Escherichia coli mediated resistance of Entamoeba histolytica to oxidative stress is triggered by oxaloacetate

Amebiasis, a global intestinal parasitic disease, is due to Entamoeba histolytica. This parasite, which feeds on bacteria in the large intestine of its human host, can trigger a strong inflammatory response upon invasion of the colonic mucosa. Whereas information about the mechanisms which are used by the parasite to cope with oxidative and nitrosative stresses during infection is available, knowledge about the contribution of bacteria to these mechanisms is lacking. In a recent study, we demonstrated that enteropathogenic Escherichia coli O55 protects E. histolytica against oxidative stress. Resin-assisted capture (RAC) of oxidized (OX) proteins coupled to mass spectrometry (OX-RAC) was used to investigate the oxidation status of cysteine residues in proteins present in E. histolytica trophozoites incubated with live or heat-killed E. coli O55 and then exposed to H2O2-mediated oxidative stress. We found that the redox proteome of E. histolytica exposed to heat-killed E. coli O55 is enriched with proteins involved in redox homeostasis, lipid metabolism, small molecule metabolism, carbohydrate derivative metabolism, and organonitrogen compound biosynthesis. In contrast, we found that proteins associated with redox homeostasis were the only OX-proteins that were enriched in E. histolytica trophozoites which were incubated with live E. coli O55. These data indicate that E. coli has a profound impact on the redox proteome of E. histolytica. Unexpectedly, some E. coli proteins were also co-identified with E. histolytica proteins by OX-RAC. We demonstrated that one of these proteins, E. coli malate dehydrogenase (EcMDH) and its product, oxaloacetate, are key elements of E. coli-mediated resistance of E. histolytica to oxidative stress and that oxaloacetate helps the parasite survive in the large intestine. We also provide evidence that the protective effect of oxaloacetate against oxidative stress extends to Caenorhabditis elegans.


Isotope Patterns Sequenced
The total number of isotope patterns sequenced by tandem MS.
Isotope Patterns Sequenced (z>1) The total number of isotope patterns sequenced by tandem MS with a charge state of 2 or more.

Isotope Patterns Sequenced [%]
The percentage of isotope patterns sequenced by tandem MS.
Isotope Patterns Sequenced (z>1) [%] The percentage of isotope patterns sequenced by tandem MS with a charge state of 2 or more.

Isotope Patterns Repeatedly Sequenced
The total number of isotope patterns repeatedly sequenced (i.e. 1 or more times) by tandem MS.

Isotope Patterns Repeatedly Sequenced [%]
The percentage of isotope patterns repeatedly sequenced (i.e. 1 or more times) by tandem MS.

Evidence
The evidence file combines all the information about the identified peptides and normally is the only file required for processing the results. Additional information about the peptides, modifications, proteins, etc. can be found in the other files by unique identifier linkage.

Sequence
The identified AA sequence of the peptide.

Length
The length of the sequence stored in the column 'Sequence'.

Modifications
Post-translational modifications contained within the identified peptide sequence.
Modified sequence Sequence representation including the post-translational modifications (abbreviation of the modification in brackets before the modified AA). The sequence is always surrounded by underscore characters ('_').
Carbamidomethyl ( Carbamidomethyl (C) Score Diffs Sequence representation for each of the possible PTM positions in each possible configuration, the difference is calculated between the identification score with the PTM added to that position and the best scoring identification where no PTM is added to that position. When this value is negative, it is unlikely that the particular modification is located at this position.
Oxidation (M) Score Diffs Sequence representation for each of the possible PTM positions in each possible configuration, the difference is calculated between the identification score with the PTM added to that position and the best scoring identification where no PTM is added to that position. When this value is negative, it is unlikely that the particular modification is located at this position.
Oxidation(C) Score Diffs Sequence representation for each of the possible PTM positions in each possible configuration, the difference is calculated between the identification score with the PTM added to that position and the best scoring identification where no PTM is added to that position. When this value is negative, it is unlikely that the particular modification is located at this position.
Oxidation(WYF) Score Diffs Sequence representation for each of the possible PTM positions in each possible configuration, the difference is calculated between the identification score with the PTM added to that position and the best scoring identification where no PTM is added to that position. When this value is negative, it is unlikely that the particular modification is located at this position.
Acetyl (Protein N-term) The number of occurrences of the modification 'Acetyl (Protein N-term) '.

Carbamidomethyl (C)
The number of occurrences of the modification 'Carbamidomethyl (C)'.

Oxidation (M)
The number of occurrences of the modification 'Oxidation (M)'.

Oxidation(C)
The number of occurrences of the modification 'Oxidation(C)'.

Oxidation(WYF)
The number of occurrences of the modification 'Oxidation(WYF)'.
Missed cleavages Number of missed enzymatic cleavages.

Proteins
The identifiers of the proteins this particular peptide is associated with.

Leading Proteins
The identifiers of the proteins in the proteinGroups file, with this protein as best match, this particular peptide is associated with. When multiple matches are found here, the best scoring protein can be found in the 'Leading Razor Protein' column.

Leading Razor Protein
The identifier of the best scoring protein, from the proteinGroups file this, this peptide is associated to.

Type
The type of MS/MS spectrum this sequence is derived from. MSMS -MS/MS for an unidentified peak. ISO-MSMS -MS/MS from an identified isotope cluster. MULTI-MSMS -MS/MS from an identified labeling cluster.

Raw file
The name of the RAW-file the mass spectral data was derived from.

MS/MS m/z
The m/z used for fragmentation (not necessarily the monoisotopic m/z).

Charge
The charge-state of the precursor ion. m/z The recalibrated mass-over-charge value of the precursor ion.

Mass
The predicted monoisotopic mass of the identified peptide sequence.

Resolution
The resolution of precursor ion measured in Full Width at Half Maximum (FWHM).

Uncalibrated -Calibrated m/z [ppm]
The difference between the uncalibrated and recalibrated mass-over-charge value of the precursor ion measured in parts-per-million. This gives an indication of the mass drift in the original data, which was automatically corrected by MaxQuant.
Uncalibrated -Calibrated m/z [Da] The difference between the uncalibrated and recalibrated mass-over-charge value of the precursor ion measured in parts-per-million. This gives an indication of the mass drift in the original data, which was automatically corrected by MaxQuant.
Mass Error [ppm] Mass error of the recalibrated mass-over-charge value of the precursor ion in comparison to the predicted monoisotopic mass of the identified peptide sequence in parts per million.

Mass Error [Da]
Mass error of the recalibrated mass-over-charge value of the precursor ion in comparison to the predicted monoisotopic mass of the identified peptide sequence in milli-Dalton.

Uncalibrated Mass Error [ppm]
Mass error of the uncalibrated mass-over-charge value of the precursor ion in comparison to the predicted monoisotopic mass of the identified peptide sequence.
Note: This column can contain missing values (denoted as NaN).

Uncalibrated Mass Error [Da]
Mass error of the uncalibrated mass-over-charge value of the precursor ion in comparison to the predicted monoisotopic mass of the identified peptide sequence.
Note: This column can contain missing values (denoted as NaN).
Max intensity m/z 0 Summed up eXtracted Ion Current (XIC) of all isotopic clusters associated with the identified AA sequence. In case of a labeled experiment this is the total intensity of all the isotopic patterns in the label cluster.

Retention time
The uncalibrated retention time in minutes in the elution profile of the precursor ion.

Retention length
The total retention time of the peak (last timepoint -first timepoint).

Calibrated retention time
The recalibrated retention time in minutes in the elution profile of the precursor ion.
Calibrated retention time start The recalibrated retention start in minutes in the elution profile of the precursor ion.
Calibrated retention time finish The recalibrated retention finish in minutes in the elution profile of the precursor ion.

Retention time calibration
The difference in minutes between the uncalibrated and recalibrated retention time. This gives an indication of the retention time drift in the original data, which was automatically corrected by MaxQuant.
Note: This column can contain missing values (NaN).
Match time difference When the option 'match between runs' is used in MaxQuant, this value indicates the time difference between the feature from the raw file it was taken from and the feature from the raw file it was matched to.
Match m/z difference When the option 'match between runs' is used in MaxQuant, this value indicates the m/z difference between the feature from the raw file it was taken from and the feature from the raw file it was matched to.
Match q-value This is the q-value for features that have been identified by 'matching between runs'.
Match score The andromeda score of the MS/MS identification that is the source of this identification by 'matching between runs'.
Number of data points The number of data points (peak centroids) collected for this peptide feature.

Number of scans
The number of MS scans that the 3d peaks of this peptide feature are overlapping with.

Number of isotopic peaks
The number of isotopic peaks contained in this peptide feature.
PIF Short for Parent Ion Fraction; indicates the fraction the target peak makes up of the total intensity in the inclusion window.
Fraction of total spectrum The percentage the ion intensity makes up of the total intensity of the whole spectrum.

Base peak fraction
The percentage the parent ion intensity in comparison to the highest peak in the MS spectrum.

PEP
Posterior Error Probability of the identification. This value essentially operates as a p-value, where smaller is more significant.

MS/MS Count
The number of sequencing events for this sequence, which matches the number of identifiers stored in the column 'MS/MS IDs'. This number is independent of the times the AA sequence has been identified through (other) modifications (e.g. heavy label, oxidation, etc.), about which information can be found in the columns 'Labeling State' and 'Modification'.

MS/MS Scan Number
The RAW-file derived scan number of the MS/MS with the highest peptide identification score (the highest score is stored in the column 'Score').

Score
Andromeda score for the best associated MS/MS spectrum.
Delta score Score difference to the second best identified peptide.

Combinatorics
Number of possible distributions of the modifications over the peptide sequence.

Intensity
Summed up eXtracted Ion Current (XIC) of all isotopic clusters associated with the identified AA sequence. In case of a labeled experiment this is the total intensity of all the isotopic patterns in the label cluster.

Reverse
When marked with '+', this particular peptide was found to be part of a protein derived from the reversed part of the decoy database. These should be removed for further data analysis.
Potential contaminant When marked with '+', this particular peptide was found to be part of a commonly occurring contaminant. These should be removed for further data analysis.
id A unique (consecutive) identifier for each row in the evidence table, which is used to cross-link the information in this file with the information stored in the other files.

Protein group IDs
The identifier of the protein-group this redundant peptide sequence is associated with, which can be used to look up the extended protein information in the file 'proteinGroups.txt'. As a single peptide can be linked to multiple proteins (e.g. in the case of razor-proteins), multiple id's can be stored here separated by a semicolon. As a protein can be identified by multiple peptides, the same id can be found in different rows.
Peptide ID The identifier of the non-redundant peptide sequence.
Mod. peptide ID Identifier of the associated modification summary stored in the file 'modificationSpecificPeptides.txt'.

Peptides
The peptides table contains information on the identified peptides in the processed raw-files.

Sequence
The amino acid sequence of the identified peptide.
N-term cleavage window Sequence window from -8 to 8 around the N-terminal cleavage site of this peptide.
C-term cleavage window Sequence window from -8 to 8 around the C-terminal cleavage site of this peptide.
Amino acid before The amino acid in the protein sequence before the peptide.
First amino acid The amino acid in the first position of the peptide sequence.
Second amino acid The amino acid in the first position of the peptide sequence.
Second last amino acid The amino acid in the last position of the peptide sequence.
Last amino acid The amino acid in the last position of the peptide sequence.
Amino acid after The amino acid in the protein sequence after the peptide.

A Count
The number of instances of the 'A' amino acid contained within the sequence.

R Count
The number of instances of the 'R' amino acid contained within the sequence.

N Count
The number of instances of the 'N' amino acid contained within the sequence.

D Count
The number of instances of the 'D' amino acid contained within the sequence.

C Count
The number of instances of the 'C' amino acid contained within the sequence.

Q Count
The number of instances of the 'Q' amino acid contained within the sequence.

E Count
The number of instances of the 'E' amino acid contained within the sequence.

G Count
The number of instances of the 'G' amino acid contained within the sequence.

H Count
The number of instances of the 'H' amino acid contained within the sequence.

I Count
The number of instances of the 'I' amino acid contained within the sequence.

L Count
The number of instances of the 'L' amino acid contained within the sequence.

K Count
The number of instances of the 'K' amino acid contained within the sequence.

M Count
The number of instances of the 'M' amino acid contained within the sequence.

F Count
The number of instances of the 'F' amino acid contained within the sequence.

P Count
The number of instances of the 'P' amino acid contained within the sequence.

S Count
The number of instances of the 'S' amino acid contained within the sequence.

T Count
The number of instances of the 'T' amino acid contained within the sequence.

W Count
The number of instances of the 'W' amino acid contained within the sequence.

Y Count
The number of instances of the 'Y' amino acid contained within the sequence.

V Count
The number of instances of the 'V' amino acid contained within the sequence.

U Count
The number of instances of the 'U' amino acid contained within the sequence.

Length
The length of the sequence stored in the column "Sequence".
Missed cleavages Number of missed enzymatic cleavages.

Mass
Monoisotopic mass of the peptide.

Proteins
Identifiers of proteins this peptide is associated with.
Leading razor protein Identifiers of the best scoring protein this peptide is associated with.
Start position Position of the first amino acid of this peptide in the protein sequence. (one-based) End position Position of the last amino acid of this peptide in the protein sequence. (one-based) Unique (Groups) When marked with '+', this particular peptide is unique to a single protein group in the proteinGroups file.

Unique (Proteins)
When marked with '+', this particular peptide is unique to a single protein sequence in the fasta file(s).

Intensity
Summed up eXtracted Ion Current (XIC) of all isotopic clusters associated with the identified AA sequence. In case of a labeled experiment this is the total intensity of all the isotopic patterns in the label cluster.
Intensity Control 1 Summed up eXtracted Ion Current (XIC) of all isotopic clusters associated with the identified AA sequence. In case of a labeled experiment this is the total intensity of all the isotopic patterns in the label cluster. Intensity Control 2 Summed up eXtracted Ion Current (XIC) of all isotopic clusters associated with the identified AA sequence. In case of a labeled experiment this is the total intensity of all the isotopic patterns in the label cluster.
Intensity Control 3 Summed up eXtracted Ion Current (XIC) of all isotopic clusters associated with the identified AA sequence. In case of a labeled experiment this is the total intensity of all the isotopic patterns in the label cluster.
Intensity H2O2 1 Summed up eXtracted Ion Current (XIC) of all isotopic clusters associated with the identified AA sequence. In case of a labeled experiment this is the total intensity of all the isotopic patterns in the label cluster.
Intensity H2O2 2 Summed up eXtracted Ion Current (XIC) of all isotopic clusters associated with the identified AA sequence. In case of a labeled experiment this is the total intensity of all the isotopic patterns in the label cluster.
Intensity H2O2 3 Summed up eXtracted Ion Current (XIC) of all isotopic clusters associated with the identified AA sequence. In case of a labeled experiment this is the total intensity of all the isotopic patterns in the label cluster.

Reverse
When marked with '+', this particular peptide was found to be part of a protein derived from the reversed part of the decoy database. These should be removed for further data analysis.

Potential contaminant
When marked with '+', this particular peptide was found to be part of a commonly occurring contaminant. These should be removed for further data analysis.
id A unique (consecutive) identifier for each row in the peptides table, which is used to cross-link the information in this table with the information stored in the other tables.

Protein group IDs
The identifiers of the protein groups this peptide was linked to, referenced against the proteinGroups

Sequence
The identified AA sequence of the peptide.

Modifications
Post-translational modifications contained within the sequence. When no modifications exist, this is set to 'unmodified'.

Mass
Charge corrected mass of the precursor ion.

Mass Fractional Part
The values after the decimal point (ie value -floor(value)).

Protein Groups
IDs of the protein groups to whoch this peptide belongs.

Proteins
The identifiers of the proteins this particular peptide is associated with.
Unique (Groups) When marked with '+', this particular peptide is unique to a single protein group in the proteinGroups file.
Unique (Proteins) When marked with '+', this particular peptide is unique to a single protein sequence in the fasta file(s).

Retention time
Retention time in minutes averaged over the evidence entries belonging to this modification-specific peptide.
Calibrated retention time Calibrated retention time averaged over the evidence entries belonging to this modification-specific peptide. Obviously this only makes sense if retention time recalibration has been performed which is the case when matching between run is selected.

Charges
All charge states that have been observed.

PEP
Posterior Error Probability of the identification. This value essentially operates as a p-value, where smaller is more significant.

MS/MS scan number
The RAW-file derived scan number of the MS/MS with the highest peptide identification score (the highest score is stored in the column 'Score').

Raw file
The name of the RAW-file the mass spectral data was derived from.

Score
Andromeda score for the best identified among the associated MS/MS spectra.
Delta score Score difference to the second best identified peptide.

Intensity
Summed up eXtracted Ion Current (XIC) of all isotopic clusters associated with the identified AA sequence. In case of a labeled experiment this is the total intensity of all the isotopic patterns in the label cluster.
Intensity Control 1 Summed up eXtracted Ion Current (XIC) of all isotopic clusters associated with the identified AA sequence. In case of a labeled experiment this is the total intensity of all the isotopic patterns in the label cluster.
Intensity Control 2 Summed up eXtracted Ion Current (XIC) of all isotopic clusters associated with the identified AA sequence. In case of a labeled experiment this is the total intensity of all the isotopic patterns in the label cluster.
Intensity Control 3 Summed up eXtracted Ion Current (XIC) of all isotopic clusters associated with the identified AA sequence. In case of a labeled experiment this is the total intensity of all the isotopic patterns in the label cluster.
Intensity H2O2 1 Summed up eXtracted Ion Current (XIC) of all isotopic clusters associated with the identified AA sequence. In case of a labeled experiment this is the total intensity of all the isotopic patterns in the label cluster.
Intensity H2O2 2 Summed up eXtracted Ion Current (XIC) of all isotopic clusters associated with the identified AA sequence. In case of a labeled experiment this is the total intensity of all the isotopic patterns in the label cluster.
Intensity H2O2 3 Summed up eXtracted Ion Current (XIC) of all isotopic clusters associated with the identified AA sequence. In case of a labeled experiment this is the total intensity of all the isotopic patterns in the label cluster.

Reverse
When marked with '+', this particular peptide was found to be part of a protein derived from the reversed part of the decoy database. These should be removed for further data analysis.
Potential contaminant When marked with '+', this particular peptide was found to be part of a commonly occurring contaminant. These should be removed for further data analysis.
id A unique (consecutive) identifier for each row in the peptides table, which is used to cross-link the information in this table with the information stored in the other tables.

Protein group IDs
The identifiers of the protein groups this peptide was linked to, referenced against the proteinGroups table.
Peptide ID Identifier of the associated peptide sequence summary, which can be found in the file 'peptides.txt'.
Evidence IDs Identifier(s) for analyzed peptide evidence associated with the protein group referenced against the evidences

Name Separator Description
Proteins Identifiers of proteins this site is associated with.
Positions within proteins For each protein identifier in the 'Proteins' column you find here the psoition of the site in the respective protein sequence. The index of the first amino acid in the sequence is 1.

Leading proteins
Protein Identifier of the protein this peptide is associated with.

Fasta headers
Descriptions of proteins this peptide is associated with.
Localization prob Score diff PEP The posterior error probability (PEP) of the best identified modified peptide containing this site.

Score
The Andromeda score of the best identified modified peptide containing this site. Delta score The Andromeda delta score of the best identified modified peptide containing this site.

Score for localization
The Andromeda score of the MS/MS spectrum used for calculating the localization score for this site.

Mass error [ppm]
Mass error of the recalibrated mass-over-charge value of the precursor ion in comparison to the predicted monoisotopic mass of the identified peptide sequence.

Intensity
Summed up eXtracted Ion Current (XIC) of all isotopic clusters associated with the identified AA sequence. In case of a labeled experiment this is the total intensity of all the isotopic patterns in the label cluster.

Intensity___1
Summed up eXtracted Ion Current (XIC) of all isotopic clusters associated with the identified AA sequence. In case of a labeled experiment this is the total intensity of all the isotopic patterns in the label cluster.

Intensity___2
Summed up eXtracted Ion Current (XIC) of all isotopic clusters associated with the identified AA sequence. In case of a labeled experiment this is the total intensity of all the isotopic patterns in the label cluster.

Intensity___3
Summed up eXtracted Ion Current (XIC) of all isotopic clusters associated with the identified AA sequence. In case of a labeled experiment this is the total intensity of all the isotopic patterns in the label cluster.

Ratio mod/base
Intensity Control 1 Summed up eXtracted Ion Current (XIC) of all isotopic clusters associated with the identified AA sequence. In case of a labeled experiment this is the total intensity of all the isotopic patterns in the label cluster.
Intensity Control 2 Summed up eXtracted Ion Current (XIC) of all isotopic clusters associated with the identified AA sequence. In case of a labeled experiment this is the total intensity of all the isotopic patterns in the label cluster.
Intensity Control 3 Summed up eXtracted Ion Current (XIC) of all isotopic clusters associated with the identified AA sequence. In case of a labeled experiment this is the total intensity of all the isotopic patterns in the label cluster.
Intensity H2O2 1 Summed up eXtracted Ion Current (XIC) of all isotopic clusters associated with the identified AA sequence. In case of a labeled experiment this is the total intensity of all the isotopic patterns in the label cluster.
Intensity H2O2 2 Summed up eXtracted Ion Current (XIC) of all isotopic clusters associated with the identified AA sequence. In case of a labeled experiment this is the total intensity of all the isotopic patterns in the label cluster.
Intensity H2O2 3 Summed up eXtracted Ion Current (XIC) of all isotopic clusters associated with the identified AA sequence. In case of a labeled experiment this is the total intensity of all the isotopic patterns in the label cluster. Intensity Control 1___1 Summed up eXtracted Ion Current (XIC) of all isotopic clusters associated with the identified AA sequence. In case of a labeled experiment this is the total intensity of all the isotopic patterns in the label cluster.
Intensity Control 1___2 Summed up eXtracted Ion Current (XIC) of all isotopic clusters associated with the identified AA sequence. In case of a labeled experiment this is the total intensity of all the isotopic patterns in the label cluster.
Intensity Control 1___3 Summed up eXtracted Ion Current (XIC) of all isotopic clusters associated with the identified AA sequence. In case of a labeled experiment this is the total intensity of all the isotopic patterns in the label cluster.
Intensity Control 2___1 Summed up eXtracted Ion Current (XIC) of all isotopic clusters associated with the identified AA sequence. In case of a labeled experiment this is the total intensity of all the isotopic patterns in the label cluster.
Intensity Control 2___2 Summed up eXtracted Ion Current (XIC) of all isotopic clusters associated with the identified AA sequence. In case of a labeled experiment this is the total intensity of all the isotopic patterns in the label cluster.
Intensity Control 2___3 Summed up eXtracted Ion Current (XIC) of all isotopic clusters associated with the identified AA sequence. In case of a labeled experiment this is the total intensity of all the isotopic patterns in the label cluster.
Intensity Control 3___1 Summed up eXtracted Ion Current (XIC) of all isotopic clusters associated with the identified AA sequence. In case of a labeled experiment this is the total intensity of all the isotopic patterns in the label cluster.
Intensity Control 3___2 Summed up eXtracted Ion Current (XIC) of all isotopic clusters associated with the identified AA sequence. In case of a labeled experiment this is the total intensity of all the isotopic patterns in the label cluster.
Intensity Control 3___3 Summed up eXtracted Ion Current (XIC) of all isotopic clusters associated with the identified AA sequence. In case of a labeled experiment this is the total intensity of all the isotopic patterns in the label cluster.
Intensity H2O2 1___1 Summed up eXtracted Ion Current (XIC) of all isotopic clusters associated with the identified AA sequence. In case of a labeled experiment this is the total intensity of all the isotopic patterns in the label cluster.

Intensity H2O2 1___2
Summed up eXtracted Ion Current (XIC) of all isotopic clusters associated with the identified AA sequence. In case of a labeled experiment this is the total intensity of all the isotopic patterns in the label cluster.
Intensity H2O2 1___3 Summed up eXtracted Ion Current (XIC) of all isotopic clusters associated with the identified AA sequence. In case of a labeled experiment this is the total intensity of all the isotopic patterns in the label cluster.
Intensity H2O2 2___1 Summed up eXtracted Ion Current (XIC) of all isotopic clusters associated with the identified AA sequence. In case of a labeled experiment this is the total intensity of all the isotopic patterns in the label cluster.
Intensity H2O2 2___2 Summed up eXtracted Ion Current (XIC) of all isotopic clusters associated with the identified AA sequence. In case of a labeled experiment this is the total intensity of all the isotopic patterns in the label cluster.
Intensity H2O2 2___3 Summed up eXtracted Ion Current (XIC) of all isotopic clusters associated with the identified AA sequence. In case of a labeled experiment this is the total intensity of all the isotopic patterns in the label cluster.
Intensity H2O2 3___1 Summed up eXtracted Ion Current (XIC) of all isotopic clusters associated with the identified AA sequence. In case of a labeled experiment this is the total intensity of all the isotopic patterns in the label cluster. Intensity H2O2 3___2 Summed up eXtracted Ion Current (XIC) of all isotopic clusters associated with the identified AA sequence. In case of a labeled experiment this is the total intensity of all the isotopic patterns in the label cluster.
Intensity H2O2 3___3 Summed up eXtracted Ion Current (XIC) of all isotopic clusters associated with the identified AA sequence. In case of a labeled experiment this is the total intensity of all the isotopic patterns in the label cluster. Reverse When marked with '+', this particular peptide was found to be part of a protein derived from the reversed part of the protein sequence database. These should be removed for further data analysis.
Potential contaminant When marked with '+', this particular peptide was found to be part of a commonly occurring contaminant. These should be removed for further data analysis.
id A unique (consecutive) identifier for each row in the site table, which is used to cross-link the information in this file with the information stored in the other files.

Protein group IDs
The identifier of the protein-group this peptide sequence is associated with, which can be used to look up the extended protein information in the file 'proteinGroups.txt'. As a single peptide can be linked to multiple proteins (e.g. in the case of razor-proteins), multiple id's can be stored here separated by a semicolon. As a protein can be identified by multiple peptides, the same id can be found in different rows.

Positions
The positions of the modifications in the protein amino acid sequence.

Position
The position of the modification in the protein amino acid sequence.
Peptide IDs Identifier(s) of the associated peptide sequence(s) summary, which can be found in the file 'peptides.txt'.
Mod. peptide IDs Identifier(s) of the associated peptide sequence(s) summary, which can be found in the file 'modificationSpecificPeptides.txt'.
Evidence IDs Identifier(s) for analyzed peptide evidence associated with the protein group referenced against the evidences table.

MS/MS IDs
The identifiers of the MS/MS scans identifying this peptide, referenced against the msms Positions within proteins For each protein identifier in the 'Proteins' column you find here the psoition of the site in the respective protein sequence. The index of the first amino acid in the sequence is 1.

Leading proteins
Protein Identifier of the protein this peptide is associated with.

Fasta headers
Descriptions of proteins this peptide is associated with.
Localization prob Score diff PEP The posterior error probability (PEP) of the best identified modified peptide containing this site.

Score
The Andromeda score of the best identified modified peptide containing this site. Delta score The Andromeda delta score of the best identified modified peptide containing this site.

Score for localization
The Andromeda score of the MS/MS spectrum used for calculating the localization score for this site.

Mass error [ppm]
Mass error of the recalibrated mass-over-charge value of the precursor ion in comparison to the predicted monoisotopic mass of the identified peptide sequence.

Intensity
Summed up eXtracted Ion Current (XIC) of all isotopic clusters associated with the identified AA sequence. In case of a labeled experiment this is the total intensity of all the isotopic patterns in the label cluster.

Intensity___1
Summed up eXtracted Ion Current (XIC) of all isotopic clusters associated with the identified AA sequence. In case of a labeled experiment this is the total intensity of all the isotopic patterns in the label cluster.

Intensity___2
Summed up eXtracted Ion Current (XIC) of all isotopic clusters associated with the identified AA sequence. In case of a labeled experiment this is the total intensity of all the isotopic patterns in the label cluster.

Intensity___3
Summed up eXtracted Ion Current (XIC) of all isotopic clusters associated with the identified AA sequence. In case of a labeled experiment this is the total intensity of all the isotopic patterns in the label cluster.

Ratio mod/base
Intensity Control 1 Summed up eXtracted Ion Current (XIC) of all isotopic clusters associated with the identified AA sequence. In case of a labeled experiment this is the total intensity of all the isotopic patterns in the label cluster.
Intensity Control 2 Summed up eXtracted Ion Current (XIC) of all isotopic clusters associated with the identified AA sequence. In case of a labeled experiment this is the total intensity of all the isotopic patterns in the label cluster.
Intensity Control 3 Summed up eXtracted Ion Current (XIC) of all isotopic clusters associated with the identified AA sequence. In case of a labeled experiment this is the total intensity of all the isotopic patterns in the label cluster.
Intensity H2O2 1 Summed up eXtracted Ion Current (XIC) of all isotopic clusters associated with the identified AA sequence. In case of a labeled experiment this is the total intensity of all the isotopic patterns in the label cluster.
Intensity H2O2 2 Summed up eXtracted Ion Current (XIC) of all isotopic clusters associated with the identified AA sequence. In case of a labeled experiment this is the total intensity of all the isotopic patterns in the label cluster.
Intensity H2O2 3 Summed up eXtracted Ion Current (XIC) of all isotopic clusters associated with the identified AA sequence. In case of a labeled experiment this is the total intensity of all the isotopic patterns in the label cluster. Intensity Control 1___1 Summed up eXtracted Ion Current (XIC) of all isotopic clusters associated with the identified AA sequence. In case of a labeled experiment this is the total intensity of all the isotopic patterns in the label cluster.
Intensity Control 1___2 Summed up eXtracted Ion Current (XIC) of all isotopic clusters associated with the identified AA sequence. In case of a labeled experiment this is the total intensity of all the isotopic patterns in the label cluster.
Intensity Control 1___3 Summed up eXtracted Ion Current (XIC) of all isotopic clusters associated with the identified AA sequence. In case of a labeled experiment this is the total intensity of all the isotopic patterns in the label cluster.
Intensity Control 2___1 Summed up eXtracted Ion Current (XIC) of all isotopic clusters associated with the identified AA sequence. In case of a labeled experiment this is the total intensity of all the isotopic patterns in the label cluster.
Intensity Control 2___2 Summed up eXtracted Ion Current (XIC) of all isotopic clusters associated with the identified AA sequence. In case of a labeled experiment this is the total intensity of all the isotopic patterns in the label cluster.
Intensity Control 2___3 Summed up eXtracted Ion Current (XIC) of all isotopic clusters associated with the identified AA sequence. In case of a labeled experiment this is the total intensity of all the isotopic patterns in the label cluster.
Intensity Control 3___1 Summed up eXtracted Ion Current (XIC) of all isotopic clusters associated with the identified AA sequence. In case of a labeled experiment this is the total intensity of all the isotopic patterns in the label cluster.
Intensity Control 3___2 Summed up eXtracted Ion Current (XIC) of all isotopic clusters associated with the identified AA sequence. In case of a labeled experiment this is the total intensity of all the isotopic patterns in the label cluster.
Intensity Control 3___3 Summed up eXtracted Ion Current (XIC) of all isotopic clusters associated with the identified AA sequence. In case of a labeled experiment this is the total intensity of all the isotopic patterns in the label cluster.
Intensity H2O2 1___1 Summed up eXtracted Ion Current (XIC) of all isotopic clusters associated with the identified AA sequence. In case of a labeled experiment this is the total intensity of all the isotopic patterns in the label cluster.
Intensity H2O2 1___2 Summed up eXtracted Ion Current (XIC) of all isotopic clusters associated with the identified AA sequence. In case of a labeled experiment this is the total intensity of all the isotopic patterns in the label cluster.
Intensity H2O2 1___3 Summed up eXtracted Ion Current (XIC) of all isotopic clusters associated with the identified AA sequence. In case of a labeled experiment this is the total intensity of all the isotopic patterns in the label cluster.
Intensity H2O2 2___1 Summed up eXtracted Ion Current (XIC) of all isotopic clusters associated with the identified AA sequence. In case of a labeled experiment this is the total intensity of all the isotopic patterns in the label cluster.
Intensity H2O2 2___2 Summed up eXtracted Ion Current (XIC) of all isotopic clusters associated with the identified AA sequence. In case of a labeled experiment this is the total intensity of all the isotopic patterns in the label cluster.
Intensity H2O2 2___3 Summed up eXtracted Ion Current (XIC) of all isotopic clusters associated with the identified AA sequence. In case of a labeled experiment this is the total intensity of all the isotopic patterns in the label cluster.
Intensity H2O2 3___1 Summed up eXtracted Ion Current (XIC) of all isotopic clusters associated with the identified AA sequence. In case of a labeled experiment this is the total intensity of all the isotopic patterns in the label cluster. Intensity H2O2 3___2 Summed up eXtracted Ion Current (XIC) of all isotopic clusters associated with the identified AA sequence. In case of a labeled experiment this is the total intensity of all the isotopic patterns in the label cluster.
Intensity H2O2 3___3 Summed up eXtracted Ion Current (XIC) of all isotopic clusters associated with the identified AA sequence. In case of a labeled experiment this is the total intensity of all the isotopic patterns in the label cluster.

Reverse
When marked with '+', this particular peptide was found to be part of a protein derived from the reversed part of the protein sequence database. These should be removed for further data analysis.
Potential contaminant When marked with '+', this particular peptide was found to be part of a commonly occurring contaminant. These should be removed for further data analysis.
id A unique (consecutive) identifier for each row in the site table, which is used to cross-link the information in this file with the information stored in the other files.

Protein group IDs
The identifier of the protein-group this peptide sequence is associated with, which can be used to look up the extended protein information in the file 'proteinGroups.txt'. As a single peptide can be linked to multiple proteins (e.g. in the case of razor-proteins), multiple id's can be stored here separated by a semicolon. As a protein can be identified by multiple peptides, the same id can be found in different rows.

Positions
The positions of the modifications in the protein amino acid sequence.

Position
The position of the modification in the protein amino acid sequence.
Peptide IDs Identifier(s) of the associated peptide sequence(s) summary, which can be found in the file 'peptides.txt'.
Mod. peptide IDs Identifier(s) of the associated peptide sequence(s) summary, which can be found in the file 'modificationSpecificPeptides.txt'.
Evidence IDs Identifier(s) for analyzed peptide evidence associated with the protein group referenced against the evidences

Name Separator Description
Proteins Identifiers of proteins this site is associated with.
Positions within proteins For each protein identifier in the 'Proteins' column you find here the psoition of the site in the respective protein sequence. The index of the first amino acid in the sequence is 1.

Leading proteins
Protein Identifier of the protein this peptide is associated with.

Fasta headers
Descriptions of proteins this peptide is associated with.
Localization prob Score diff PEP The posterior error probability (PEP) of the best identified modified peptide containing this site.

Score
The Andromeda score of the best identified modified peptide containing this site. Delta score The Andromeda delta score of the best identified modified peptide containing this site.

Score for localization
The Andromeda score of the MS/MS spectrum used for calculating the localization score for this site.

Mass error [ppm]
Mass error of the recalibrated mass-over-charge value of the precursor ion in comparison to the predicted monoisotopic mass of the identified peptide sequence.

Intensity
Summed up eXtracted Ion Current (XIC) of all isotopic clusters associated with the identified AA sequence. In case of a labeled experiment this is the total intensity of all the isotopic patterns in the label cluster.

Intensity___1
Summed up eXtracted Ion Current (XIC) of all isotopic clusters associated with the identified AA sequence. In case of a labeled experiment this is the total intensity of all the isotopic patterns in the label cluster.

Intensity___2
Summed up eXtracted Ion Current (XIC) of all isotopic clusters associated with the identified AA sequence. In case of a labeled experiment this is the total intensity of all the isotopic patterns in the label cluster.

Intensity___3
Summed up eXtracted Ion Current (XIC) of all isotopic clusters associated with the identified AA sequence. In case of a labeled experiment this is the total intensity of all the isotopic patterns in the label cluster.

Ratio mod/base
Intensity Control 1 Summed up eXtracted Ion Current (XIC) of all isotopic clusters associated with the identified AA sequence. In case of a labeled experiment this is the total intensity of all the isotopic patterns in the label cluster.
Intensity Control 2 Summed up eXtracted Ion Current (XIC) of all isotopic clusters associated with the identified AA sequence. In case of a labeled experiment this is the total intensity of all the isotopic patterns in the label cluster.
Intensity Control 3 Summed up eXtracted Ion Current (XIC) of all isotopic clusters associated with the identified AA sequence. In case of a labeled experiment this is the total intensity of all the isotopic patterns in the label cluster.
Intensity H2O2 1 Summed up eXtracted Ion Current (XIC) of all isotopic clusters associated with the identified AA sequence. In case of a labeled experiment this is the total intensity of all the isotopic patterns in the label cluster.
Intensity H2O2 2 Summed up eXtracted Ion Current (XIC) of all isotopic clusters associated with the identified AA sequence. In case of a labeled experiment this is the total intensity of all the isotopic patterns in the label cluster.
Intensity H2O2 3 Summed up eXtracted Ion Current (XIC) of all isotopic clusters associated with the identified AA sequence. In case of a labeled experiment this is the total intensity of all the isotopic patterns in the label cluster. Intensity Control 1___1 Summed up eXtracted Ion Current (XIC) of all isotopic clusters associated with the identified AA sequence. In case of a labeled experiment this is the total intensity of all the isotopic patterns in the label cluster.
Intensity Control 1___2 Summed up eXtracted Ion Current (XIC) of all isotopic clusters associated with the identified AA sequence. In case of a labeled experiment this is the total intensity of all the isotopic patterns in the label cluster.
Intensity Control 1___3 Summed up eXtracted Ion Current (XIC) of all isotopic clusters associated with the identified AA sequence. In case of a labeled experiment this is the total intensity of all the isotopic patterns in the label cluster.
Intensity Control 2___1 Summed up eXtracted Ion Current (XIC) of all isotopic clusters associated with the identified AA sequence. In case of a labeled experiment this is the total intensity of all the isotopic patterns in the label cluster.
Intensity Control 2___2 Summed up eXtracted Ion Current (XIC) of all isotopic clusters associated with the identified AA sequence. In case of a labeled experiment this is the total intensity of all the isotopic patterns in the label cluster.
Intensity Control 2___3 Summed up eXtracted Ion Current (XIC) of all isotopic clusters associated with the identified AA sequence. In case of a labeled experiment this is the total intensity of all the isotopic patterns in the label cluster.
Intensity Control 3___1 Summed up eXtracted Ion Current (XIC) of all isotopic clusters associated with the identified AA sequence. In case of a labeled experiment this is the total intensity of all the isotopic patterns in the label cluster.
Intensity Control 3___2 Summed up eXtracted Ion Current (XIC) of all isotopic clusters associated with the identified AA sequence. In case of a labeled experiment this is the total intensity of all the isotopic patterns in the label cluster.
Intensity Control 3___3 Summed up eXtracted Ion Current (XIC) of all isotopic clusters associated with the identified AA sequence. In case of a labeled experiment this is the total intensity of all the isotopic patterns in the label cluster.
Intensity H2O2 1___1 Summed up eXtracted Ion Current (XIC) of all isotopic clusters associated with the identified AA sequence. In case of a labeled experiment this is the total intensity of all the isotopic patterns in the label cluster.

Intensity H2O2 1___2
Summed up eXtracted Ion Current (XIC) of all isotopic clusters associated with the identified AA sequence. In case of a labeled experiment this is the total intensity of all the isotopic patterns in the label cluster.
Intensity H2O2 1___3 Summed up eXtracted Ion Current (XIC) of all isotopic clusters associated with the identified AA sequence. In case of a labeled experiment this is the total intensity of all the isotopic patterns in the label cluster.
Intensity H2O2 2___1 Summed up eXtracted Ion Current (XIC) of all isotopic clusters associated with the identified AA sequence. In case of a labeled experiment this is the total intensity of all the isotopic patterns in the label cluster.
Intensity H2O2 2___2 Summed up eXtracted Ion Current (XIC) of all isotopic clusters associated with the identified AA sequence. In case of a labeled experiment this is the total intensity of all the isotopic patterns in the label cluster.
Intensity H2O2 2___3 Summed up eXtracted Ion Current (XIC) of all isotopic clusters associated with the identified AA sequence. In case of a labeled experiment this is the total intensity of all the isotopic patterns in the label cluster.
Intensity H2O2 3___1 Summed up eXtracted Ion Current (XIC) of all isotopic clusters associated with the identified AA sequence. In case of a labeled experiment this is the total intensity of all the isotopic patterns in the label cluster. Intensity H2O2 3___2 Summed up eXtracted Ion Current (XIC) of all isotopic clusters associated with the identified AA sequence. In case of a labeled experiment this is the total intensity of all the isotopic patterns in the label cluster.
Intensity H2O2 3___3 Summed up eXtracted Ion Current (XIC) of all isotopic clusters associated with the identified AA sequence. In case of a labeled experiment this is the total intensity of all the isotopic patterns in the label cluster. Reverse When marked with '+', this particular peptide was found to be part of a protein derived from the reversed part of the protein sequence database. These should be removed for further data analysis.
Potential contaminant When marked with '+', this particular peptide was found to be part of a commonly occurring contaminant. These should be removed for further data analysis.
id A unique (consecutive) identifier for each row in the site table, which is used to cross-link the information in this file with the information stored in the other files.

Protein group IDs
The identifier of the protein-group this peptide sequence is associated with, which can be used to look up the extended protein information in the file 'proteinGroups.txt'. As a single peptide can be linked to multiple proteins (e.g. in the case of razor-proteins), multiple id's can be stored here separated by a semicolon. As a protein can be identified by multiple peptides, the same id can be found in different rows.

Positions
The positions of the modifications in the protein amino acid sequence.

Position
The position of the modification in the protein amino acid sequence.
Peptide IDs Identifier(s) of the associated peptide sequence(s) summary, which can be found in the file 'peptides.txt'.
Mod. peptide IDs Identifier(s) of the associated peptide sequence(s) summary, which can be found in the file 'modificationSpecificPeptides.txt'.
Evidence IDs Identifier(s) for analyzed peptide evidence associated with the protein group referenced against the evidences table.

MS/MS IDs
The identifiers of the MS/MS scans identifying this peptide, referenced against the msms

Name Separator Description
Proteins Identifiers of proteins this site is associated with.
Positions within proteins For each protein identifier in the 'Proteins' column you find here the psoition of the site in the respective protein sequence. The index of the first amino acid in the sequence is 1.

Leading proteins
Protein Identifier of the protein this peptide is associated with.

Fasta headers
Descriptions of proteins this peptide is associated with.
Localization prob Score diff PEP The posterior error probability (PEP) of the best identified modified peptide containing this site.

Score
The Andromeda score of the best identified modified peptide containing this site. Delta score The Andromeda delta score of the best identified modified peptide containing this site.

Score for localization
The Andromeda score of the MS/MS spectrum used for calculating the localization score for this site.

Mass error [ppm]
Mass error of the recalibrated mass-over-charge value of the precursor ion in comparison to the predicted monoisotopic mass of the identified peptide sequence.

Intensity
Summed up eXtracted Ion Current (XIC) of all isotopic clusters associated with the identified AA sequence. In case of a labeled experiment this is the total intensity of all the isotopic patterns in the label cluster.

Intensity___1
Summed up eXtracted Ion Current (XIC) of all isotopic clusters associated with the identified AA sequence. In case of a labeled experiment this is the total intensity of all the isotopic patterns in the label cluster.

Intensity___2
Summed up eXtracted Ion Current (XIC) of all isotopic clusters associated with the identified AA sequence. In case of a labeled experiment this is the total intensity of all the isotopic patterns in the label cluster.

Intensity___3
Summed up eXtracted Ion Current (XIC) of all isotopic clusters associated with the identified AA sequence. In case of a labeled experiment this is the total intensity of all the isotopic patterns in the label cluster.

Ratio mod/base
Intensity Control 1 Summed up eXtracted Ion Current (XIC) of all isotopic clusters associated with the identified AA sequence. In case of a labeled experiment this is the total intensity of all the isotopic patterns in the label cluster.
Intensity Control 2 Summed up eXtracted Ion Current (XIC) of all isotopic clusters associated with the identified AA sequence. In case of a labeled experiment this is the total intensity of all the isotopic patterns in the label cluster.
Intensity Control 3 Summed up eXtracted Ion Current (XIC) of all isotopic clusters associated with the identified AA sequence. In case of a labeled experiment this is the total intensity of all the isotopic patterns in the label cluster.
Intensity H2O2 1 Summed up eXtracted Ion Current (XIC) of all isotopic clusters associated with the identified AA sequence. In case of a labeled experiment this is the total intensity of all the isotopic patterns in the label cluster.
Intensity H2O2 2 Summed up eXtracted Ion Current (XIC) of all isotopic clusters associated with the identified AA sequence. In case of a labeled experiment this is the total intensity of all the isotopic patterns in the label cluster.
Intensity H2O2 3 Summed up eXtracted Ion Current (XIC) of all isotopic clusters associated with the identified AA sequence. In case of a labeled experiment this is the total intensity of all the isotopic patterns in the label cluster. Intensity Control 1___1 Summed up eXtracted Ion Current (XIC) of all isotopic clusters associated with the identified AA sequence. In case of a labeled experiment this is the total intensity of all the isotopic patterns in the label cluster.
Intensity Control 1___2 Summed up eXtracted Ion Current (XIC) of all isotopic clusters associated with the identified AA sequence. In case of a labeled experiment this is the total intensity of all the isotopic patterns in the label cluster.
Intensity Control 1___3 Summed up eXtracted Ion Current (XIC) of all isotopic clusters associated with the identified AA sequence. In case of a labeled experiment this is the total intensity of all the isotopic patterns in the label cluster.
Intensity Control 2___1 Summed up eXtracted Ion Current (XIC) of all isotopic clusters associated with the identified AA sequence. In case of a labeled experiment this is the total intensity of all the isotopic patterns in the label cluster.
Intensity Control 2___2 Summed up eXtracted Ion Current (XIC) of all isotopic clusters associated with the identified AA sequence. In case of a labeled experiment this is the total intensity of all the isotopic patterns in the label cluster.
Intensity Control 2___3 Summed up eXtracted Ion Current (XIC) of all isotopic clusters associated with the identified AA sequence. In case of a labeled experiment this is the total intensity of all the isotopic patterns in the label cluster.
Intensity Control 3___1 Summed up eXtracted Ion Current (XIC) of all isotopic clusters associated with the identified AA sequence. In case of a labeled experiment this is the total intensity of all the isotopic patterns in the label cluster.
Intensity Control 3___2 Summed up eXtracted Ion Current (XIC) of all isotopic clusters associated with the identified AA sequence. In case of a labeled experiment this is the total intensity of all the isotopic patterns in the label cluster.
Intensity Control 3___3 Summed up eXtracted Ion Current (XIC) of all isotopic clusters associated with the identified AA sequence. In case of a labeled experiment this is the total intensity of all the isotopic patterns in the label cluster.
Intensity H2O2 1___1 Summed up eXtracted Ion Current (XIC) of all isotopic clusters associated with the identified AA sequence. In case of a labeled experiment this is the total intensity of all the isotopic patterns in the label cluster.

Intensity H2O2 1___2
Summed up eXtracted Ion Current (XIC) of all isotopic clusters associated with the identified AA sequence. In case of a labeled experiment this is the total intensity of all the isotopic patterns in the label cluster.
Intensity H2O2 1___3 Summed up eXtracted Ion Current (XIC) of all isotopic clusters associated with the identified AA sequence. In case of a labeled experiment this is the total intensity of all the isotopic patterns in the label cluster.
Intensity H2O2 2___1 Summed up eXtracted Ion Current (XIC) of all isotopic clusters associated with the identified AA sequence. In case of a labeled experiment this is the total intensity of all the isotopic patterns in the label cluster.
Intensity H2O2 2___2 Summed up eXtracted Ion Current (XIC) of all isotopic clusters associated with the identified AA sequence. In case of a labeled experiment this is the total intensity of all the isotopic patterns in the label cluster.
Intensity H2O2 2___3 Summed up eXtracted Ion Current (XIC) of all isotopic clusters associated with the identified AA sequence. In case of a labeled experiment this is the total intensity of all the isotopic patterns in the label cluster.
Intensity H2O2 3___1 Summed up eXtracted Ion Current (XIC) of all isotopic clusters associated with the identified AA sequence. In case of a labeled experiment this is the total intensity of all the isotopic patterns in the label cluster. Intensity H2O2 3___2 Summed up eXtracted Ion Current (XIC) of all isotopic clusters associated with the identified AA sequence. In case of a labeled experiment this is the total intensity of all the isotopic patterns in the label cluster.
Intensity H2O2 3___3 Summed up eXtracted Ion Current (XIC) of all isotopic clusters associated with the identified AA sequence. In case of a labeled experiment this is the total intensity of all the isotopic patterns in the label cluster. Reverse When marked with '+', this particular peptide was found to be part of a protein derived from the reversed part of the protein sequence database. These should be removed for further data analysis.
Potential contaminant When marked with '+', this particular peptide was found to be part of a commonly occurring contaminant. These should be removed for further data analysis.
id A unique (consecutive) identifier for each row in the site table, which is used to cross-link the information in this file with the information stored in the other files.

Protein group IDs
The identifier of the protein-group this peptide sequence is associated with, which can be used to look up the extended protein information in the file 'proteinGroups.txt'. As a single peptide can be linked to multiple proteins (e.g. in the case of razor-proteins), multiple id's can be stored here separated by a semicolon. As a protein can be identified by multiple peptides, the same id can be found in different rows.

Positions
The positions of the modifications in the protein amino acid sequence.

Position
The position of the modification in the protein amino acid sequence.
Peptide IDs Identifier(s) of the associated peptide sequence(s) summary, which can be found in the file 'peptides.txt'.
Mod. peptide IDs Identifier(s) of the associated peptide sequence(s) summary, which can be found in the file 'modificationSpecificPeptides.txt'.
Evidence IDs Identifier(s) for analyzed peptide evidence associated with the protein group referenced against the evidences table.

MS/MS IDs
The identifiers of the MS/MS scans identifying this peptide, referenced against the msms The Protein Groups table contains information on the identified proteins in the processed raw-files. Each single row contains the group of proteins that could be reconstructed from a set of peptides.

Name Separator Description
Protein IDs Identifier(s) of protein(s) contained in the protein group. They are sorted by number of identified peptides in descending order.

Majority protein IDs
These are the IDs of those proteins that have at least half of the peptides that the leading protein has.
Peptide counts (all) Number of peptides associated with each protein in protein group, occuring in the order as the protein IDs occur in the 'Protein IDs' column. Here distinct peptide sequences are counted. Modified forms or different charges are counted as one peptide.
Peptide counts (razor+unique) Number of peptides associated with each protein in protein group, occuring in the order as the protein IDs occur in the 'Protein IDs' column. Here distinct peptide sequences are counted. Modified forms or different charges are counted as one peptide.
Peptide counts (unique) Number of peptides associated with each protein in protein group, occuring in the order as the protein IDs occur in the 'Protein IDs' column. Here distinct peptide sequences are counted. Modified forms or different charges are counted as one peptide.
Fasta headers Fasta headers(s) of protein(s) contained within the group.
Number of proteins Number of proteins contained within the group. This corresponds to the number of entries in the colum 'Protein IDs'.

Peptides
The total number of peptide sequences associated with the protein group (i.e. for all the proteins in the group).
Razor + unique peptides The total number of razor + unique peptides associated with the protein group (i.e. these peptides are shared with another protein group).

Unique peptides
The total number of unique peptides associated with the protein group (i.e. these peptides are not shared with another protein group). Percentage of the sequence that is covered by the identified peptides of the best protein sequence contained in the group.
Unique + razor sequence coverage [%] Percentage of the sequence that is covered by the identified unique and razor peptides of the best protein sequence contained in the group.

Unique sequence coverage [%]
Percentage of the sequence that is covered by the identified unique peptides of the best protein sequence contained in the group.

Mol. weight [kDa]
Molecular weight of the leading protein sequence contained in the protein group.

Sequence length
The length of the leading protein sequence contained in the group.

Sequence lengths
The length of all sequences of the proteins contained in the group.
Q-value This is the ratio of reverse to forward protein groups.

Score
Protein score which is derived from peptide posterior error probabilities.

Sequence coverage Control 1 [%]
Percentage of the sequence that is covered by the identified peptides in this sample of the longest protein sequence contained within the group.

Sequence coverage Control 2 [%]
Percentage of the sequence that is covered by the identified peptides in this sample of the longest protein sequence contained within the group.

Sequence coverage Control 3 [%]
Percentage of the sequence that is covered by the identified peptides in this sample of the longest protein sequence contained within the group.

Sequence coverage H2O2 1 [%]
Percentage of the sequence that is covered by the identified peptides in this sample of the longest protein sequence contained within the group.

Sequence coverage H2O2 2 [%]
Percentage of the sequence that is covered by the identified peptides in this sample of the longest protein sequence contained within the group.

Sequence coverage H2O2 3 [%]
Percentage of the sequence that is covered by the identified peptides in this sample of the longest protein sequence contained within the group.

Intensity
Summed up eXtracted Ion Current (XIC) of all isotopic clusters associated with the identified AA sequence. In case of a labeled experiment this is the total intensity of all the isotopic patterns in the label cluster.
Intensity Control 1 Summed up eXtracted Ion Current (XIC) of all isotopic clusters associated with the identified AA sequence. In case of a labeled experiment this is the total intensity of all the isotopic patterns in the label cluster.
Intensity Control 2 Summed up eXtracted Ion Current (XIC) of all isotopic clusters associated with the identified AA sequence. In case of a labeled experiment this is the total intensity of all the isotopic patterns in the label cluster.
Intensity Control 3 Summed up eXtracted Ion Current (XIC) of all isotopic clusters associated with the identified AA sequence. In case of a labeled experiment this is the total intensity of all the isotopic patterns in the label cluster.
Intensity H2O2 1 Summed up eXtracted Ion Current (XIC) of all isotopic clusters associated with the identified AA sequence. In case of a labeled experiment this is the total intensity of all the isotopic patterns in the label cluster.
Intensity H2O2 2 Summed up eXtracted Ion Current (XIC) of all isotopic clusters associated with the identified AA sequence. In case of a labeled experiment this is the total intensity of all the isotopic patterns in the label cluster.
Intensity H2O2 3 Summed up eXtracted Ion Current (XIC) of all isotopic clusters associated with the identified AA sequence. In case of a labeled experiment this is the total intensity of all the isotopic patterns in the label cluster.

Reverse
When marked with '+', this particular protein group contains no protein, made up of at least 50% of the peptides of the leading protein, with a peptide derived from the reversed part of the decoy database. These should be removed for further data analysis. The 50% rule is in place to prevent spurious protein hits to erroneously flag the protein group as reverse.
Potential contaminant When marked with '+', this particular protein group was found to be a commonly occurring contaminant. These should be removed for further data analysis.
id A unique (consecutive) identifier for each row in the proteinGroups table, which is used to cross-link the information in this file with the information stored in the other files.
Peptide IDs Identifier(s) of the associated peptide sequence(s) summary, which can be found in the file 'peptides.txt'.
Peptide is razor Indicates for each peptide ID if it is a razor or group unique peptide (true) or a non unique non razor peptide (false).

Name Separator Description
Raw file Name of the raw file the spectral data was extracted from.

Type
The type of detection for the peptide. SILAC -A SILAC pair was detected. ISO -An isotope pattern was detected.

Charge
The charge state of the peptide. m/z The mass divided by the charge of the charged peptide.

Mass
The mass of the neutral peptide ((m/z-proton) * charge).
Uncalibrated m/z m/z before recalibrations have been applied.

Resolution
The resolution of the peak detected for the peptide measured in Full Width at Half Maximum (FWHM).

Number of data points
The number of data points (peak centroids) collected for this peptide feature.

Number of scans
The number of MS scans that the 3d peaks of this peptide feature are overlapping with.

Number of isotopic peaks
The number of isotopic peaks contained in this peptide feature.
PIF Short for Parent Ion Fraction; indicates the fraction the target peak makes up of the total intensity in the inclusion window.

Mass fractional part
The values after the radix point (ie value -floor(value)).

Mass deficit
Empirically derived deviation measure to the next nearest integer scaled to center around 0. Can be used to visually detect contaminants in a plot setting Mass against this value. m*a+b -round(m*a+b) m: the peptide mass a: 0.999555 b: -0.10

Mass precision [ppm]
The precision of the mass detection of the peptide in parts-permillion.
Max intensity m/z 0 Summed up eXtracted Ion Current (XIC) of all isotopic clusters associated with the identified AA sequence. In case of a labeled experiment this is the total intensity of all the isotopic patterns in the label cluster.

Retention time
The retention time of the peak detected for the peptide measured in minutes.

Retention Length
The total retention time width of the peak (last timepoint -first timepoint) in seconds.

Retention Length (FWHM)
The full width at half maximum value retention time width of the peak in seconds.

Min scan number
The first scan-number at which the peak was encountered.

Max scan number
The last scan-number at which the peak was encountered.

Identified
When marked with '+' this particular MS/MS scan was identified as a peptide; when marked with '-' no identification was made.

MS/MS IDs
Unique identifier linking this identification to the MS/MS scans.

Sequence
The identified AA sequence of the peptide.

Length
The length of the sequence stored in the column "Sequence".

Modifications
Post-translational modifications contained within the sequence. When no modifications exist, this is set to 'unmodified'.
Note: This column only set when this MS/MS spectrum has been identified.
Modified sequence Sequence representation of the peptide including location(s) of modified AAs.
Note: This column only set when this MS/MS spectrum has been identified.

Proteins
Identifiers of proteins this peptide is associated with.
Note: This column only set when this MS/MS spectrum has been identified.

Score
The score of the identification (higher is better).
Note: This column only set when this MS/MS spectrum has been identified.

Intensity
Summed up eXtracted Ion Current (XIC) of all isotopic clusters associated with the identified AA sequence. In case of a labeled experiment this is the total intensity of all the isotopic patterns in the label cluster.

Intensities
The intensity values of the isotopes.

MS/MS Count
The number of MS/MS spectra recorded for the peptide.

MSMS Scan Numbers
The scan numbers where the MS/MS spectra were recorded.

MSMS Isotope Indices
Indices of the isotopic peaks that the MS/MS spectra reside on. A value of 0 corresponds to the monoisotopic peak.

MS scans
The msScans table contains information about the full scans, which can be used to verify data quality and generated useful statistics about the interaction between the samples and LC.

Name Separator Description
Raw file The name of the RAW-file the mass spectral data originates from.

Scan number
The scan number (defined in the raw-file) at which the full scan was made.

Scan index
The consecutive index of this full scan.

Retention time
The retention time at which the full scan was made.

Cycle time
The total time (full scan including the tandem MS scans) this full scan has taken up.

Ion injection time
The total injection time that was required to capture the specified amount of ions. This value is limited by a maximum, which can be used to determine whether the time has maxed out (indicative of a bad acquisition).

Base peak intensity
The intensity of the most intense ion in the spectrum.

Total ion current
The total intensity acquired in the full scan.

MS/MS count
The number of tandem MS scans that were made based on this full scan (e.g. a top 10 method selects the top 10 most intense ions in the scan and fragments those).

Mass calibration
The applied mass correction in Th to the full scan.

Peak length
The average time between the start and the end of the peaks detected in the full scan.

Isotope pattern length
The average time between the start and the end of the isotope patterns detected in the full scan.

Multiplet length
The average time between the start and the end of the isotope patterns of the labeling multiplets detected in the full scan.
Peaks / s The average number of peaks detected per second of chromatography.
Single peaks / s The average number of single peaks detected per second of chromatography.
Isotope patterns / s The average number of isotope patterns detected per second of chromatography.
Single isotope patterns / s The average number of single isotope patterns detected per of second chromatography.
Multiplets / s The average number of labeling multiplets detected per of second chromatography.
Identified multiplets / s The percentage of labeling multiplets actually identified.

Multiplet identification rate [%]
The percentage of the detected labeling multiplets that were identified.

MS/MS / s
The average number of MS/MS events per second of chromatography.
Identified MS/MS / s The average number of identified MS/MS events per second of chromatography.

MS/MS identification rate [%]
The percentage of tandem MS scans that were identified.

Intens Comp Factor
Taken from the Thermo RAW file.

CTCD Comp
Taken from the Thermo RAW file.

RawOvFtT
For Thermo Fisher only. TIC estimation done with the orbitrap cell.

AGC Fill
Taken from the Thermo RAW file.

Raw file
The name of the RAW-file the mass spectral data was derived from. For time of flight instruments only.

Base peak intensity
The intensity of the most intense ion in the spectrum.

Elapsed time
The time the MS/MS scan took to complete.

Identified
When marked with '+' this particular MS/MS scan was identified as a peptide; when marked with '-' no identification was made.

MS/MS IDs
Unique identifier linking this identification to the MS/MS scans.

Sequence
The identified AA sequence of the peptide.

Length
The length of the sequence stored in the column "Sequence".
Filtered peaks Number of peaks after the 'top X per 100 Da' filtering.
m/z Recalibrated m/z of the precursor ion.

Mass
Charge corrected mass of the precursor ion.

Charge
Charge state of the precursor ion.

Type
The type of precursor ion as identified by MaxQuant. ISOisotopic cluster. PEAK -single peak. MULTI -labeling cluster.

Fragmentation
The type of fragmentation used to create the MS/MS spectrum. CID -Collision Induced Dissociation. HCD -High energy Collision induced Dissociation. ETD -Electron Transfer Dissociation.

Mass analyzer
The mass analyzer used to record the MS/MS spectrum. ITMS -Ion trap. FTMS -Fourier transform ICR or orbitrap cell. TOF -Time of flight.

Parent intensity fraction
The percentage the parent ion intensity makes up of the total intensity in the selection window.
Fraction of total spectrum The percentage the parent ion intensity makes up of the total intensity of the whole MS spectrum.
Base peak fraction The percentage the parent ion intensity in comparison to the highest peak in he MS spectrum.
Precursor full scan number The full scan number where the precursor ion was selected for fragmentation.

Precursor intensity
The intensity of the precursor ion at the scannumber it was selected.
Precursor apex fraction The fraction the intensity of the precursor ion makes up of the peak (apex) intensity.
Precursor apex offset How many full scans the precursor ion is offset from the peak (apex) position.
Precursor apex offset time How much time the precursor ion is offset from the peak (apex) position.

Scan event number
This number indicates which MS/MS scan this one is in the consecutive order of the MS/MS scans that are acquired after an MS scan.

Modifications
Post-translational modifications contained within the sequence. When no modifications exist, this is set to 'unmodified'.
Note: This column only set when this MS/MS spectrum has been identified.
Modified sequence Sequence representation of the peptide including location(s) of modified AAs.
Note: This column only set when this MS/MS spectrum has been identified.

Proteins
Identifiers of proteins this peptide is associated with.
Note: This column only set when this MS/MS spectrum has been identified.

Score
The score of the identification (higher is better).
Note: This column only set when this MS/MS spectrum has been identified.

Experiment
Intens Comp Factor Taken from the Thermo RAW file.

CTCD Comp
Taken from the Thermo RAW file.

RawOvFtT
For Thermo Fisher only. TIC estimation done with the orbitrap cell.

AGC Fill
Taken from the Thermo RAW file.

Scan index
Consecutive index of the MS/MS spectrum.

MS scan index
Consecutive index of the MS spectrum prior to this MS/MS spectrum.
MS scan number Scan number of the MS spectrum prior to this MS/MS spectrum.

Raw file
The name of the RAW file the mass spectral data was read from.

Scan number
The RAW-file derived scan number of the MS/MS spectrum.

Scan index
The consecutive index of the MS/MS spectrum.

Sequence
The identified AA sequence of the peptide.

Length
The length of the sequence stored in the column "Sequence".
Missed cleavages Number of missed enzymatic cleavages.

Modifications
Post-translational modifications contained within the identified peptide sequence.
Modified sequence Sequence representation including the post-translational modifications (abbreviation of the modification in brackets before the modified AA). The sequence is always surrounded by underscore characters ('_').

Proteins
The identifiers of the proteins the identified peptide is associated with.

Charge
The charge state of the precursor ion.

Fragmentation
The type of fragmentation used to create the MS/MS spectrum. CID -Collision Induced Dissociation. HCD -High energy Collision induced Dissociation. ETD -Electron Transfer Dissociation.

Mass analyzer
The mass analyzer used to record the MS/MS spectrum. ITMS -Ion trap. FTMS -Fourier transform ICR or orbitrap cell. TOF -Time of flight.

Type
The type of precursor ion as identified by MaxQuant. ISOisotopic cluster. PEAK -single peak. MULTI -labeling cluster.

Scan event number
Isotope index m/z The mass-over-charge of the precursor ion.

Mass
The charge corrected mass of the precursor ion.

Mass Error [ppm]
Mass error of the recalibrated mass-over-charge value of the precursor ion in comparison to the predicted monoisotopic mass of the identified peptide sequence.

Simple Mass Error [ppm]
Retention time The uncalibrated retention time in minutes where the MS/MS spectrum has been acquired.

PEP
Posterior Error Probability of the identification. This value essentially operates as a p-value, where smaller is more significant.

Score
Andromeda score for the best associated MS/MS spectrum.
Delta score Score difference to the second best identified peptide with a different amino acid sequence.
Score diff Score difference to the second best positioning of modifications identified peptide with the same amino acid sequence.

Localization prob
Combinatorics Number of possible distributions of the modifications over the peptide sequence.
PIF Short for Parent Ion Fraction; indicates the fraction the target peak makes up of the total intensity in the inclusion window.

Fraction of total spectrum
The percentage the parent ion intensity makes up of the total intensity of the whole spectrum.
Base peak fraction The percentage the parent ion intensity in comparison to the highest peak in he MS spectrum.

Precursor Full ScanNumber
The full scannumber where the precursor ion was selected for fragmentation.

Precursor Intensity
The intensity of the precursor ion at the scannumber it was selected.

Precursor Apex Fraction
The fraction the intensity of the precursor ion makes up of the peak (apex) intensity.
Precursor Apex Offset How many full scans the precursor ion is offset from the peak (apex) position.
Precursor Apex Offset Time How much time the precursor ion is offset from the peak (apex) position.

Matches
The species of the peaks in the fragmentation spectrum after TopN filtering.

Intensities
The intensities of the peaks in the fragmentation spectrum after TopN filtering.

Mass Deviations [Da]
The mass deviation of each peak in the fragmentation spectrum in absolute mass units.

Mass Deviations [ppm]
The mass deviation of each peak in the fragmentation spectrum in parts per million.

Masses
The masses-over-charge of the peaks in the fragmentation spectrum.

Number of Matches
The number of peaks matching to the predicted fragmentation spectrum.

Intensity coverage
The fraction of intensity in the MS/MS spectrum that is annotated.

Peak coverage
The fraction of peaks in the MS/MS spectrum that are annotated.
Neutral loss level How many neutral losses were applied to each fragment in the Andromeda scoring.
ETD identification type For ETD spectra several different combinations of ion series are scored. Here the highest scoring combination is indicated Reverse When marked with '+', this particular peptide was found to be part of a protein derived from the reversed part of the decoy database. These should be removed for further data analysis.

All scores
All sequences All modified sequences id A unique (consecutive) identifier for each row in the msms table, which is used to cross-link the information in this file with the information stored in the other files.

Protein group IDs
The identifier of the protein-group this redundant peptide sequence is associated with, which can be used to look up the extended protein information in the file 'proteinGroups.txt'. As a single peptide can be linked to multiple proteins (e.g. in the case of razor-proteins), multiple id's can be stored here separated by a semicolon. As a protein can be identified by multiple peptides, the same id can be found in different rows.
Peptide ID The identifier of the non-redundant peptide sequence.
Mod. peptide ID Identifier of the associated modification summary stored in the file 'modificationSpecificPeptides.txt'.
Evidence ID Identifier of the associated evidence stored in the file 'evidence.txt'.
Carbamidomethyl (C) site IDs Identifier of the oxidation summary stored in the file 'Carbamidomethyl (C)Sites.txt'.

Oxidation (M) site IDs
Identifier of the oxidation summary stored in the file 'Oxidation (M)Sites.txt'.
Oxidation(C) site IDs Identifier of the oxidation summary stored in the file 'Oxidation(C)Sites.txt'.
Oxidation(WYF) site IDs Identifier of the oxidation summary stored in the file 'Oxidation(WYF)Sites.txt'.

Name Separator Description
id A unique (consecutive) identifier for each row in the AIF MS/MS table, which is used to cross-link the information in this file with the information stored in the other files.

Protein group IDs
The identifier of the protein group this redundant peptide sequence is associated with, which can be used to look up the extended protein information in the file 'proteinGroups.txt'. As a single peptide can be linked to multiple proteins (e.g. in the case of razor-proteins), multiple id's can be stored here separated by a semicolon. As a protein can be identified by multiple peptides, the same id can be found in different rows.
Peptide ID The identifier of the non-redundant peptide sequence.
Mod. peptide ID Identifier of the associated modification summary stored in the file 'modificationSpecificPeptides.txt'.
Evidence ID Identifier for analyzed peptide evidence associated with the protein group referenced against the evidences

Raw file
Name of the RAW file the spectral data was extracted from, which led to the identification of this peptide.

Sequence
The identified AA sequence of the peptide.

Length
The length of the sequence stored in the column "Sequence".

Missed Cleavages
Number of missed enzymatic cleavages.

Modifications
Post-translational modifications contained within the sequence. When no modifications exist, this is set to 'unmodified'. Note: This column only set when this MS/MS spectrum has been identified.
Modified Sequence Sequence representation of the peptide including location(s) of modified AAs. Note: This column only set when this MS/MS spectrum has been identified.

Proteins
The IPI identifiers of the proteins the identified peptide is associated with.

Charge
The charge of the precursor ion. m/z The mass-over-charge of the precursor ion.

Mass
The charge corrected mass of the precursor ion.

Retention time
The uncalibrated retention time in minutes in the elution profile of the precursor ion.

Precursor intensity
The intensity of the precursor ion.

PEP
Posterior Error Probability of the identification. This value essentially operates as a p-value, where smaller is more significant.

Score
Andromeda identification score for the MS/MS spectrum.
Delta score Score difference to the second best identified peptide.

Combinatorics
Number of possible distributions of the modifications over the peptide sequence.

Intensities
The intensities of the peaks in the fragmentation spectrum after top-N filtering.

Mass Deviations
The search engine allowed mass deviations of the peaks in the fragmentation spectrum.

Masses
The masses-over-charge of the peaks in the fragmentation spectrum.

Number of Matches
Reverse When marked with '+', this particular peptide was found to be part of a protein derived from the reversed part of the decoy database. These should be removed for further data analysis.