The First Community-Wide, Comparative Cross-linking Mass Spectrometry Study

Claudio Iacobucci; Christine Piotrowski; Ruedi Aebersold; Bruno C Amaral; Philip C Andrews; Katja Bernfur; Christoph H Borchers; Nicholas I Brodie; James E Bruce; Yong Cao; Stéphane Chaignepain; Juan D Chavez; Stéphane Claverol; Jurgen Cox; Trisha N Davis; Gianluca Degliesposti; Meng-Qiu Dong; Nufar Edinger; Cecilia Emanuelsson; Marina Gay; Francisco Gomes-Neto; Fabio Cesar Gozzo; Craig B Gutierrez; Caroline Haupt; Albert J R Heck; Frank 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-Fereira; Robert Ninnis; Petr Novák; Francis J O'Reilly; Matthias Pelzing; Evgeniy V Petrotchenko; Lolita Piersimoni; Manolo Plasencia; Tara L Pukala; Kasper D Rand; Juri Rappsilber; Dana Reichman; 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 J Trnka; Marta Vilaseca; Rosa Viner; Yufei Xiang; Şule Yılmaz; Alex Zelter; Daniel S Ziemianowicz; Alexander Leitner; Andrea Sinz

doi:10.1021/acs.analchem.9b00658

The First Community-Wide, Comparative Cross-linking Mass Spectrometry Study

Claudio Iacobucci, Christine Piotrowski, Ruedi Aebersold, Bruno C Amaral, Philip C Andrews, Katja Bernfur, Christoph H Borchers, Nicholas I Brodie, James E Bruce, Yong Cao, Stéphane Chaignepain, Juan D Chavez, Stéphane Claverol, Jurgen Cox, Trisha N Davis, Gianluca Degliesposti, Meng-Qiu Dong, Nufar Edinger, Cecilia Emanuelsson, Marina GayFrancisco Gomes-Neto, Fabio Cesar Gozzo, Craig B Gutierrez, Caroline Haupt, Albert J R Heck, Frank 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-Fereira, Robert Ninnis, Petr Novák, Francis J O'Reilly, Matthias Pelzing, Evgeniy V Petrotchenko, Lolita Piersimoni, Manolo Plasencia, Tara L Pukala, Kasper D Rand, Juri Rappsilber, Dana Reichman, 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 J Trnka, Marta Vilaseca, Rosa Viner, Yufei Xiang, Şule Yılmaz, Alex Zelter, Daniel S Ziemianowicz, Alexander Leitner, Andrea Sinz^*

^*Corresponding author for this work

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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
Journal	Analytical Chemistry
Volume	91
Issue number	11
Pages (from-to)	6953-6961
ISSN	0003-2700
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. C., Bernfur, K., Borchers, C. H., Brodie, N. I., Bruce, J. E., Cao, Y., Chaignepain, S., Chavez, J. D., Claverol, S., Cox, J., Davis, T. N., Degliesposti, G., Dong, M-Q., Edinger, N., Emanuelsson, C., ... Sinz, A. (2019). The First Community-Wide, Comparative Cross-linking Mass Spectrometry Study. Analytical Chemistry, 91(11), 6953-6961. https://doi.org/10.1021/acs.analchem.9b00658

Iacobucci, C, Piotrowski, C, Aebersold, R, Amaral, BC, Andrews, PC, Bernfur, K, Borchers, CH, Brodie, NI, Bruce, JE, Cao, Y, Chaignepain, S, Chavez, JD, Claverol, S, Cox, J, Davis, TN, Degliesposti, G, Dong, M-Q, Edinger, N, Emanuelsson, C, Gay, M, Gomes-Neto, F, Gozzo, FC, Gutierrez, CB, 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-Fereira, AGC, Ninnis, R, Novák, P, O'Reilly, FJ, Pelzing, M, Petrotchenko, EV, Piersimoni, L, Plasencia, M, Pukala, TL, Rand, KD, Rappsilber, J, Reichman, 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, MJ, Vilaseca, M, Viner, R, Xiang, Y, Yılmaz, Ş, Zelter, A, Ziemianowicz, DS, Leitner, A & Sinz, A 2019, 'The 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

@article{b0c4a3034ff147bdb7c9ce0ef7cace62,

title = "The 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 Andrews, {Philip C} and Katja Bernfur and Borchers, {Christoph H} and Brodie, {Nicholas I} and Bruce, {James E} and Yong Cao and St{\'e}phane Chaignepain and Chavez, {Juan D} and St{\'e}phane Claverol and Jurgen Cox and Davis, {Trisha N} and Gianluca Degliesposti and Meng-Qiu Dong and Nufar Edinger and Cecilia Emanuelsson and Marina Gay and Francisco Gomes-Neto and Gozzo, {Fabio Cesar} and Gutierrez, {Craig B} and Caroline Haupt and Heck, {Albert J R} and Frank 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-Fereira, {Ana G C} and Robert Ninnis and Petr Nov{\'a}k and O'Reilly, {Francis J} and Matthias Pelzing and Petrotchenko, {Evgeniy V} and Lolita Piersimoni and Manolo Plasencia and Pukala, {Tara L} and Rand, {Kasper D} and Juri Rappsilber and Dana Reichman 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 Trnka, {Michael J} and Marta Vilaseca and Rosa Viner and Yufei Xiang and {\c S}ule Yılmaz and Alex Zelter and Ziemianowicz, {Daniel S} 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 = "Industrial And Engineering Chemistry Analytical Edition",

issn = "0003-2700",

publisher = "American Chemical Society",

number = "11",

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TY - JOUR

T1 - The 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 C

AU - Bernfur, Katja

AU - Borchers, Christoph H

AU - Brodie, Nicholas I

AU - Bruce, James E

AU - Cao, Yong

AU - Chaignepain, Stéphane

AU - Chavez, Juan D

AU - Claverol, Stéphane

AU - Cox, Jurgen

AU - Davis, Trisha N

AU - Degliesposti, Gianluca

AU - Dong, Meng-Qiu

AU - Edinger, Nufar

AU - Emanuelsson, Cecilia

AU - Gay, Marina

AU - Gomes-Neto, Francisco

AU - Gozzo, Fabio Cesar

AU - Gutierrez, Craig B

AU - Haupt, Caroline

AU - Heck, Albert J R

AU - Herzog, Frank

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-Fereira, Ana G C

AU - Ninnis, Robert

AU - Novák, Petr

AU - O'Reilly, Francis J

AU - Pelzing, Matthias

AU - Petrotchenko, Evgeniy V

AU - Piersimoni, Lolita

AU - Plasencia, Manolo

AU - Pukala, Tara L

AU - Rand, Kasper D

AU - Rappsilber, Juri

AU - Reichman, 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 J

AU - Vilaseca, Marta

AU - Viner, Rosa

AU - Xiang, Yufei

AU - Yılmaz, Şule

AU - Zelter, Alex

AU - Ziemianowicz, Daniel S

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 - Journal article

C2 - 31045356

SN - 0003-2700

VL - 91

SP - 6953

EP - 6961

JO - Industrial And Engineering Chemistry Analytical Edition

JF - Industrial And Engineering Chemistry Analytical Edition

IS - 11

ER -

The First Community-Wide, Comparative Cross-linking Mass Spectrometry Study

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