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theGreatHerrLeberttheGreatHerrLebert
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Merge pull request #374 from theGreatHerrLebert/feature/intensity-variation-timsim-dda
Feature/intensity variation timsim dda
2 parents 10f78c7 + 71d9b01 commit 70129db

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Lines changed: 312 additions & 2 deletions

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‎imspy/examples/timsim-configs/TIMSIM-DDA-HeLa-G15-10K-from-template.toml‎

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[main_settings]
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save_path = "/scratch/timsim/submission/examples/"
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reference_path = "/scratch/timsim/submission/blanks/dda/plain/K240723_003_S1-A3_1_2774.d"
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fasta_path = "/media/hd02/data/fasta/hela/plain/hela.fasta"
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experiment_name = "TIMSIM-DDA-HELA-10K-002"
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acquisition_type = "DDA"
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use_reference_layout = true
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reference_in_memory = false
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sample_peptides = true
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add_decoys = false
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proteome_mix = false
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silent_mode = false
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from_existing = true
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existing_path = "/scratch/timsim/submission/examples/TIMSIM-DDA-HELA-10K-001"
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apply_fragmentation = true
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[peptide_digestion]
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num_sample_peptides = 10000
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missed_cleavages = 2
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min_len = 7
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max_len = 30
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cleave_at = "KR"
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restrict = "P"
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[peptide_intensity]
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intensity_mean = 5
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intensity_min = 4
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intensity_max = 8
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sample_occurrences = true
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intensity_value = 6
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[isotopic_pattern]
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isotope_k = 8
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isotope_min_intensity = 1
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isotope_centroid = true
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[distribution_settings]
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gradient_length = 900.0
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sigma_alpha_rt = 1
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sigma_beta_rt = 1
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k_lower_rt = 0.1
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k_upper_rt = 2
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k_alpha_rt = 1
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k_beta_rt = 1
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z_score = 0.99
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target_p = 0.999
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sampling_step_size = 0.0001
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use_inverse_mobility_std_mean = false
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inverse_mobility_std_mean = 0.0075
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[phosphorylation_settings]
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phospho_mode = false
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[noise_settings]
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add_noise_to_signals = true
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mz_noise_precursor = true
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precursor_noise_ppm = 6.5
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mz_noise_fragment = true
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fragment_noise_ppm = 6.5
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mz_noise_uniform = false
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add_real_data_noise = true
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reference_noise_intensity_max = 9999999
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down_sample_factor = 0.5
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[charge_state_probabilities]
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p_charge = 0.5
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min_charge_contrib = 0.25
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[dda_settings]
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precursors_every = 7
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max_precursors = 8
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exclusion_width = 25
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precursor_intensity_threshold = 1000
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selection_mode = "topN"
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[property_variation_settings]
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rt_variation_std = 15
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ion_mobility_variation_std = 0.008
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intensity_variation_std = 0.02
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[performance_settings]
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num_threads = -1
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batch_size = 256

‎imspy/examples/timsim-configs/TIMSIM-DDA-HeLa-G15-10K.toml‎

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[main_settings]
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save_path = "/scratch/timsim/submission/examples/"
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reference_path = "/scratch/timsim/submission/blanks/dda/plain/K240723_003_S1-A3_1_2774.d"
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fasta_path = "/media/hd02/data/fasta/hela/plain/hela.fasta"
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experiment_name = "TIMSIM-DDA-HELA-10K-001"
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acquisition_type = "DDA"
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use_reference_layout = true
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reference_in_memory = false
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sample_peptides = true
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add_decoys = false
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proteome_mix = false
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silent_mode = false
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from_existing = false
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existing_path = ""
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apply_fragmentation = true
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[peptide_digestion]
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num_sample_peptides = 10000
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missed_cleavages = 2
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min_len = 7
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max_len = 30
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cleave_at = "KR"
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restrict = "P"
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[peptide_intensity]
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intensity_mean = 5
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intensity_min = 4
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intensity_max = 8
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sample_occurrences = true
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intensity_value = 6
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[isotopic_pattern]
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isotope_k = 8
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isotope_min_intensity = 1
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isotope_centroid = true
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[distribution_settings]
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gradient_length = 900.0
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sigma_alpha_rt = 1
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sigma_beta_rt = 1
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k_lower_rt = 0.1
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k_upper_rt = 2
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k_alpha_rt = 1
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k_beta_rt = 1
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z_score = 0.99
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target_p = 0.999
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sampling_step_size = 0.0001
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use_inverse_mobility_std_mean = false
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inverse_mobility_std_mean = 0.0075
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[phosphorylation_settings]
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phospho_mode = false
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[noise_settings]
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add_noise_to_signals = true
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mz_noise_precursor = true
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precursor_noise_ppm = 6.5
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mz_noise_fragment = true
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fragment_noise_ppm = 6.5
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mz_noise_uniform = false
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add_real_data_noise = true
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reference_noise_intensity_max = 9999999
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down_sample_factor = 0.5
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[charge_state_probabilities]
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p_charge = 0.5
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min_charge_contrib = 0.25
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[dda_settings]
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precursors_every = 7
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max_precursors = 8
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exclusion_width = 25
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precursor_intensity_threshold = 1000
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selection_mode = "topN"
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[property_variation_settings]
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rt_variation_std = 15
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ion_mobility_variation_std = 0.008
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intensity_variation_std = 0.02
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[performance_settings]
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num_threads = -1
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batch_size = 256

‎imspy/examples/timsim-configs/TIMSIM-DIA-HeLa-G15-10K-from-template.toml‎

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[main_settings]
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save_path = "/scratch/timsim/submission/examples/"
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reference_path = "/scratch/timsim/submission/blanks/dia/G241217_012_Slot2-2_1_16313.d"
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fasta_path = "/media/hd02/data/fasta/hela/plain/hela.fasta"
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experiment_name = "TIMSIM-DIA-G15-HeLa10K-002"
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acquisition_type = "DIA"
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use_reference_layout = true
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reference_in_memory = false
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sample_peptides = true
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add_decoys = false
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proteome_mix = false
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silent_mode = false
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from_existing = true
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existing_path = "/scratch/timsim/submission/examples/TIMSIM-DIA-G15-HeLa10K-001"
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apply_fragmentation = true
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[peptide_digestion]
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num_sample_peptides = 10000
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missed_cleavages = 2
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min_len = 7
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max_len = 30
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cleave_at = "KR"
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restrict = "P"
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[peptide_intensity]
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intensity_mean = 5
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intensity_min = 4
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intensity_max = 8
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sample_occurrences = true
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intensity_value = 6
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[isotopic_pattern]
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isotope_k = 8
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isotope_min_intensity = 1
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isotope_centroid = true
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[distribution_settings]
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gradient_length = 900.0
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mean_std_rt = 0.9
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variance_std_rt = 0.2
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mean_skewness = 1.5
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variance_skewness = 0.01
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z_score = 0.99
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target_p = 0.999
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sampling_step_size = 0.0001
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[phosphorylation_settings]
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phospho_mode = false
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[noise_settings]
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add_noise_to_signals = true
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mz_noise_precursor = true
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precursor_noise_ppm = 6.5
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mz_noise_fragment = true
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fragment_noise_ppm = 6.5
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mz_noise_uniform = false
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add_real_data_noise = true
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reference_noise_intensity_max = 150000
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down_sample_factor = 0.5
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[property_variation_settings]
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rt_variation_std = 15
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ion_mobility_variation_std = 0.008
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intensity_variation_std = 0.02
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[charge_state_probabilities]
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p_charge = 0.5
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min_charge_contrib = 0.25
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[performance_settings]
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num_threads = -1
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batch_size = 256

‎imspy/examples/timsim-configs/TIMSIM-DIA-HeLa-G15-10K.toml‎

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[main_settings]
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save_path = "/scratch/timsim/submission/examples/"
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reference_path = "/scratch/timsim/submission/blanks/dia/G241217_012_Slot2-2_1_16313.d"
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fasta_path = "/media/hd02/data/fasta/hela/plain/hela.fasta"
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experiment_name = "TIMSIM-DIA-G15-HeLa10K-001"
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acquisition_type = "DIA"
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use_reference_layout = true
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reference_in_memory = false
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sample_peptides = true
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add_decoys = false
11+
proteome_mix = false
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silent_mode = false
13+
from_existing = false
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existing_path = ""
15+
apply_fragmentation = true
16+
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[peptide_digestion]
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num_sample_peptides = 10000
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missed_cleavages = 2
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min_len = 7
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max_len = 30
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cleave_at = "KR"
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restrict = "P"
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[peptide_intensity]
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intensity_mean = 5
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intensity_min = 4
28+
intensity_max = 8
29+
sample_occurrences = true
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intensity_value = 6
31+
32+
[isotopic_pattern]
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isotope_k = 8
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isotope_min_intensity = 1
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isotope_centroid = true
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[distribution_settings]
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gradient_length = 900.0
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mean_std_rt = 0.9
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variance_std_rt = 0.2
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mean_skewness = 1.5
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variance_skewness = 0.01
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z_score = 0.99
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target_p = 0.999
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sampling_step_size = 0.0001
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[phosphorylation_settings]
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phospho_mode = false
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[noise_settings]
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add_noise_to_signals = true
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mz_noise_precursor = true
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precursor_noise_ppm = 6.5
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mz_noise_fragment = true
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fragment_noise_ppm = 6.5
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mz_noise_uniform = false
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add_real_data_noise = true
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reference_noise_intensity_max = 150000
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down_sample_factor = 0.5
60+
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[property_variation_settings]
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rt_variation_std = 15
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ion_mobility_variation_std = 0.008
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intensity_variation_std = 0.02
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[charge_state_probabilities]
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p_charge = 0.5
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min_charge_contrib = 0.25
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[performance_settings]
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num_threads = -1
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batch_size = 256

‎imspy/imspy/simulation/timsim/jobs/simulate_proteins.py‎

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@@ -131,8 +131,8 @@ def protein_to_peptides(fasta,
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return peptide_set
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except Exception as e:
134-
print(f"Error generating peptides: {e}")
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print("This error can usually be safely ignored when using TIMSIM ...")
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# print(f"Error generating peptides: {e}")
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# print("This error can usually be safely ignored when using TIMSIM ...")
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return None
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