Supplementary Information: An open data format for visualization and analysis of cross-linked mass spectrometry results
Michael R. Hoopmann1*, Eric W. Deutsch1, Luis Mendoza1, David Shteynberg1, Robert L. Moritz1
1Institute for Systems Biology, Seattle, Washington 98109, USA
* Corresponding Author: , 206-732-1200
Table of Contents
1. Cross-link algorithm search parameters
2. Supplemental Figure 1: pepXML extension syntax for cross-link and loop-link PSMs
3. Supplemental Figures 2-4: pepXML representation of the same PSM from pLink, Protein Prospector, and Kojak, respectively.
1. Cross-link algorithm search parameters
[pLink]
enzyme.name=Trypsin
max_miss_site=2
mod.fixed.total=1
mod.fixed.1=Carbamidomethyl[C]
mod.variable.total=1
mod.variable.1=Oxidation[M]
linker.total=1
linker.name1=BS3
noninterexport=true
peptide_tol_total=1
peptide_tol1=10
peptide_tol_type1=ppm
peptide_tol_base1=0.000000
peptide_tol_base_type1=Da
filter_peptide_tol_base=0
filter_peptide_tol_lb=-10
filter_peptide_tol_ub=10
filter_peptide_tol_type=ppm
evalue_max=1000
[Protein Prospector]
allow_non_specific:at 0 termini
const_mod:Carbamidomethyl (C)
enzyme:Trypsin
expect_calc_method:Linear Tail Fit
fragment_masses_tolerance:25
fragment_masses_tolerance_units:ppm
full_pi_range:1
high_pi:10.0
instrument_name:ESI-Q-high-res
link_aa:C->C
link_search_type:DSS
low_pi:3.0
max_hits:9999999
max_saved_tag_hits:1000
missed_cleavages:3
mod_c_term_type:Peptide
mod_comp_ion:K
mod_defect:0.00048
mod_end_nominal:4038
mod_max_z:4
mod_n_term:1
mod_n_term_type:Protein
mod_range_type:Da
mod_start_nominal:438
mod_uncleaved:1
msms_full_mw_range:1
msms_max_modifications:2
msms_max_peaks:200
msms_max_reported_hits:5
msms_mod_AA:Acetyl (Protein N-term)
msms_mod_AA:Acetyl+Oxidation (Protein N-term M)
msms_mod_AA:Gln->pyro-Glu (N-term Q)
msms_mod_AA:Met-loss (Protein N-term M)
msms_mod_AA:Met-loss+Acetyl (Protein N-term M)
msms_mod_AA:Oxidation (M)
msms_mod_AA:Xlink:DSS1 (Protein N-term)
msms_mod_AA:Xlink:DSS1 (Uncleaved K)
msms_mod_AA:Xlink:DSS2 (Protein N-term)
msms_mod_AA:Xlink:DSS2 (Uncleaved K)
msms_parent_mass_systematic_error:0
msms_parent_mass_tolerance:10
msms_parent_mass_tolerance_units:ppm
msms_pk_filter:Max MSMS Pks
msms_precursor_charge_range:2 3 4 5
msms_prot_high_mass:125000
msms_prot_low_mass:1000
parent_mass_convert:monoisotopic
use_instrument_ion_types:1
[Kojak]
export_percolator = 1
export_pepXML = 1
percolator_version = 2.08
enrichment = 0
instrument = 0
MS1_centroid = 0
MS2_centroid = 1
MS1_resolution = 15000
MS2_resolution = 7500
cross_link = 1 1 138.0680742 BS3
mono_link = 1 156.0786
fixed_modification = C 57.02146
modification = M 15.9949
diff_mods_on_xl = 0
max_mods_per_peptide = 0
mono_links_on_xl = 0
enzyme = [KR]|{P}
fragment_bin_offset = 0.0
fragment_bin_size = 0.03
ion_series_A = 0
ion_series_B = 1
ion_series_C = 0
ion_series_X = 0
ion_series_Y = 1
ion_series_Z = 0
use_comet_xcorr = 0
decoy_filter = reverse
max_miscleavages = 2
max_peptide_mass = 5000.0
min_peptide_mass = 500.0
max_spectrum_peaks = 0
ppm_tolerance_pre = 10.0
prefer_precursor_pred =2
spectrum_processing = 1
top_count = 300
truncate_prot_names = 0
2. Supplemental Figure 1: pepXML extension syntax for cross-link and loop-link PSMs
Supplemental Figure 1: pepXML extension syntax examples. A) Example of two cross-linked peptides. Cross-linked status is specified using the xlink_type attribute. All peptide information contained in the search_hit element is superseded with the peptides specified in the linked_peptide elements. B) Example of a loop-linked PSM. All peptide information is stored in the search_hit element, as is typically done with shotgun results. Information regarding the looped cross-linker is provided in the xlink element.
3. Supplemental Figures 2-4: pepXML representation of the same PSM from pLink, Protein Prospector, and Kojak, respectively.
Each figure shows the same PSM represented in pepXML using the cross-link extension. The pepXML extension accommodates search algorithm-specific scores and information.
Supplemental Figure 2: pLink PSM in pepXML.
Supplemental Figure 3: Protein Prospector PSM in pepXML.
Supplemental Figure 4: Kojak PSM in pepXML.