JUMPlion is a software tool for quantifying proteomics data generated by data-independent acquisition mass spectrometry (DIA-MS).
JUMPlion can be installed via pip and is compatible with both Windows and Linux.
conda create -n jumplion python=3.12
conda activate jumplion
conda install mono # Required on Linux for reading Thermo .raw files; skip this step on Windows
pip install "jumplion[gui] @ git+https://github.com/yingxue-fu/jumplion.git"After installation, the easiest way to begin your analysis is by launching the JUMPlion GUI from the terminal:
jumplion-guiAn HTTP address will appear in the terminal. Paste it into your browser to open the interface.
On the Home page, click Start Analysis to navigate to the parameter settings page. Enter the paths to the required input files, then click Settings to configure the parameters. For most parameters, the default values are sufficient. Once all settings are complete, click Run to begin the analysis.
JUMPlion can also be used in command-line mode. See the Parameters section below for a list of supported parameters and commands. For convenience, you can generate a parameter file in the current working directory, fill in the required inputs, and then run the program:
jumplion --gen-params jumplion.params
jumplion jumplion.params1. DIA-MS Files
Supported mass spectrometry file formats include:
- Bruker
.d(diaPASEF) - Thermo Fisher
.raw .mzMLfiles converted from.raw
2. Precursor-Level Identification Report
This file is a table listing identified precursors for each run, along with their retention time (RT), ion mobility (IM, for timsTOF data), and precursor-level q-value.
Example:
| Run | Precursor.Id | RT | IM | Q.Value |
|---|---|---|---|---|
| Run_1 | AAAAAAALQAK2 | 8.13581 | 0.8512 | 8.96e-06 |
| Run_2 | AAAAAAALQAK2 | 8.12073 | 0.8535 | 0.00141 |
| Run_3 | AAAAAAALQAK2 | 8.10539 | 0.8548 | 0.00165 |
| Run_1 | AAAIGIDLGTTYSCVGVFQHGK3 | 32.08232 | 0.9773 | 8.96e-06 |
| Run_2 | AAAIGIDLGTTYSCVGVFQHGK3 | 32.11453 | 0.9774 | 1.41e-05 |
| Run_3 | AAAIGIDLGTTYSCVGVFQHGK3 | 32.11588 | 0.9798 | 0.00125 |
A DIA-NN identification report (for example, report.parquet) can be used directly because it already contains all required columns. Identification results from other search engines may require additional formatting.
3. Spectral library
The spectral library provides the information needed to extract XICs from raw data. It should include:
- precursor information (for example, m/z, charge, and peptide sequence)
- product ion information (for example, m/z, charge, and ion type such as b/y ions)
- protein annotation for each precursor
Supported spectral library formats include:
.csv.tsv.parquet
A DIA-NN spectral library file (for example, report-lib.parquet) can be used directly.
4. Sample meta file
A sample metadata file in .csv format should contain the grouping information or biological condition for each sample.
Example:
| Sample | Group |
|---|---|
| Run_1 | A |
| Run_2 | A |
| Run_3 | A |
| Run_4 | A |
| Run_5 | B |
| Run_6 | B |
| Run_7 | B |
| Run_8 | B |
5. FASTA file(s) (optional)
If provided, the FASTA file(s) will be used to calculate the protein coverage percentages and draw the protein coverage plot in GUI.
6. Output directory
Specify the directory where output results will be saved.
To test run JUMPlion using demo data, you can download all required inputs from the following link: https://drive.google.com/drive/folders/1Ew8SVq0riDzyl5rywLWcTfUmfcPSglld?usp=drive_link
The data are derived from the following published study: Wang, J., Huang, Y., Lu, F., et al. Benchmarking informatics workflows for data-independent acquisition single-cell proteomics. Nature Communications 16, 10276 (2025). https://doi.org/10.1038/s41467-025-65174-4
The expected runtime for the demo on a standard desktop computer is approximately 15 minutes.
The output is organized into two folders:
- intermediate: contains mass calibration results, RT/IM prediction results, and extracted XIC data for each run.
- publication: contains XIC-level, precursor-level, and protein-level quantification results
The table below lists all parameters and commands supported by JUMPlion.
| Category | Parameter | Command | Description | Values |
|---|---|---|---|---|
| Inputs | input_runs | --input-runs | Paths to DIA-MS files. Supports .raw/.mzML files for Thermo instruments and diaPASEF .d files for timsTOF instruments. |
|
| prec_ids | --prec-ids | Path to the precursor-level identification table. | ||
| spec_lib | --spec-lib | Path to the spectral library (supports .tsv, .csv, and .parquet formats). |
||
| sample_meta | --sample-meta | Path to the sample metadata file (supports .csv format). |
||
| out_dir | --out-dir | Directory where output files will be saved. | ||
| Reuse existing results | skip_id_process | --skip-id-process | Skip the ID result processing step and use previously saved filtered spectral library and precursor RT/IM table. | 0 = no, 1 = yes, default: 0 |
| use_saved_xic | --use-saved-xic | Use existing XIC files generated by a previous analysis to save time. | 0 = no, 1 = yes, default: 0 | |
| use_xic_report | --use-xic-report | Use an existing XIC-level quantification report file. | 0 = no, 1 = yes, default: 0 | |
| ID results processing | min_runs_quant | --min-runs-quant | Minimum number of runs in which a precursor must be identified to be quantified. | default: 3 |
| min_runs_model | --min-runs-model | Minimum number of runs in which a precursor must be identified to be used for building the RT/IM prediction model. | default: 3 | |
| min_runs_cal | --min-runs-cal | Minimum number of runs in which a precursor must be identified to be used for mass calibration. | default: 6 | |
| max_qvalue_cal | --max-qvalue-cal | Maximum q-value (FDR) for a precursor to be used for mass calibration. | default: 0.0001 | |
| max_mass_cal | --max-mass-cal | Maximum number of precursors used for mass calibration. | default: 5000 | |
| XIC extraction | n_xic_points | --n-xic-points | Number of data points to extract for each XIC. | default: 21 |
| mass_calibration | --mass-calibration | Whether to perform mass calibration. | 0 = no, 1 = yes, default: 1 | |
| mass_cal_acc | --mass-cal-acc | Calibration mass accuracy (ppm). | default: 30.0 | |
| fix_mass_acc | --fix-mass-acc | Whether to use fixed MS1/MS2 mass accuracy. | 0 = no, 1 = yes, default: 0 | |
| mass_acc_ms2 | --mass-acc-ms2 | MS2 mass accuracy (ppm). | default: 15.0 | |
| mass_acc_ms1 | --mass-acc-ms1 | MS1 mass accuracy (ppm). | default: 15.0 | |
| individual_mass_acc | --individual-mass-acc | Whether to determine MS1/MS2 mass accuracy for each individual run. | 0 = no, 1 = yes, default: 0 | |
| im_window_cal | --im-window-cal | IM window used for calibration. | default: 0.03 | |
| fix_im_window | --fix-im-window | Whether to use a fixed IM window. | 0 = no, 1 = yes, default: 0 | |
| im_window | --im-window | IM window. | default: 0.01 | |
| individual_im_window | --individual-im-window | Whether to determine the IM window for each individual run. | 0 = no, 1 = yes, default: 0 | |
| max_prec_num | --max-prec-num | Maximum number of precursor XICs (monoisotopic + isotopic) to extract. | default: 5 | |
| min_prod_num | --min-prod-num | Minimum number of product ions required for a precursor to be quantified. | default: 3 | |
| max_prod_num | --max-prod-num | Maximum number of product ions used for precursor quantification. | default: 6 | |
| XIC quantification | optimal_xic_source | --optimal-xic-source | MS level used to define the optimal XIC. | ms1_ms2 = MS1/MS2, ms1 = MS1 only, ms2 = MS2 only, default: ms1_ms2 |
| intf_removal | --intf-removal | Whether to perform interference removal for an XIC. | 0 = off, 1 = on, default: 1 | |
| intf_factor_ms1 | --intf-factor-ms1 | Interference filtering factor for MS1-level XICs. | default: 1.2 | |
| intf_factor_ms2 | --intf-factor-ms2 | Interference filtering factor for MS2-level XICs. | default: 1.5 | |
| Precursor quantification | use_raw_ms1 | --use-raw-ms1 | Whether to use raw MS1-level XIC quantities when summarizing to the precursor-level. | 0 = no, 1 = yes, default: 0 |
| use_raw_ms2 | --use-raw-ms2 | Whether to use raw MS2-level XIC quantities when summarizing to the precursor-level. | 0 = no, 1 = yes, default: 1 | |
| lion_inference | --lion-inference | Whether to perform LION-based inference for missing XIC quantities | 0 = off, 1 = on, default: 1 | |
| lion_value_scale | --lion-value-scale | The scaling factor applied to the local minimum used in LION | default: 1.0 | |
| Precursor normalization | normalization | --normalization | Whether to perform normalization at the precursor level. | 0 = off, 1 = on, default: 1 |
| norm_species | --norm-species | Species of peptides used for intensity normalization. | default: HUMAN | |
| norm_method | --norm-method | Normalization method. | median or mean, default: median |
|
| trim_percentage | --trim-percentage | Percentage trimmed from each side for normalization. | default: 5 | |
| Protein quantification | prec_quant_level | --prec-quant-level | Level of precursor quantification used for protein summarization. | ms1_ms2 = MS1/MS2 integration, ms1 = MS1 only, ms2 = MS2 only, default: ms1_ms2 |
| min_prec_count | --min-prec-count | Minimum number of precursors required for a protein to be retained in the final quantification table. | default: 2 | |
| min_pep_count | --min-pep-count | Minimum number of peptides required for a protein to be retained in the final quantification table. | default: 1 | |
| fastas | --fastas | Path(s) to FASTA file(s). |