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Project PXD042173

Summary

Title

Proteome-scale recombinant standard datasets for XL-MS

Description

This submission includes the complete set of raw data generated from the analytical standard, the concept of which is described in our manuscript "Proteome-Scale Recombinant Standards And A Robust High-Speed Search Engine To Advance Cross-Linking MS-Based Interactomics". In this study, we develop a strategy to generate a well-controlled XL-MS standard by systematically mixing and cross-linking rec...

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Sample Processing Protocol

PROTEIN MIXING AND CROSS-LINKING Ectopically expressed and purified human proteins were provided by Absea Biotechnology Ltd., Beijing. In brief, all proteins are His-tagged at the C-termini and packaged in PC3.1 expression plasmid. Lyophilized proteins were dissolved in 20 mM HEPES pH 7.8 at concentrations varying from 0.1 � 1.5 mg/mL. The dissolved proteins were mixed in pairs of two proteins acc...

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Data Processing Protocol

RAW files were searched for cross-links with Scout v. 1.4.14. Search parameters were used as following: MS1 mass tolerance, 10 ppm; MS2 mass tolerance, 20 ppm; maximum number of missed cleavages, 3; minimum peptide length, 6; peptide-mass, 0 � 4,000 Da. Cross-links were detected by searching for the cross-linker modification on lysines. Carbamidomethylation (+ 57.021 Da) on cysteines was used as a...

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Contact

Dr Diogo Borges Lima, Leibniz-Forschungsinstitut für Molekulare Pharmakologie

Dr Fan Liu, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (lab head)

Submission Date

02/05/2024

Publication Date

06/08/2024

Publication

DOI: 10.1038/s41592-024-02478-1, Des: Clasen MA, Ruwolt M, Wang C, Ruta J, Bogdanow B, Kurt LU, Zhang Z, Wang S, Gozzo FC, Chen T, Carvalho PC, Lima DB, Liu F. Proteome-scale recombinant standards and a robust high-speed search engine to advance cross-linking MS-based interactomics. Nat Methods. 2024 21(12):2327-2335

Visualizations

Name
Type
View
synthetic-dataset-allbatches-mzid
cross-linking

Project Files

Name
Type
Size (M)
Download
#
protein-construct-sequences_and_interaction-groups.xlsx
OTHER
73955 bit
599a78b9e1f9e533705f825eda653c4f0659dc76e41f5f5a4987d91d5f46f359
synthetic_dataset_allbatches-specId.ms2
PEAK
1395
10c028d97803a0abbcbdd0efb1c07fbd8a04c5a1459a3fda7bc013aeebb2e83d
synthetic_dataset_allbatches.mzid
RESULT
362
21f491b8f9997d86564a3ca7d6085de69c4f7743998ed4b15842e443995bd426
L1_20211004_MxR_secondbatch_DSSOplate_F1_F2.raw
RAW
929
bcb0e018d02d036e0546534e6ba9998e74d123c2d46cec7ecf1a450ef1ce6f11
L1_20210811_MxR_FDR_firstbatch_DSSOplate_E5.raw
RAW
1009
60008d4f9ef82151fb2ecbefa268d6f16b3ec5dd6d4243d92a595c4d81b7d43e
L1_20211004_MxR_secondbatch_DSSOplate_C5_152127.raw
RAW
812
e5c5499ee0df7febd322b16015041723467a8ba6f9fb3c97410b0634743529b7
L1_20240412_MxR_FDR_fifthbatch_DSSO_B9_B10.raw
RAW
1538
ce93a2aef4d0f5925950f0bd35bdabad3c62b4f9823ed03bb6a5fbf9c0d720ad
L1_20211004_MxR_secondbatch_DSSOplate_E5_E6.raw
RAW
877
e1078d948a7f7b8adde9eb8a26bd5e5aa90213f806d02df60147d2c359825ca7
L1_20240412_MxR_FDR_fifthbatch_DSSO_C11.raw
RAW
1513
8d36d86234e730e7759f5407f1cf45b0ef65a00f8ec6b0953e63e0715a9e71fd
L1_20240412_MxR_FDR_fifthbatch_DSSO_C2.raw
RAW
1465
e3f73ba6af74767fb66eab4b6ad81b34b1f3546b87ed8619be7592448fee6858
L1_20240412_MxR_FDR_fifthbatch_DSSO_B7_B8.raw
RAW
1508
c25e36fbf9fd594b837f8ce71e91e390642929a9d118f53b7be8ba3b4d62af5b
L1_20240412_MxR_FDR_fifthbatch_DSSO_B11_B12.raw
RAW
1432
7a446e4b601da275da6116c5fbf5ad9d2c9740dfb443eb93c1422f8973ab673b
L1_20211004_MxR_secondbatch_DSSOplate_F5_F6.raw
RAW
994
268bb124bd4d7b6b6c9991e6f786dcc4657ddbc466793155c47ecc4f1db18976
L1_20210811_MxR_FDR_firstbatch_DSSOplate_E10.raw
RAW
907
ccaacf94cd6510d3a37051afc5a8458e15065b51fb86e91b840f4120eeeefd9b
L1_20240412_MxR_FDR_fifthbatch_DSSO_C4.raw
RAW
1544
b9744674bbb763a78841c6984607fc025181ed6654727c8d38a2bd483c763307
L1_20240412_MxR_FDR_fifthbatch_DSSO_D7.raw
RAW
1571
1b6a0b4cdc27181d0ee36073255e73e6c04143c12d1d61aeaf6831ea1037ed09
L1_20240412_MxR_FDR_fifthbatch_DSSO_G5_G6.raw
RAW
1920
5906c98ac2011554a7a6900a50fd0dac40ed69ee5a695ca84aae8b376d0f47ee
L1_20240412_MxR_FDR_fifthbatch_DSSO_D1.raw
RAW
1395
dbdc33cdf5a02aad72f2c3e341e72c142ca428abae33f59b86a718b9f93485e7
L1_20240412_MxR_FDR_fifthbatch_DSSO_E7_E8.raw
RAW
1943
c0444b8c5369271c8c75d96ee4f8c5f50a09afb60dea4a08e8db723eb316fcc5
L1_20210811_MxR_FDR_firstbatch_DSSOplate_D10_remeasure.raw
RAW
1097
4a4f60ff9695d95713fc5ff76dc5b5318468f3755168a9e969976b5b298762bd
    Total 183 items
  • 1
  • 2
  • 3
  • 10
    • 20 /page

Experimental Design (Samples)

Properties

Organism
Organism part

Unknown

Diseases

Unknown

Modification
Instrument
Software

Unknown

Experiment Type

Chemical cross-linking coupled with mass spectrometry proteomics

Data-dependent acquisition

Quantification

Unknown

Dataset reuses

Not available

Number of files

RAW (178), SEARCH (0), PEAK (1), RESULT (1), OTHER (3)

License

Similar Studies

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