Panda-UV Update Log

v2.0 Update (2026-04-16)

Requirements

Panda-UV runs on Python 3.7+ with the following dependencies:

Package	Version	Description
pyteomics	≥4.5.6	Mass spectrometry data processing
pandas	≥1.3.5	Data manipulation
numpy	≥1.21.0	Numerical computing
plotly	≥5.14.1	Visualization
PyQt5	≥5.15.9	GUI framework
tqdm	≥4.60.0	Progress bar (for prsm_parser.py)
Averagine	built-in	Isotopic envelope calculation (C++ wrapped)

Isotope Calculation:

• Averagine library (built-in, C++ wrapped) is used for theoretical isotope envelope calculations
• Reference: Rockwood, A.L., & Haimi, P. (2006). Efficient calculation of accurate masses of isotopic peaks. J. Am. Soc. Mass Spectrom., 17(3), 415-419.

Installation:

# Using conda environment file
conda env create -f requirements.yml
conda activate Panda-UV

# Or using pip
pip install pyteomics pandas numpy plotly PyQt5 tqdm

---

1. Parameter Structure Refactoring

1.1 Unified Parameter File Format

Item	v1.0 (Old)	v2.0 (New)
File Format	YAML	JSON
Modification Config	Separate file paths	Embedded data structure
Scan Processing	Single scan_id	Multiple scans list
PRSM Mapping	None	prsm_id dictionary

1.2 Parameter Changes

New Parameters:

Parameter	Type	Default	Description
scans	list	[]	List of scan IDs to process
prsm_id	dict	{}	Mapping from scan to prsm_id
thread	int	1	Number of threads for parallel processing
msalign_file_dir	str	""	Path to msalign file (replaces deconv_mass_file_dir)

Renamed/Modified Parameters:

Old Name	New Name	Change
deconv_mass_file_dir	msalign_file_dir	Renamed
fixed_mod_file_dir	fixed_mod	File path → Embedded data structure
unlocalized_mod_file_dir	unloc_mod	File path → Embedded data structure
scan_id	scans	Single value → List
None	sequence	New, dict type

Deprecated Parameters:

• fixed_mod_file_dir
• unlocalized_mod_file_dir
• deconv_mass_file_dir

1.3 Modification Data Structure Changes

Old v1.0 fixed_mod (file path):

fixed_mod_file_dir: "path/to/fixed_mod.csv"
# CSV format: name, formula, loc

New v2.0 fixed_mod (embedded data):

"fixed_mod": {
  "header": ["name", "formula", "loc"],
  "1920": [["Acetyl", "C2H2O", 1]],
  "4139": [["Acetyl", "C2H2O", 1], ["Carbamidomethyl", "C2H3NO", 2]]
}

New v2.0 unloc_mod:

"unloc_mod": {
  "header": ["name", "formula", "start_loc", "end_loc", "ion type"],
  "3876": [["heme", "C34H31O4Fe", "any", "any", "any"]]
}

New v2.0 prsm_id:

"prsm_id": {
  "1563": 0,
  "1570": 1,
  "1920": 100
}

---

2. GUI Interface Refactoring

2.1 Layout System Upgrade

Issue	Solution
Components crowded/overlapping	Qt Layout Manager (QGridLayout, QVBoxLayout, QHBoxLayout)
Layout broken on window resize	Set minimum window size (1300x950)
Fixed coordinate positioning	Responsive layout

2.2 New Table Components

Table	Columns	Function
Scan-Sequence	Scan, Sequence	Configure protein sequence for each scan
Fixed mod	Scan, name, formula, loc	Configure fixed modifications per scan
Unlocalized mod	Scan, name, formula, start_loc, end_loc, ion type	Configure variable modifications
PRSM ID	Scan, prsm_id	Configure scan to prsm_id mapping

2.3 Input Validation System

Validation Rules:

Field	Validation	Error Message
Scan	Non-empty, integer	"Scan must be an integer, got 'xxx'"
Sequence	Non-empty	"Sequence cannot be empty"
loc	Integer	"'loc' must be an integer, got 'xxx'"
start_loc/end_loc	Integer or "any"	"'start_loc' must be an integer or 'any', got 'xxx'"
PRSM ID	Integer	"PRSM ID must be an integer, got 'xxx'"

Error Display Features:

• Error cells highlighted (light red background #FFC8C8)
• Summary error message dialog
• Pre-save completeness check

---

3. Core Functionality Enhancements

3.1 Multi-threaded Parallel Processing

Parameter: thread - Number of threads

Behavior:

• thread = 1: Single-threaded sequential processing
• thread > 1: Parallel processing using ThreadPoolExecutor

GUI Location: Right settings panel → "Thread count" control

3.2 Batch Scan Processing

Old version: Can only process one scan at a time (scan_id parameter)

New version: Can configure multiple scans simultaneously, each with its own:

• Protein sequence
• Fixed modifications
• Variable modifications
• PRSM ID

---

4. Code Architecture Optimization

4.1 Module Integration

Old Version	New Version
PandaUV_main.py	PandaUV_core.py (PandaUV class)
Standalone functions	Class methods
Scattered param classes	Unified Param class

4.2 Main Classes and Methods

# Param class
class Param:
    def get_param_template()  # Get default parameter template
    def save_param()         # Save parameters to JSON
    def read_param()         # Load parameters from JSON

# PandaUV class
class PandaUV:
    def run()                 # Single-threaded run
    def run_parallel()        # Multi-threaded run
    def initialize()          # Initialize environment
    def match()               # Single scan matching

---

5. Usage Method Changes

5.1 Parameter File Creation Workflow

Old version:

1. Prepare fixed_mod.csv file
2. Prepare unlocalized_mod.csv file
3. Enter file paths in GUI
4. Save parameters

New version:

1. Add scan and sequence in Scan-Sequence table in GUI
2. Add modifications in Fixed mod table (directly embedded)
3. Add variable modifications in Unlocalized mod table
4. Configure mapping in PRSM ID table
5. Save parameters (automatically generates JSON)

5.2 Parameter File Examples

v1.0 (YAML):

sequence: 'MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG'
deconv_mass_file_dir: 'path/to/deconv_mass.csv'
fixed_mod_file_dir: 'path/to/fixed_mod.csv'
unlocalized_mod_file_dir: 'path/to/unloc_mod.csv'
scan_id: 3871
mass_calibration: true
ms_calibration: true
mass_mode: 'M'
terminal_mass_error: 10

v2.0 (JSON):

{
  "sequence": {
    "1563": "MQIFVKTLTGKTITLEVEPSDTIENV...",
    "1570": "SGRGKGGLETKGPSSSEL..."
  },
  "scans": [1563, 1570, 1612],
  "msalign_file_dir": "path/to/msalign.msalign",
  "fixed_mod": {
    "header": ["name", "formula", "loc"],
    "1563": [["Acetyl", "C2H2O", 1]],
    "1570": [["Carbamidomethyl", "C2H3NO", 2]]
  },
  "unloc_mod": {
    "header": ["name", "formula", "start_loc", "end_loc", "ion type"],
    "1563": [["heme", "C34H31O4Fe", "any", "any", "any"]]
  },
  "prsm_id": {
    "1563": 0,
    "1570": 1,
    "1612": 10
  },
  "thread": 4,
  "mass_calibration": false,
  "ms_calibration": false,
  "mass_mode": "M",
  "terminal_mass_error": 10
}

6.3 Example Datasets

example_param_Ub_monomer.json

• Dataset Location: examples/20200110_ubiquitin_193nm_1_2mj_monomer_Z6_1428_1
• Description: Single protein (Ubiquitin) example demonstrating basic Panda-UV usage
• Data Source: UVPD mass spectrometry data of Ubiquitin monomer
• Use Case: Demonstrates single protein analysis with fixed and variable modifications

example_param_OT_rep1_toppic1.5.4.json

• Dataset Location: examples/CPTAC_Intact_rep1_15Jan15_Bane_C2-14-08-02RZ
• Description: Complex dataset from CPTAC intact proteomics study
• Data Source: Park, J., et al. "Informed-Proteomics: open-source software package for top-down proteomics." Nat. Methods 14.9 (2017): 909-914.
• Search Method: TopPIC v1.5.4 (Top-down proteomics identification and characterization)
• Parameter Generation: Generated using prsm_parse.py based on TopPIC search results
• Reference: Basharat, A.R., Ning, X., & Liu, X. "EnvCNN: a convolutional neural network model for evaluating isotopic envelopes in top-down mass-spectral deconvolution." Anal. Chem. 92.11 (2020): 7778-7785.

Related References:

• Park, J., et al. "Informed-Proteomics: open-source software package for top-down proteomics." Nat. Methods 14.9 (2017): 909-914.
• Basharat, A.R., Ning, X., & Liu, X. "EnvCNN: a convolutional neural network model for evaluating isotopic envelopes in top-down mass-spectral deconvolution." Anal. Chem. 92.11 (2020): 7778-7785.

---

7. Citation

If you use Panda-UV in your research, please cite:

Panda-UV: Zhu, Y., et al. "Panda-UV Unlocks Deeper Protein Characterization with Internal Fragments in Ultraviolet Photodissociation Mass Spectrometry." Anal. Chem. 96.21 (2024): 8474-8483.

---

v2.1 Update (2026-04-21)

Removed R Dependency

Dependency Changes

Change	Description
Removed	rpy2 package and R environment dependency
Removed	r_env_dir parameter
Changed	Averagine library (based on emass, built-in C++ wrapped) for isotope envelope calculations

Code Changes

File	Change
PandaUV_core.py	Removed r_source and r_lock, replaced with Averagine-based calculation
PandaUV_core.py	Removed r_env_dir parameter from template
PandaUV_GUI.py	Removed R env dir input field
Scoring_function_utils.py	Replaced R-based get_iso_peak_arr with Averagine.formula_to_iso

Citation

emass provides efficient isotopic envelope calculations without requiring R runtime:

• Rockwood, A.L., & Haimi, P. (2006). Efficient calculation of accurate masses of isotopic peaks. J. Am. Soc. Mass Spectrom., 17(3), 415-419.

Threading Fix

• Added global lock (self.lock) for thread-safe isotope calculations
• Lock protects averagine module calls in multi-threaded processing

---

Original Version (v1.0 - 2023-08-18)

• Basic GUI and CLI implementation
• Single scan processing mode
• Separate file storage for modification data
• Core fragment matching algorithm
• PCC scoring system
• Mass calibration functionality