Description from Proteome Xchange: "Mlh3 internally tagged with Flag was pulled down from synchronous meiotic cells at t = 4 h in meiosis, in order to identify its interacting partners involved in meiotic crossover formation"

Sample Processing Protocol from PRIDE: "2.1010 cells of VBD1674 strain at 4 h in meiosis were harvested, washed two times with ice-cold TNG buffer (50 mM Tris/HCl pH 8; 150 mM NaCl, 10% Glycerol; 1 mM PMSF; 1X Complete Mini EDTA-Free (Roche); 1X PhosSTOP (Roche)) and flash-frozen in liquid nitrogen. Frozen cells were mechanically ground in liquid nitrogen with the 6775 Freezer/Mill cryogenic grinder (SPEX SamplePrep). The resulting powder was resuspended in 25 mL of lysis buffer (50 mM Tris/HCl pH 7.5; 1 mM EDTA; 0.5% NP40; 10% glycerol; 150 mM NaCl; 1X Complete Mini EDTA-Free (Roche); 1X PhosSTOP (Roche), 210 U/mL benzonase (Sigma)) and incubated 1 h at 4°C with rotation. The lysate was cleared by centrifugation at 8000 g for 10 min and pre-cleared by pre-incubated with 100 μl Mouse IgG−Agarose beads (A0919 Sigma) without antibody for 2 h at 4°C on wheel. The pre-cleared lysate was incubated with 100 μl of washed and buffer equilibrated anti-Flag magnetic beads (Sigma-Aldrich, St. Louis, MO) for 2 h at 4°C. The beads were washed once with lysis buffer and three times with washing buffer (20 mM Tris/HCl pH 7.5; 0.5 mM EDTA; 0.1% tween; 10% glycerol; 150 mM NaCl; 5 mM MgCl2; 0.5 mM PMSF; 1X Complete Mini EDTA-Free (Roche, Switzerland); 1X PhosSTOP (Roche)). Proteins were eluted with 5 bed volume of elution buffer (20 mM Tris/HCl pH 8; 0.5 mM EDTA; 0.1% tween; 10% glycerol; 150 mM NaCl; 5 mM MgCl2; 0.5 mM PMSF; 1X Complete Mini EDTA-Free (Roche); 1X PhosSTOP (Roche); 100 μg/mL Flag peptide) for 2 h at 4°C. Proteins were separated by SDS-PAGE, stained with colloidal blue, and bands covering the entire lane were excised for each sample. In-gel digestion was performed overnight by using trypsin/LysC (Promega, Madison, WI). Peptides extracted from each band were analyzed by nanoLC-MS/MS using an Ultimate 3000 system (Dionex, Thermo Scientific, Waltham, MA) coupled to a TripleTOFTM 6600 mass spectrometer (ABSciex)."

Article Information

The work involved in developing the dataset and benchmarking its use of machine learning is set out in the article ‘IoMT-TrafficData: Dataset and Tools for Benchmarking Intrusion Detection in Internet of Medical Things’. DOI: 10.1109/ACCESS.2024.3437214.

Please do cite the aforementioned article when using this dataset.

Abstract

The increasing importance of securing the Internet of Medical Things (IoMT) due to its vulnerabilities to cyber-attacks highlights the need for an effective intrusion detection system (IDS). In this study, our main objective was to develop a Machine Learning Model for the IoMT to enhance the security of medical devices and protect patients’ private data. To address this issue, we built a scenario that utilised the Internet of Things (IoT) and IoMT devices to simulate real-world attacks. We collected and cleaned data, pre-processed it, and provided it into our machine-learning model to detect intrusions in the network. Our results revealed significant improvements in all performance metrics, indicating robustness and reproducibility in real-world scenarios. This research has implications in the context of IoMT and cybersecurity, as it helps mitigate vulnerabilities and lowers the number of breaches occurring with the rapid growth of IoMT devices. The use of machine learning algorithms for intrusion detection systems is essential, and our study provides valuable insights and a road map for future research and the deployment of such systems in live environments. By implementing our findings, we can contribute to a safer and more secure IoMT ecosystem, safeguarding patient privacy and ensuring the integrity of medical data.

ZIP Folder Content

The ZIP folder comprises two main components: Captures and Datasets. Within the captures folder, we have included all the captures used in this project. These captures are organized into separate folders corresponding to the type of network analysis: BLE or IP-Based. Similarly, the datasets folder follows a similar organizational approach. It contains datasets categorized by type: BLE, IP-Based Packet, and IP-Based Flows.

To cater to diverse analytical needs, the datasets are provided in two formats: CSV (Comma-Separated Values) and pickle. The CSV format facilitates seamless integration with various data analysis tools, while the pickle format preserves the intricate structures and relationships within the dataset.

This organization enables researchers to easily locate and utilize the specific captures and datasets they require, based on their preferred network analysis type or dataset type. The availability of different formats further enhances the flexibility and usability of the provided data.

Datasets' Content

Within this dataset, three sub-datasets are available, namely BLE, IP-Based Packet, and IP-Based Flows. Below is a table of the features selected for each dataset and consequently used in the evaluation model within the provided work.

Identified Key Features Within Bluetooth Dataset

Feature	Meaning
btle.advertising_header	BLE Advertising Packet Header
btle.advertising_header.ch_sel	BLE Advertising Channel Selection Algorithm
btle.advertising_header.length	BLE Advertising Length
btle.advertising_header.pdu_type	BLE Advertising PDU Type
btle.advertising_header.randomized_rx	BLE Advertising Rx Address
btle.advertising_header.randomized_tx	BLE Advertising Tx Address
btle.advertising_header.rfu.1	Reserved For Future 1
btle.advertising_header.rfu.2	Reserved For Future 2
btle.advertising_header.rfu.3	Reserved For Future 3
btle.advertising_header.rfu.4	Reserved For Future 4
btle.control.instant	Instant Value Within a BLE Control Packet
btle.crc.incorrect	Incorrect CRC
btle.extended_advertising	Advertiser Data Information
btle.extended_advertising.did	Advertiser Data Identifier
btle.extended_advertising.sid	Advertiser Set Identifier
btle.length	BLE Length
frame.cap_len	Frame Length Stored Into the Capture File
frame.interface_id	Interface ID
frame.len	Frame Length Wire
nordic_ble.board_id	Board ID
nordic_ble.channel	Channel Index
nordic_ble.crcok	Indicates if CRC is Correct
nordic_ble.flags	Flags
nordic_ble.packet_counter	Packet Counter
nordic_ble.packet_time	Packet time (start to end)
nordic_ble.phy	PHY
nordic_ble.protover	Protocol Version

Identified Key Features Within IP-Based Packets Dataset

Feature	Meaning
http.content_length	Length of content in an HTTP response
http.request	HTTP request being made
http.response.code	Sequential number of an HTTP response
http.response_number	Sequential number of an HTTP response
http.time	Time taken for an HTTP transaction
tcp.analysis.initial_rtt	Initial round-trip time for TCP connection
tcp.connection.fin	TCP connection termination with a FIN flag
tcp.connection.syn	TCP connection initiation with SYN flag
tcp.connection.synack	TCP connection establishment with SYN-ACK flags
tcp.flags.cwr	Congestion Window Reduced flag in TCP
tcp.flags.ecn	Explicit Congestion Notification flag in TCP
tcp.flags.fin	FIN flag in TCP
tcp.flags.ns	Nonce Sum flag in TCP
tcp.flags.res	Reserved flags in TCP
tcp.flags.syn	SYN flag in TCP
tcp.flags.urg	Urgent flag in TCP
tcp.urgent_pointer	Pointer to urgent data in TCP
ip.frag_offset	Fragment offset in IP packets
eth.dst.ig	Ethernet destination is in the internal network group
eth.src.ig	Ethernet source is in the internal network group
eth.src.lg	Ethernet source is in the local network group
eth.src_not_group	Ethernet source is not in any network group
arp.isannouncement	Indicates if an ARP message is an announcement

Identified Key Features Within IP-Based Flows Dataset

Feature	Meaning
proto	Transport layer protocol of the connection
service	Identification of an application protocol
orig_bytes	Originator payload bytes
resp_bytes	Responder payload bytes
history	Connection state history
orig_pkts	Originator sent packets
resp_pkts	Responder sent packets
flow_duration	Length of the flow in seconds
fwd_pkts_tot	Forward packets total
bwd_pkts_tot	Backward packets total
fwd_data_pkts_tot	Forward data packets total
bwd_data_pkts_tot	Backward data packets total
fwd_pkts_per_sec	Forward packets per second
bwd_pkts_per_sec	Backward packets per second
flow_pkts_per_sec	Flow packets per second
fwd_header_size	Forward header bytes
bwd_header_size	Backward header bytes
fwd_pkts_payload	Forward payload bytes
bwd_pkts_payload	Backward payload bytes
flow_pkts_payload	Flow payload bytes
fwd_iat	Forward inter-arrival time
bwd_iat	Backward inter-arrival time
flow_iat	Flow inter-arrival time
active	Flow active duration

The aim of the project was to purify Xenopus replisome from replicationg chromatin assembled in Xenopus laevis egg extract. To this end recombinant Cdc45-TEV-His10-FLAG5 was expressed in bacteria and purified. 4 ml of Xenopus laevis egg extract was activated into interphase and supplemented with 10 ng/µl of demembranated sperm DNA, 70 nM recombinant Cdc45, 40 µM aphidicolin, 5 mM caffeine and incubated at 23°C for 60 min. Chromatin was isolated in ANIB100 buffer (50 mM HEPES pH 7.6, 100 mM KOAc, 10 mM MgOAc, 2.5 mM Mg-ATP, 0.5 mM spermidine, 0.3 mM spermine, 1 µg/ml of each aprotinin, leupeptin and pepstatin, 25 mM β-glycerophosphate, 0.1 mM Na3VO4 and 10 mM 2-chloroacetamide) as described previously (Gillespie, Gambus et al. 2012). Chromatin pellets re-suspended in ANIB100 containing 20% sucrose. Protein complexes were released from chromatin by digestion with 4 U/µl benzonase nuclease (E1014-25KU, Sigma) and sonicated for 5 min using a sonicator with settings: 30 sec on, 30 sec off, low power (Bioruptor Diagenode UCD-200). Immunoprecipitation was performed using 100 µl of anti-FLAG M2 magnetic beads (Sigma-Aldrich). Before elution the sample was washed four times with 1 ml of ANIB100 20% sucrose, ANIB100 20% sucrose 0.1% Triton X-100, ANIB100 and elution buffer (25 mM HEPES pH 7.5, 100 mM KAc, 5 mM MgAc, 1 mM ATP and 0.02% NP-40), respectively. The sample was eluted adding 250 µM 3xFLAG peptide (Stratech) to 200 µl of elution buffer and a small proportion of it analysed by mass spectrometry.

Comparison of the UF-5000 BACT-Info flags and urine culture results.