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MSFragger

Ultrafast and comprehensive peptide identification in mass spectrometry–based proteomics

Guide to FragPipe results

Output files will depend on the workflow used and how experiments/groups are set on the ‘Workflow’ tab. This page lists the different output files generated by FragPipe. Main report files are either comma-separated (csv) or tab-separated (tsv), and their column contents are described here. Outputs that take the name of the input LC-MS file are shown with the generic ‘filename’ placeholder here.

Log files are saved automatically (with a timestamp) if an analysis finishes successfully, but they can also be exported (with the ‘Export Log’ button on the ‘Run’ tab) to help with troubleshooting if an analysis fails.

FragPipe also uses various configuration and intermediate files listed here.

Also see our guide to using FragPipe.

Main report files

TMT/iTRAQ reports

Isobaric labeling reports are found in the ‘tmt-report’ folder. Two sets of isobaric labeling quantification reports are generated by TMT-Integrator, one set with abundances and one with ratios. Files containing ‘ratio’ in the file name report ratio to the reference/bridge channel in each plex if specified, or a ratio to the average abundance within each plex (virtual reference approach. Files containing ‘abundance’ are generated by converting ratio tables back to the intensity (ion abundance) scale.

Other reports
Log files
Configuration files
Intermediate files




psm.tsv

psm.tsv files contain FDR-filtered search results, where each row contains a peptide-spectrum match (PSM). A separate psm.tsv file will be generated for each experiment specified on the ‘Workflow’ tab. Contents of each column are listed below.

Spectrum MS/MS spectrum identifier, follows the format (file name).(scan #).(scan #).(charge)

Spectrum File name of originating identification file

Peptide peptide amino acid sequence, any modifications not included (‘stripped’ peptide sequence)

Modified Peptide peptide sequence including modifications, modified residues are followed by brackets containing the integer mass (in Da) of the residue plus the modification; blank if peptide is unmodified

Peptide Length number of residues in the peptide sequence

Charge charge state of the identified peptide

Retention retention time (in seconds)

Observed Mass mass of the identified peptide (in Da)

Calibrated Observed Mass mass of the identified peptide after m/z calibration (in Da)

Observed M/Z mass-to-charge ratio of the peptide ion

Calibrated Observed M/Z mass-to-charge ratio of the peptide ion after m/z calibration

Calculated Peptide Mass theoretical peptide mass based on identified sequence and modifications

Calculated M/Z theoretical peptide mass-to-charge ratio based on identified sequence and modifications

Delta Mass difference between calibrated observed peptide mass and calculated peptide mass (in Da)

Expectation expectation value from statistical modeling with PeptideProphet, lower values indicate higher likelihood

Hyperscore similarity score between observed and theoretical spectra, higher values indicate greater similarity

Nextscore similarity score (hyperscore) of second-highest scoring match for the spectrum

PeptideProphet Probability confidence score determined by PeptideProphet, higher values indicate greater confidence

Number of Enzymatic Termini 2 = fully-enzymatic, 1 = semi-enzymatic, 0 = non-enzymatic

Number of Missed Cleavages number of potential enzymatic cleavage sites within the identified sequence

Intensity relative abundance (peak intensity) of the precursor ion

Ion Mobility TIMS transit time of the precursor ion (1/K0)

Assigned Modifications variable modifications (listed by mass in Da) with modified residue and location within the peptide

Observed Modifications modifications from Delta Mass values as mapped to Unimod entries

Number of Phospho Sites count of phosphorylation sites within the peptide

Phospho Site Localization location and probability (calculated by PTMProphet) of phosphorylation site(s) within the peptide

Is Unique whether the identified sequence maps to a single identified protein (FALSE if shared between multiple proteins identified in the experiment)

Protein protein sequence header corresponding to the identified peptide sequence; this will be the selected razor protein if the peptide maps to multiple proteins (in this case, other mapped proteins are listed in the ‘Mapped Proteins’ column)

Protein ID protein identifier (primary accession number) for the selected protein

Entry Name entry name for the selected protein

Gene gene name for the selected protein

Protein Description name of the selected protein

Mapped Genes additional genes the identified peptide may originate from

Mapped Proteins additional proteins the identified peptide maps to

Is Used whether the PSM is used in protein quantification (‘TRUE’ means this PSM’s intensity contributes to protein abundance)

Purity Precursor ion intensity as a percentage of total ion intensity in the MS1 scan.

(additional columns for TMT/iTRAQ channels if used, where each contains the relative reporter ion abundances for that PSM)


filename.tsv

[filename].tsv files are generated by mass offset or open search workflows, and contain unfiltered MSFragger search results (peptide-spectrum matches) plus localization information. A separate psm.tsv file will be generated for each individual spectral file. Contents of each column are listed below.

scannum scan number of the MS/MS spectrum within the spectral file

precursor_neutral_mass neutral mass of the identified peptide ion as measured (in Da)

retention_time MS/MS spectrum retention time (in minutes)

charge charge state of the identified peptide ion

hit_rank position of the identification within all matches to the spectrum (1=highest scoring match)

peptide stripped amino acid sequence of the identified peptide

peptide_prev_aa amino acid directly preceding the identified peptide within the mapped protein sequence

peptide_next_aa amino acid directly following the identified peptide within the mapped protein sequence

protein complete FASTA header of the originating protein sequence

num_matched_ions count of fragment ions matching the identified peptide sequence (includes mass-shifted ions from localization-aware matching)

tot_num_ions total count of theoretical fragment ions from the peptide

calc_neutral_pep_mass theoretical mass of the identified peptide ion (in Da)

massdiff difference between measured and theoretical precursor neutral mass

num_tol_term number of enzymatic termini (2=fully enzymatic, 1=semi-enzymatic, 0=non-enzymatic)

num_missed_cleavages number of missed enzymatic cleavage sites in the identified peptide sequence

modification_info position, identity, and mass of each identified modification specified as fixed or variable in the search (does not include mass differences from open or mass offset searches), multiple modifications are comma-separated

hyperscore similarity score between observed and theoretical spectra, higher values indicate greater similarity

nextscore similarity score (hyperscore) of second-highest scoring match for the spectrum

expectscore expectation score of the peptide-spectrum match, lower values indicate higher likelihood

best_locs peptide sequence with most probable delta mass (massdiff) locations indicated with lowercase letters

score_without_delta_mass similarity score (hyperscore) if no delta mass is included on the peptide

best_score_with_delta_mass similarity score (hyperscore) if the indicated delta mass (massdiff) is included on the peptide

second_best_score_with_delta_mass similarity score (hyperscore) of the second-highest scoring match if the indicated delta mass (massdiff) is included on the peptide

delta_score similarity score difference between best_score_with_delta_mass and second_best_score_with_delta_mass

alternative_proteins FASTA headers of any additional proteins the identified peptide maps to, list separated by @@


modifications.tsv

modifications.tsv files are generated by open search workflows and contain counts of FDR-filtered PSMs per 0.1 Da mass shift bin. A separate modifications.tsv file will be generated for each experiment. Column contents are listed below.

Mass Bin Delta mass value (in 0.1 Da increments)

PSMs with Assigned Modifications Number of peptide-spectrum matches with a variable modification (i.e. specified in the search) that falls in this delta mass bin

PSMs with Observed Modifications Number of peptide-spectrum matches found with a mass shift that falls in this delta mass bin


ion.tsv

ion.tsv files contain FDR-filtered search results, where each row contains a peptide sequence with a certain charge and modification state. A separate ion.tsv file will be generated for each experiment specified on the ‘Workflow’ tab. Contents of each column are listed below.

Peptide Sequence peptide amino acid sequence, any modifications not included (‘stripped’ peptide sequence)

Modified Sequence peptide sequence including modifications, modified residues are followed by brackets containing the integer mass (in Da) of the residue plus the modification; blank if peptide is unmodified

Peptide Length number of residues in the peptide sequence

M/Z calculated (theoretical) peptide mass-to-charge ratio based on identified sequence and modifications Charge peptide ion charge state

Observed Mass calculated mass of the identified peptide (in Da)

Probability confidence score determined by PeptideProphet, higher values indicate greater confidence

Expectation expectation value from statistical modeling with PeptideProphet, lower values indicate higher likelihood

Spectral Count number of corresponding PSMs

Intensity peptide ion abundance

Assigned Modifications variable modifications (listed by modification mass in Da) with modified residue and location within the peptide

Observed Modifications for peptides identified with non-zero delta masses (from open or mass offset searches), modifications mapping to a Unimod entry of the corresponding delta mass are listed here

Protein protein sequence header corresponding to the identified peptide sequence; this will be the selected razor protein if the peptide maps to multiple proteins (in this case, other mapped proteins are listed in the ‘Mapped Proteins’ column)

Protein ID UniProt protein identifier (primary accession number)

Entry Name entry name for the selected protein

Gene gene name for the selected protein

Protein Description name of the selected protein

Mapped Genes additional genes the identified peptide may originate from

Mapped Proteins additional proteins the identified peptide maps to

(additional columns for TMT/iTRAQ channels if applicable, each contains relative reporter ion abundances)


peptide.tsv

peptide.tsv files contain FDR-filtered search results, where each row is an identified peptide sequence. A separate peptide.tsv file will be generated for each experiment specified on the ‘Workflow’ tab. Contents of each column are listed below.

Peptide peptide amino acid sequence, no modifications included (‘stripped’ peptide sequence)

Peptide Length number of residues in the peptide sequence

Charges peptide ion charge state(s)

Probability confidence score determined by PeptideProphet, higher values indicate greater confidence

Spectral Count number of corresponding PSMs

Intensity relative abundance (peak intensity) of the precursor ion

Assigned Modifications variable modifications (listed by mass in Da) with modified residue and location within the peptide

Observed Modifications for peptides identified with non-zero delta masses (from open or mass offset searches), modifications mapping to a Unimod entry of the corresponding delta mass are listed here

Protein protein sequence header corresponding to the identified peptide sequence; this will be the selected razor protein if the peptide maps to multiple proteins (in this case, other mapped proteins are listed in the ‘Mapped Proteins’ column)

Protein ID protein identifier (primary accession number) for the selected protein

Entry Name entry name for the selected protein

Gene gene name for the selected protein

Protein Description name of the selected protein

Mapped Genes additional genes the identified peptide may originate from

Mapped Proteins additional proteins the identified peptide maps to

(additional columns for TMT/iTRAQ channels if applicable, each contains relative reporter ion abundances)


protein.tsv

protein.tsv files contain FDR-filtered protein results, where each row is an identified protein group. A separate protein.tsv file will be generated for each experiment specified on the ‘Workflow’ tab. Contents of each column are listed below.

Group protein group number

SubGroup protein subgroup identifier

Protein protein sequence header

Protein ID UniProt protein identifier (primary accession number)

Entry Name protein entry name

Gene gene name

Length number of residues in protein sequence

Percent Coverage percent of protein sequence observed

Organism species of identified protein

Protein Description protein name

Protein Existence type of evidence that supports the existence of the protein

Protein Probability confidence score determined by ProteinProphet

Top Peptide Probability best peptide probability of supporting peptides

Stripped Peptides total number of unique stripped (unmodified) sequences in support of the protein

Total Peptide Ions total number of peptide ions (including modifications) in support of the protein

Unique Peptide Ions number of peptide ions (including modifications) that do not map to other identified proteins

Razor Peptide Ions total number of peptides ions (including modifications) in support of the protein identification

Total Spectral Count total number of PSMs in support of the protein

Unique Spectral Count total number of PSMs that do not map to other identified proteins

Razor Spectral Count total number of PSMs in support of the protein identification

Total Intensity sum of all (unique+razor) peptide abundances

Unique Intensity sum of peptide abundances (only those that do not map to another identified protein)

Razor Intensity sum of PSM abundances from razor peptides

Razor Assigned Modifications sum of PSM abundances from razor peptides containing variable modifications

Razor Observed Modifications sum of PSM abundances from razor peptides containing modifications from Delta Mass values

Indistinguishable Proteins proteins that are equally supported by the evidence and cannot be distinguished from the identification in the ‘Protein’ column

(additional columns for TMT/iTRAQ channels if applicable, each contains relative reporter ion abundances)


combined_peptide.tsv

combined_peptide.tsv files contain FDR-filtered peptides from all experimental groups, where each row is a (stripped) peptide sequence. Contents of each column are listed below.

Sequence peptide amino acid sequence, any modifications not included (‘stripped’ peptide sequence)

Charge States all observed charge states for the peptide in the experiment

Probability peptide-level confidence score determined by PeptideProphet, higher values indicate greater confidence

Assigned Modifications all variable modifications of the peptide found in the experiment, each listed by mass in Da with modified residue and location within the peptide sequence

Gene gene name of the protein corresponding to the identified peptide sequence; this will be from the selected razor protein if the peptide maps to multiple proteins

Protein protein sequence header corresponding to the identified peptide sequence; this will be the selected razor protein if the peptide maps to multiple proteins (in this case, other mapped proteins are listed in the ‘Mapped Proteins’ column)

Protein ID protein identifier (primary accession number) for the selected protein

Protein Description name of the selected protein

[experiment] Spectral Count count of peptide-spectrum matches (PSMs) in the sample that support the peptide identification

[experiment] Intensity summed precursor intensities of supporting PSMs


combined_protein.tsv

combined_protein.tsv files contain FDR-filtered proteins from all experimental groups, where each row is a protein group. Contents of each column are listed below.

Protein Group protein group as calculated by ProteinProphet

SubGroup protein sub-group as calculated by ProteinProphet

Protein protein sequence header corresponding to the identified peptide sequence inferred from combined evidence; this will be the selected razor protein if the peptide maps to multiple proteins

Protein ID protein identifier (primary accession number) for the selected protein

Entry Name entry name for the selected protein

Gene Name gene name for the selected protein

Protein Length number of amino acid sequences in the selected protein

Coverage percent of total protein length represented by the identified peptides

Organism species corresponding to the protein identification

Protein Existence type of evidence for the existence of the protein

Description name of the selected protein

Protein Probability confidence score determined by ProteinProphet from combined evidence, higher values indicate greater confidence

Top Peptide Probability highest PeptideProphet confidence score from all peptides that map to the protein

Unique Stripped Peptides number of unique peptide sequences mapping to the protein

Summarized Total Spectral Count total number of PSMs with sequences mapping to the selected protein, includes shared PSMs

Summarized Unique Spectral Count number of PSMs with sequences mapping only to the selected protein

Summarized Razor Spectral Count number of PSMs where the selected protein is the razor assignment for that PSM

[experiment] Total Spectral Count total number of PSMs in the sample with sequences mapping to the selected protein, includes shared PSMs

[experiment] Unique Spectral Count number of PSMs in the sample with sequences mapping only to the selected protein

[experiment] Razor Spectral Count number of PSMs in the sample where the selected protein is the razor assignment for that PSM

[experiment] Total Intensity summed precursor intensities from all PSMs in the sample with sequences mapping to the selected protein (including shared PSMs)

[experiment] Unique Intensity summed precursor intensities from all PSMs in the sample with sequences mapping only to the selected protein

[experiment] Razor Intensity summed precursor intensities from all PSMs in the sample where the selected protein is the razor assignment for that PSM

Indistinguishable Proteins proteins that cannot be distinguished from the selected protein given all sequences/evidence identified in the experiment


global.profile.tsv

global.profile.tsv reports the most prominent features from PTM-Shepherd analysis of mass shifts observed from FDR-filtered open search results. Each row corresponds to a different detected mass shift. Unless otherwise indicated, values are summed from all datasets in the analysis. Column contents are listed below.

peak_apex apex of the detected delta mass peak (in Da)

peak_lower lower bound of the detected peak (Da), determined by precursor tolerance or the detection of an adjacent peak

peak_upper upper bound of the detected peak (Da), determined by precursor tolerance or the detection of an adjacent peak

PSMs the number of PSMs contained within the peak boundary (bin), reported for each dataset if multiple datasets are used as input

peak_signal relative measure of peak prominence/quality. In noisy regions of the delta mass histogram, values are penalized

percent_also_in_unmodified the percentage of PSMs in this mass bin with a corresponding PSM in the unmodified bin

mapped_mass_1 primary modification annotation derived from Unimod, all isobaric modifications listed and separated by “/”

mapped_mass_2 if the delta mass peak is a combination of two masses, a second modification annotation is listed here. As with mapped_mass_1, all isobaric modifications are listed and separated by “/”

similarity MS/MS spectral similarity of modified peptides compared to their unmodified counterparts. When multiple modified-unmodified comparisons are done for a single peptide, these cosine similarity scores are averaged for the peptide. The peptide scores are then averaged across all peptides in the mass shift bin. These comparisons are only done for peptides of the same charge state.

rt_shift retention time shift comparing modified peptides to their unmodified counterparts. When multiple modified-unmodified comparisons are done for a single peptide, the retention time shifts are averaged for the peptide. The peptide shifts are then averaged across all peptides in the mass shift bin. Individual comparisons are only done for peptides in the same LC-MS run. Units are usually seconds but can vary by instrument type

localized_PSMs number of PSMs for this delta mass that showed at least one additional matched ion when the mass shift is placed on a residue

n-term_localization_rate percentage of PSMs with an uninterrupted string of localized residues from the N-terminus. This is calculated differently from other enrichment scores due to the difference in assumptions underlying N-terminal and residue-specific localization, so these values cannot be directly compared to the amino acid enrichment scores.

AA1 amino acid/residue most enriched (most likely to harbor the mass shift) compared to other residues

AA1_enrichment_score equivalent to the odds the delta mass is localized to AA1 compared to other residues

AA1_psm_count weighted number of PSMs where the mass shift localized to AA1. Shifts localizing to multiple residues are divided by the number of localized residues in the spectra, so this is an estimated number of PSMs localized to a particular residue

(same enrichment_score, and psm_count columns for AA2 and AA3 if multiple amino acids are likely to harbor the mass shift)

[experiment]_PSMs number of PSMs with a mass shift in this bin

[experiment]_percent_PSMs number of PSMs from the previous column as a percentage of total PSMs

[experiment]_peptides number of unique peptide sequences with a mass shift in this bin

[experiment]_percent_also_in_unmodified percentage of peptide sequences with a mass shift in this bin that are also found in the zero mass shift bin




global.modsummary.tsv

global.modsummary.tsv is a modification-centric table generated from PTM-Shepherd summarization of mass shifts observed in open search workflows. Contents of each column are listed below.

Modification Name/annotation of the modification (as found in the global.profile.tsv file)

Theoretical Mass Shift The theoretical mass of the modification from Unimod if annotated, or the peak apex of an unannotated modification

[experiment]_PSMs Number of PSMs with the modification, including any row from the global.profile.tsv file where the modification appears (e.g., a ‘Methylation’ entry in the will include PSMs corresponding to both ‘Methylation’ and ‘Methylation + First isotopic peak’)

[experiment]_percent_PSMs The number of PSMs from the previous column as a percentage of the total PSMs


filename_quant.csv

filename_quant.csv contains label-free quantification information from IonQuant. These quantification values will also be included in the psm.tsv, peptide.tsv, and protein.tsv reports.

scan_num scan number of the MS/MS spectrum within the LC-MS file

compensation_voltage FAIMS compensation voltage for the scan if applicable

peptide stripped amino acid sequence of the identified peptide

modified_peptide peptide sequence plus variable modifications

calculated_MZ theoretical mass-to-charge value of the identified peptide

uncalibrated_precursor_MZ observed mass-to-charge value prior to calibration

calibrated_precursor_MZ observed mass-to-charge value after calibration by MSFragger

uncalibrated_ppm difference between calculated and observed peptide mass (in parts per million) prior to calibration

calibrated_ppm difference between calculated and observed peptide mass (in parts per million) after calibration by MSFragger

retention_time retention time at which the MS/MS scan was taken (usually in seconds but units can vary by instrument type)

charge precursor charge state

apex_scan_num scan number closest to the apex intensity of the precursor

relative_mass_deviation

apex_retention_time retention time of the precursor’s apex intensity (usually in seconds but units can vary by instrument type)

retention_time_begin time the traced precursor feature is first observed

retention_time_end time the traced precursor feature is last observed

intensity summed precursor feature intensity (including all isotopic peaks)

intensity0 precursor intensity at the 0th isotopic peak

intensity1 precursor intensity at the 1st isotopic peak

intensity2 precursor intensity at the 2nd isotopic peak

ppm0 intensity-weighted ppm error of the 0th isotope peak

ppm1 intensity-weighted ppm error of the 1st isotope peak

ppm2 intensity-weighted ppm error of the 2nd isotope peak

hyperscore similarity score between observed and theoretical spectra, higher values indicate greater similarity


gene

Report_[abundance/ratio]_groupby=gene_protNorm=[MD]_gu=[0].tsv contains isobaric quantification information summarized from the psm.tsv tables by TMT-Integrator to the gene level. If ‘Group by’ is set to ‘Gene level’ (default for non-modification centric quantification workflows) in the ‘Quant (Isobaric)’ tab of FragPipe, only gene-level reports will be generated. Set ‘Group by’ to ‘All’ to also generate protein and peptide-level reports. (Ratios are channel abundance / reference channel abundance, so [channel] - ReferenceIntensity in the tables since values are log2-transformed.)

Index gene name (works best if the analyses were run with properly-formatted FASTA sequence databases, see this page for more information)

NumberPSM total peptide-spectrum matches mapping to the gene that are used in quantification

Proteins names of the proteins mapping to the gene

MaxPepProb highest PeptideProphet probability of the PSMs mapping to the gene

ReferenceIntensity real reference channel abundance if one has been provided, otherwise these values are virtual reference abundances from the average abundance across the channels, more information here

[sample/channel name] normalized and log2 transformed abundance/ratio for the given reporter ion channel from summarization to the gene level


protein

Report_[abundance/ratio]_groupby=protein_protNorm=[MD]_gu=[0].tsv contains isobaric quantification information summarized from the psm.tsv tables by TMT-Integrator to the protein level. If ‘Group by’ is set to ‘Protein’ in the ‘Quant (Isobaric)’ tab of FragPipe, only protein-level reports will be generated. Set ‘Group by’ to ‘All’ to also generate gene and peptide-level reports. (Ratios are channel abundance / reference channel abundance, so [channel] - ReferenceIntensity in the tables since values are log2-transformed.)

Index protein name (FASTA sequence header)

NumberPSM total peptide-spectrum matches mapping to the gene that are used in quantification

Gene originating gene name for the protein

MaxPepProb highest PeptideProphet probability of the PSMs mapping to the protein that are used in quantification

ReferenceIntensity real reference channel abundance if one has been provided, otherwise these values are virtual reference abundances from the average abundance across the channels, more information here

[sample/channel name] normalized and log2 transformed abundance/ratio for the given reporter ion channel from summarization to the protein level


peptide

Report_[abundance/ratio]_groupby=peptide_protNorm=[MD]_gu=[0].tsv contains isobaric quantification information summarized from the psm.tsv tables by TMT-Integrator to the peptide level. If ‘Group by’ is set to ‘Peptide sequence’ in the ‘Quant (Isobaric)’ tab of FragPipe, only peptide-level reports will be generated. Set ‘Group by’ to ‘All’ to also generate gene and protein-level reports. (Ratios are channel abundance / reference channel abundance, so [channel] - ReferenceIntensity in the tables since values are log2-transformed.)

Index protein name (FASTA sequence header) with the start and end positions of the peptide within the protein sequence

Gene originating gene name for the peptide

Peptide stripped peptide sequence

MaxPepProb highest PeptideProphet probability of the PSMs with the sequence that are used in quantification

ReferenceIntensity real reference channel abundance if one has been provided, otherwise these values are virtual reference abundances from the average abundance across the channels, more information here

[sample/channel name] normalized and log2 transformed abundance/ratio for the given reporter ion channel from summarization to the stripped peptide sequence level


multi-site

Report_[abundance/ratio]_groupby=multi-site_protNorm=[MD]_gu=[0].tsv contains isobaric quantification information summarized from the psm.tsv tables by TMT-Integrator based on modification sites that have been observed and quantified together. If ‘Group by’ is set to ‘Multiple PTM sites’ in the ‘Quant (Isobaric)’ tab of FragPipe, only multi-site reports will be generated. Set ‘Group by’ to ‘All’ to generate reports at all levels. (Ratios are channel abundance / reference channel abundance, so [channel] - ReferenceIntensity in the tables since values are log2-transformed.)

Index protein name (FASTA sequence header) with the start and end positions of the potential modification sites within the protein sequence, the count of the possible sites in that sequence window, the count of localized modifications, and the list of modified sites

Gene originating gene name

Peptide stripped peptide sequence containing the modification sites, residues with localized modifications are shown in lower case

MaxPepProb highest PeptideProphet probability of the PSMs with the sequence that are used in quantification

ReferenceIntensity real reference channel abundance if one has been provided, otherwise these values are virtual reference abundances from the average abundance across the channels, more information here

[sample/channel name] normalized and log2 transformed abundance/ratio for the given reporter ion channel from summarization to the multiple-mod site level


single-site

Report_[abundance/ratio]_groupby=single-site_protNorm=[MD]_gu=[0].tsv contains isobaric quantification information summarized from the psm.tsv tables by TMT-Integrator to the level of single post-translationally modified sites. If ‘Group by’ is set to ‘Single PTM site’ in the ‘Quant (Isobaric)’ tab of FragPipe, only multi-site reports will be generated. Set ‘Group by’ to ‘All’ to generate reports at all levels. (Ratios are channel abundance / reference channel abundance, so [channel] - ReferenceIntensity in the tables since values are log2-transformed.)

Index protein name (FASTA sequence header) with the modified site location within the protein sequence

Gene originating gene name

Peptide stripped peptide sequence containing the modification sites, residues with localized modifications are shown in lower case

MaxPepProb highest PeptideProphet probability of the PSMs with the sequence that are used in quantification

ReferenceIntensity real reference channel abundance if one has been provided, otherwise these values are virtual reference abundances from the average abundance across the channels, more information here

[sample/channel name] normalized and log2 transformed abundance/ratio for the given reporter ion channel from summarization to the single modification site level (sites are quantified from PSMs with only the site of interest if available, otherwise the median of all localized sites is used if the site is only found with additional sites)


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