... Sinz, A. (2019). First community-wide, comparative cross-linking mass spectrometry study. Analytical Chemistry, 91(11), 6953-6961. https://doi.org/10.1021/acs.analchem.9b00658

@article{df8eeae9c05348a59360731d04aad141,

title = "First community-wide, comparative cross-linking mass spectrometry study",

abstract = "The number of publications in the field of chemical cross-linking combined with mass spectrometry (XL-MS) to derive constraints for protein three-dimensional structure modeling and to probe protein-protein interactions has increased during the last years. As the technique is now becoming routine for in vitro and in vivo applications in proteomics and structural biology there is a pressing need to define protocols as well as data analysis and reporting formats. Such consensus formats should become accepted in the field and be shown to lead to reproducible results. This first, community-based harmonization study on XL-MS is based on the results of 32 groups participating worldwide. The aim of this paper is to summarize the status quo of XL-MS and to compare and evaluate existing cross-linking strategies. Our study therefore builds the framework for establishing best practice guidelines to conduct cross-linking experiments, perform data analysis, and define reporting formats with the ultimate goal of assisting scientists to generate accurate and reproducible XL-MS results.",

author = "Claudio Iacobucci and Christine Piotrowski and Ruedi Aebersold and Amaral, {Bruno C.} and Philip Andrews and Katja Bernfur and Christoph Borchers and Brodie, {Nicolas I.} and Bruce, {James E.} and Yong Cao and St{\'e}phane Chaignepain and Chavez, {Juan D.} and St{\'e}phane Claverol and J{\"u}rgen Cox and Trisha Davis and Gianluca Degliesposti and Dong, {Meng Qiu} and Nufar Edinger and Cecilia Emanuelsson and Marina Gay and Michael G{\"o}tze and Francisco Gomes-Neto and Gozzo, {Fabio C.} and Craig Gutierrez and Caroline Haupt and Heck, {Albert J.R.} and Franz Herzog and Lan Huang and Hoopmann, {Michael R.} and Nir Kalisman and Oleg Klykov and Zden{\v e}k Kuka{\v c}ka and Fan Liu and Maccoss, {Michael J.} and Karl Mechtler and Ravit Mesika and Moritz, {Robert L.} and Nagarjuna Nagaraj and Victor Nesati and Neves-Ferreira, {Ana G.C.} and Robert Ninnis and Petr Nov{\'a}k and O'Reilly, {Francis J.} and Matthias Pelzing and Evgeniy Petrotchenko and Lolita Piersimoni and Manolo Plasencia and Tara Pukala and Rand, {Kasper D.} and Juri Rappsilber and Dana Reichmann and Carolin Sailer and Sarnowski, {Chris P.} and Scheltema, {Richard A.} and Carla Schmidt and Schriemer, {David C.} and Yi Shi and Skehel, {J. Mark} and Moriya Slavin and Frank Sobott and Victor Solis-Mezarino and Heike Stephanowitz and Florian Stengel and Stieger, {Christian E.} and Esben Trabjerg and Michael Trnka and Marta Vilaseca and Rosa Viner and Yufei Xiang and Sule Yilmaz and Alex Zelter and Daniel Ziemianowicz and Alexander Leitner and Andrea Sinz",

year = "2019",

month = jun,

day = "4",

doi = "10.1021/acs.analchem.9b00658",

language = "English",

volume = "91",

pages = "6953--6961",

journal = "Analytical Chemistry",

issn = "0003-2700",

publisher = "American Chemical Society",

number = "11",

}

Iacobucci, C, Piotrowski, C, Aebersold, R, Amaral, BC, Andrews, P, Bernfur, K, Borchers, C, Brodie, NI, Bruce, JE, Cao, Y, Chaignepain, S, Chavez, JD, Claverol, S, Cox, J, Davis, T, Degliesposti, G, Dong, MQ, Edinger, N, Emanuelsson, C, Gay, M, Götze, M, Gomes-Neto, F, Gozzo, FC, Gutierrez, C, Haupt, C, Heck, AJR, Herzog, F, Huang, L, Hoopmann, MR, Kalisman, N, Klykov, O, Kukačka, Z, Liu, F, Maccoss, MJ, Mechtler, K, Mesika, R, Moritz, RL, Nagaraj, N, Nesati, V, Neves-Ferreira, AGC, Ninnis, R, Novák, P, O'Reilly, FJ, Pelzing, M, Petrotchenko, E, Piersimoni, L, Plasencia, M, Pukala, T, Rand, KD, Rappsilber, J, Reichmann, D, Sailer, C, Sarnowski, CP, Scheltema, RA, Schmidt, C, Schriemer, DC, Shi, Y, Skehel, JM, Slavin, M, Sobott, F, Solis-Mezarino, V, Stephanowitz, H, Stengel, F, Stieger, CE, Trabjerg, E, Trnka, M, Vilaseca, M, Viner, R, Xiang, Y, Yilmaz, S, Zelter, A, Ziemianowicz, D, Leitner, A & Sinz, A 2019, 'First community-wide, comparative cross-linking mass spectrometry study', Analytical Chemistry, vol. 91, no. 11, pp. 6953-6961. https://doi.org/10.1021/acs.analchem.9b00658

TY - JOUR

T1 - First community-wide, comparative cross-linking mass spectrometry study

AU - Iacobucci, Claudio

AU - Piotrowski, Christine

AU - Aebersold, Ruedi

AU - Amaral, Bruno C.

AU - Andrews, Philip

AU - Bernfur, Katja

AU - Borchers, Christoph

AU - Brodie, Nicolas I.

AU - Bruce, James E.

AU - Cao, Yong

AU - Chaignepain, Stéphane

AU - Chavez, Juan D.

AU - Claverol, Stéphane

AU - Cox, Jürgen

AU - Davis, Trisha

AU - Degliesposti, Gianluca

AU - Dong, Meng Qiu

AU - Edinger, Nufar

AU - Emanuelsson, Cecilia

AU - Gay, Marina

AU - Götze, Michael

AU - Gomes-Neto, Francisco

AU - Gozzo, Fabio C.

AU - Gutierrez, Craig

AU - Haupt, Caroline

AU - Heck, Albert J.R.

AU - Herzog, Franz

AU - Huang, Lan

AU - Hoopmann, Michael R.

AU - Kalisman, Nir

AU - Klykov, Oleg

AU - Kukačka, Zdeněk

AU - Liu, Fan

AU - Maccoss, Michael J.

AU - Mechtler, Karl

AU - Mesika, Ravit

AU - Moritz, Robert L.

AU - Nagaraj, Nagarjuna

AU - Nesati, Victor

AU - Neves-Ferreira, Ana G.C.

AU - Ninnis, Robert

AU - Novák, Petr

AU - O'Reilly, Francis J.

AU - Pelzing, Matthias

AU - Petrotchenko, Evgeniy

AU - Piersimoni, Lolita

AU - Plasencia, Manolo

AU - Pukala, Tara

AU - Rand, Kasper D.

AU - Rappsilber, Juri

AU - Reichmann, Dana

AU - Sailer, Carolin

AU - Sarnowski, Chris P.

AU - Scheltema, Richard A.

AU - Schmidt, Carla

AU - Schriemer, David C.

AU - Shi, Yi

AU - Skehel, J. Mark

AU - Slavin, Moriya

AU - Sobott, Frank

AU - Solis-Mezarino, Victor

AU - Stephanowitz, Heike

AU - Stengel, Florian

AU - Stieger, Christian E.

AU - Trabjerg, Esben

AU - Trnka, Michael

AU - Vilaseca, Marta

AU - Viner, Rosa

AU - Xiang, Yufei

AU - Yilmaz, Sule

AU - Zelter, Alex

AU - Ziemianowicz, Daniel

AU - Leitner, Alexander

AU - Sinz, Andrea

PY - 2019/6/4

Y1 - 2019/6/4

N2 - The number of publications in the field of chemical cross-linking combined with mass spectrometry (XL-MS) to derive constraints for protein three-dimensional structure modeling and to probe protein-protein interactions has increased during the last years. As the technique is now becoming routine for in vitro and in vivo applications in proteomics and structural biology there is a pressing need to define protocols as well as data analysis and reporting formats. Such consensus formats should become accepted in the field and be shown to lead to reproducible results. This first, community-based harmonization study on XL-MS is based on the results of 32 groups participating worldwide. The aim of this paper is to summarize the status quo of XL-MS and to compare and evaluate existing cross-linking strategies. Our study therefore builds the framework for establishing best practice guidelines to conduct cross-linking experiments, perform data analysis, and define reporting formats with the ultimate goal of assisting scientists to generate accurate and reproducible XL-MS results.

AB - The number of publications in the field of chemical cross-linking combined with mass spectrometry (XL-MS) to derive constraints for protein three-dimensional structure modeling and to probe protein-protein interactions has increased during the last years. As the technique is now becoming routine for in vitro and in vivo applications in proteomics and structural biology there is a pressing need to define protocols as well as data analysis and reporting formats. Such consensus formats should become accepted in the field and be shown to lead to reproducible results. This first, community-based harmonization study on XL-MS is based on the results of 32 groups participating worldwide. The aim of this paper is to summarize the status quo of XL-MS and to compare and evaluate existing cross-linking strategies. Our study therefore builds the framework for establishing best practice guidelines to conduct cross-linking experiments, perform data analysis, and define reporting formats with the ultimate goal of assisting scientists to generate accurate and reproducible XL-MS results.

U2 - 10.1021/acs.analchem.9b00658

DO - 10.1021/acs.analchem.9b00658

M3 - Review article

C2 - 31045356

AN - SCOPUS:85066804197

VL - 91

SP - 6953

EP - 6961

JO - Analytical Chemistry

JF - Analytical Chemistry

SN - 0003-2700

IS - 11

ER -

First community-wide, comparative cross-linking mass spectrometry study

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