United States Department of Agriculture

Agricultural Marketing Service, Science & Technology

Pesticide Data Program

SOP No.: PDP-DATA Page 1 of 32

Title: Data and Instrumentation

Revision: 11 Replaces: 03/01/23 Effective: 03/01/24

1. Purpose:

To provide standard procedures for:

• Instruments, equipment, and injection sequence used in the USDA/AMS Pesticide Data 

Program (PDP). See SOP PDP-ADMIN for administrative requirements (e.g., 

purchase approval, PDP equipment inventory system, instructions for permission to 

salvage, transfer or dispose of equipment, etc.).

• Quantitative and qualitative analysis of pesticide residues determined for the 

USDA/AMS PDP.

• Data reduction, reporting, and submission by participating laboratories.

2. Scope:

This standard operating procedure (SOP) shall be followed by all laboratories conducting residue 

studies for PDP, including support laboratories conducting stability or other types of studies that 

may impact the program.

3. Outline of Procedures:

5. Instrumentation

5.1 SOPs and Manuals

5.2 Maintenance

5.3 Performance Verification

5.4 Records

6. Calibration

6.1 Calibration Integrity

6.2 Quantification Using Calibration Curves

6.3 Quantification Using Single Point Comparisons

6.4 Quantification of Multi-Peak Compounds

6.5 Quantification of Spikes

7. Generating Raw Data

7.1 Injection sequence description

7.2 Retention Time Criteria (Selective Detection and MS Systems) 

7.3 MS Confirmation Criteria
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SOP No.: PDP-DATA Page 2 of 32

Title: Data and Instrumentation

Revision: 11 Replaces: 03/01/23 Effective: 03/01/24

7.4 MS Documentation Criteria

8. Data Handling

8.1 Raw Data Handling

8.2 Hardcopy Data Package Requirements

9. Data Reporting

9.1 Calculations and Significant Figures

9.2 Determination of Residue Concentrations for PDP Reporting Purposes

9.3 Administrative Reporting Level

9.4 PDP Tolerance Table

9.5 Non-violative results

9.6 Presumptive Tolerance Violations (PTV) 

9.7 Tolerance Interpretation for Processed Commodities

9.8 Reporting Proficiency Testing (PT) Results

10. Data Review

11. Remote Data Entry (RDE) System

11.1 RDE System Administration

11.2 RDE System Access

11.3 RDE Data Entry

11.4 RDE Data Sign-off and Transmission

Attachment 1. Laboratory Information Form (LIF) Codes

Attachment 2. Flowchart for Reporting Codes

Attachment 3. Glossary of Mass Spectrometry Terms and Acronyms

4. References:

• Bethem, R.A., Boison, J., Gale, J., Heller, D., Lehotay, S., Loo, J., Mussler, S., Price, P., Stein, 

S., Establishing the Fitness for Purpose of Mass Spectrometric Methods, J. Am. Soc. Mass 

Spectrom. 14 (2003) 528-541 https://pubmed.ncbi.nlm.nih.gov/12745222/

• Busch, K.L., A Glossary for Mass Spectrometry, Mass Spectrometry, Supplement to LC/GC, 

17 (6S), S26-S34 (2002)

https://www.waters.com/webassets/cms/library/docs/720000807en.pdf
United States Department of Agriculture

Agricultural Marketing Service, Science & Technology

Pesticide Data Program

SOP No.: PDP-DATA Page 3 of 32

Title: Data and Instrumentation

Revision: 11 Replaces: 03/01/23 Effective: 03/01/24

• Cairns, T. and Siegmund, E.G., Regulatory Pesticide Analysis by Mass Spectrometry, 

Analytical Methods for Pesticides and Plant Growth Regulators, Ed. Gunter Zweig, Vol. 14, 

pp. 193-253, Academic Press, New York, 1982 

https://www.sciencedirect.com/science/article/pii/B9780127843148500098?via%3Dihub

• Chapman, J.R., Practical Organic Mass Spectrometry: A Guide for Chemical and Biochemical 

Analysis, 2

nd Edition, John Wiley & Sons, West Sussex, UK, 1993

• FDA Center for Veterinary Medicine, Guidance for Industry: Mass Spectrometry for 

Confirmation of the Identity of Animal Drug Residues, Final Guidance, US Department of 

Health and Human Services, Rockville, MD, Guide #118, May 1, 2003. 

https://www.fda.gov/media/70154/download

• FDACS, QA/QC Guideline Document, Section 14

https://www.fdacs.gov/content/download/89978/file/feed-rule.pdf

• FIFRA, Pesticide Emergency Exemptions, Section 18, 40 CFR Part 160

https://www.ecfr.gov/current/title-40/chapter-I/subchapter-E/part-166

• Garfield, F.M., Quality Assurance Principles for Analytical Laboratories, AOAC, 1991

• Hites, R.A., Handbook of Mass Spectra of Environmental Contaminants, Lewis Publishers, 

Boca Raton, FL, 1992

• Horwitz, W., Evaluation of Analytical Methods Used for Regulation of Foods and Drugs,

Analytical Chemistry, Vol. 54, No. 1, pp. 67A-76A, 1982

https://pubs.acs.org/doi/10.1021/ac00238a765

• Middleditch, B.S., Missler, S.R., Hines, H.B., Mass Spectrometry of Priority Pollutants,

Plenum Press, New York, 1981

https://analyticalsciencejournals.onlinelibrary.wiley.com/doi/abs/10.1002/jat.2550010615

• Mishalanie, E., Enigma Analytical, May 9, 2000

• Parker, G.A., Validation of Methods Used in the Florida Department of Agriculture and 

Consumer Services' Chemical Residue Laboratory, JAOAC, 74, No. 5, pp. 868-871, 1991

• Sphon, J.A. Use of Mass Spectrometry for Confirmation of Animal Drug Residues, J. Assoc. 

Off. Anal. Chem. 61 (1978) 1247-1252 https://pubmed.ncbi.nlm.nih.gov/721737/

• Taylor, J.K., Quality Assurance of Chemical Measurements, Lewis Publishers, 1989

https://www.semanticscholar.org/paper/Quality-assurance-of-chemical-measurements-%3ALewis-Taylor-Tranter/50f139e39d4456349b61c3e805cc5735f7e07294

• US EPA, Maintenance and calibration of equipment, 40 CFR 160.63
United States Department of Agriculture

Agricultural Marketing Service, Science & Technology

Pesticide Data Program

SOP No.: PDP-DATA Page 4 of 32

Title: Data and Instrumentation

Revision: 11 Replaces: 03/01/23 Effective: 03/01/24

https://www.ecfr.gov/current/title-40/chapter-I/subchapter-E/part-160/subpart-D/section160.63

• US EPA, Standard operating procedures, 40 CFR 160.81

https://www.govinfo.gov/app/details/CFR-2012-title40-vol25/CFR-2012-title40-vol25-sec160-

81/summary

• US EPA, Conduct of a study, 40 CFR Part 160.130

https://www.govinfo.gov/app/details/CFR-2006-title40-vol23/CFR-2006-title40-vol23-

sec160-130

• US EPA, Appendix A, 40 CFR Part 136

https://www.ecfr.gov/current/title-40/chapter-I/subchapter-D/part-136

• US EPA, Reporting of study results, 40 CFR Part 160.185

https://www.ecfr.gov/current/title-40/chapter-I/subchapter-E/part-160/subpart-J/section160.185

• US EPA, Tolerances and Exemptions from Tolerances for Pesticide Chemicals in Food, 40 

CFR Subchapter E, Part 180

https://www.ecfr.gov/current/title-40/chapter-I/subchapter-E/part-180

• US EPA/OPPTS, Processed Food/Feed, 860.1520

https://www.epa.gov/test-guidelines-pesticides-and-toxic-substances/series-860-residuechemistry-test-guidelines

• USDA/FDA, Food and Drugs, 21 CFR Part 175.105

https://www.ecfr.gov/current/title-21/chapter-I/subchapter-B/part-175/subpart-B

Note: References consulted in the preparation of this SOP document.

5. Instrumentation:

5.1 SOPs and Manuals

Each laboratory shall develop SOPs for PDP equipment operation. The SOPs shall set forth in 

sufficient detail the methods, materials, and schedules to be used in the routine inspection, 

cleaning, maintenance, testing, calibration, and/or performance verification of equipment used, 

and shall, when appropriate, specify remedial action to be taken in the event of failure or 

malfunction of equipment. SOPs and operator manuals shall be readily accessible to applicable 
United States Department of Agriculture

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Pesticide Data Program

SOP No.: PDP-DATA Page 5 of 32

Title: Data and Instrumentation

Revision: 11 Replaces: 03/01/23 Effective: 03/01/24

laboratory staff. Manufacturer’s manuals or published literature may be used as supplements to 

SOPs.

5.2 Maintenance

All instruments and other equipment used in the analysis of PDP samples shall be inspected, cleaned, 

and maintained in proper working condition to ensure the accuracy, precision, and sensitivity 

requirements specified in this SOP and PDP-QC SOP are met.

5.3 Performance Verification

Before being placed into service, an instrument shall undergo appropriate checks to establish that 

all requirements are met. See SOP PDP-QC.

5.4 Records

5.4.1 Records (e.g., logbooks) shall be maintained for all critical equipment and 

instruments. These records shall be used to document all routine and non-routine 

inspection, maintenance, and calibration activities, including the date, the identity of the 

personnel performing the activities, and any maintenance (routine or otherwise), repairs, 

or remedial actions.

5.4.2 Data packages shall reflect the specific instruments and equipment that were used 

to generate, measure, or assess the data. Data on the performance verification of 

instruments (e.g., gas chromatograph-mass selective detector (GC-MSD), etc.) utilized in 

the analysis of a data set are to be maintained by the laboratory. See Section 8 of this 

SOP for hardcopy data package requirements. See Section 7 of this SOP for mass 

spectrometry (MS) documentation requirements.

5.4.3 Calibration and/or performance verification data for balances, refrigerators, and 

other peripheral equipment do not need to be included in the submitted data packages but

shall be maintained by the laboratory.

5.4.4 See SOP PDP-ADMIN sections 5.4 and 5.5 for records storage and archival 
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SOP No.: PDP-DATA Page 6 of 32

Title: Data and Instrumentation

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requirements.

6. Calibration:

Instruments and equipment that have significant effects on test results shall be calibrated at the 

minimum frequency specified in the laboratory’s internal SOPs.

6.1 Calibration Integrity

6.1.1 Calibration integrity is defined as steady instrument response to a given amount of 

analyte over the duration of a sample run. Calibration integrity shall be determined by 

injecting standards at the beginning and end of a run to evaluate the variability in 

instrument response and any changes in retention time (see 6.1.2). Injection of a 

standard(s) between the beginning and end of a run also may be required. Calibration 

integrity shall be calculated in terms of relative percent difference (RPD), percent 

difference (%D), or percent relative standard deviation (%RSD) using the following 

equations:

RPD =

|X1 − X2|

[

X1 + X2

2

]

× 100

where X1 is the response of the first analytical standard injected and X2 is the response of 

the second standard injected;

%D =

C1 − C2

C1

× 100

where C1 is the known concentration of the standard used for quantification and C2 is the 

concentration of that standard calculated using the calibration curve:

%RSD =

SD

avg. RF

× 100
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SOP No.: PDP-DATA Page 7 of 32

Title: Data and Instrumentation

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where SD is standard deviation:

and RF is response factor, or the area or height of each standard divided by the 

concentration of that standard.

6.1.2 Standard response drift greater than 20% RPD, %D, or RSD indicate that 

additional standards within the run may be injected in order to attempt to meet the 20% 

calibration integrity requirement. Each laboratory shall document exceptions in internal 

SOPs and shall determine the number of intermediate standards required throughout the 

run to maintain calibration integrity.

6.1.3 For cases where no residues were detected in samples and only the spike recovery 

is being quantified, the requirement for calibration integrity shall be 30%.

6.2 Quantification Using Calibration Curves

6.2.1 Incurred residue(s) may be subtracted from matrix matched standards prior to 

generating the calibration curve. A laboratory may elect to subtract incurred residue(s) if 

the following conditions are met:

• Blank matrix cannot be obtained. The laboratory shall make every effort to 

obtain blank matrix such as purchasing organic produce, saving analyzed 

samples that are pesticide free, etc.

• The incurred residue is less than 2xLOQ (Limit of Quantitation).

If a laboratory elects to subtract incurred residues from matrix matched standards, they 

shall have internal procedures on how to handle the subtraction process.
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Title: Data and Instrumentation

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6.2.2 If calibration curves are used for quantification, they shall be constructed using 

standards which bracket the expected range of residue concentration. A suggested range 

is 1xLOQ to 10xLOQ. Second-order curves (i.e., quadratic) may be employed, providing 

that a sufficient number of points (i.e., minimum of five) is used to define the curve.

6.2.3 For any analyte that is quantitated using a calibration curve, the fitness of curve, 

whether first- or second-order, shall be demonstrated in the same injection sequence used 

to report the data by one of the following accepted methods:

• correlation coefficient (where R > 0.995 / R2 > 0.990),

• percent relative standard deviation (where %RSD ≤ 20), or

• percent difference of calculated vs. known standard concentration in the curve 

(where %D is within 20%).

6.2.4 The laboratory shall specify in an internal SOP the method/parameter(s) used to 

demonstrate fitness of curve.

6.2.5 Results obtained using a calibration curve shall lay within the range of the 

calibration curve. If results fall outside the calibration curve, the sample must be diluted, 

the calibration curve extended, or the procedures for single point comparisons followed. 

The procedure for extending the range of the calibration curve shall be documented in 

internal laboratory procedures. Data generated to support extension of the calibration 

curve shall be maintained and housed with the QAU (Quality Assurance Unit).

If method range has been extended beyond the highest validated level, then samples may 

be diluted for quantitation purposes. However, dilutions must be done proportionally with 

matrix so that the matrix concentration of the sample is similar to that of the analytical 

standards used to prepare the calibration curve.

6.3 Quantification Using Single Point Comparisons

Quantification using a single standard is permitted if the sample response is within 30% of the 

standard response for samples greater than LOQ; if it is not, dilution of the sample or injection of 
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SOP No.: PDP-DATA Page 9 of 32

Title: Data and Instrumentation

Revision: 11 Replaces: 03/01/23 Effective: 03/01/24

a different standard concentration shall be required. This difference shall be calculated using the 

following equation:

Xstandard − Xsample

Xstandard

× 100

where Xstandard is the response of the standard and Xsample is the response of the sample.

6.4 Quantification of Multi-Peak Compounds

Quantification of multi-peak compounds may be based on the largest peak or the sum of all the 

peaks. Summation using the instrument’s peak integration software is preferred and, when used, 

must be applied to the multi-peak compound with consistent parameters across all samples; in this 

scenario the results do not need to be coded “E” even if one or more (but not all) peaks are <LOQ. 

Otherwise, when reporting multi-peak compounds as total (each separately integrated peak 

combined) values and one or more peaks, but not all, are Below Quantifiable Level (BQL), 

determine and report the value(s) for the BQL peak(s) using either single point quantification or 

the value calculated by the data station based on the calibration table. If one or more peaks are 

less than the Limit of Detection (LOD), or LOQ where LOD=LOQ, do not include them in 

calculating the total (combined) value. In either case, code the reported value as an estimate “E” 

in the quantification field of the analytical results section.

6.5 Quantification of Spikes

6.5.1 Incurred residue(s) may be subtracted from spike recovery(ies) prior to 

calculating the percent recovery. A laboratory may elect to subtract incurred residue(s) if 

the following conditions are met:

• Blank matrix cannot be obtained. The laboratory shall make every effort to 

obtain blank matrix such as purchasing organic produce, saving analyzed 

samples that are pesticide free, etc.

• The incurred residue is less than 2xLOQ.

• The laboratory shall report blank subtracted spike recovery data by entering the 
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SOP No.: PDP-DATA Page 10 of 32

Title: Data and Instrumentation

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amount subtracted into the comments field and entering an “S” (Incurred 

Subtracted) code in the Exception field for that compound on the QA/QC 

Recovery section of the RDE.

If a laboratory elects to subtract incurred residues, they shall have internal procedures on 

how to handle the subtraction process.

6.5.2 When a 2xLOQ spike recovery value falls below 50%, by definition, these spikes 

are quantitated using responses less than the LOQ. This is an acceptable PDP practice.

6.5.3 Incurred residues, as determined using the matrix blank, shall not be subtracted 

from the spike when the residue in the matrix blank exceeds 2xLOQ. If an incurred 

residue is greater than 2xLOQ or otherwise prevents reporting of an associated QA/QC 

recovery, an “I” (Incurred Residue) code shall be entered into the Exception field for that 

compound on the QA/QC Recovery section of the RDE for recoveries that are reported.

6.5.4 Pesticides not recovered shall be reported using an “N” (Not Recovered) code in 

the Exception field for that compound on the QA/QC Recovery section of the RDE for 

the spiked pesticide.

6.5.5 Pesticides reported as estimates shall be coded as “E” (Estimate) in the Exception 

field for that compound on the QA/QC Recovery section of the RDE for recoveries that 

are reported.

6.5.6 Pesticides reported as having matrix interference shall be coded as “M” in the 

Exception field for that compound on the QA/QC Recovery section of the RDE.

6.5.7 Pesticides reported as Marginal Performing Analytes shall be coded as “P” in the 

Exception field for that compound on the QA/QC Recovery section of the RDE.

6.5.8 Pesticides reported as unvalidated shall be coded as “U” in the Exception field for 

that compound on the QA/QC Recovery section of the RDE (refer to Attachment 2,

Flowchart for Reporting Codes).
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SOP No.: PDP-DATA Page 11 of 32

Title: Data and Instrumentation

Revision: 11 Replaces: 03/01/23 Effective: 03/01/24

7. Generating Raw Data:

7.1 Injection Sequence Description

7.1.1 Each laboratory shall develop an SOP detailing an appropriate injection sequence 

to ensure data integrity and uniform response across the sample set. “Uniform response” 

shall be construed as no greater than 20% RPD, %D, or RSD between calibration 

responses (refer to Section 6.1 of this document) or 30% if a residue was not detected and 

only the spike is being quantitated.

7.1.2 Standards for each compound analyzed shall be included with every injection 

sequence. It is recommended that standards spanning the expected range of residue 

concentrations, such as 1xLOQ to 10xLOQ, be included in the sequence to allow 

construction of a calibration curve; however, construction of a calibration curve is not 

required unless a curve is used for quantification.

7.1.3 Standards must be run at a minimum of the beginning and end of the data run to 

demonstrate calibration integrity. This may be accomplished via a single standard or a 

full set of calibration curve standards.

7.1.4 Each initial analytical run shall include the reagent blank, matrix blank, spikes, 

and samples. For additional runs (i.e., reinjects/dilutions) QC samples shall be run as 

necessary (i.e., reagent or matrix interference).

7.1.5 A non-extracted LOD standard for each compound analyzed shall be run with 

each data set as a diagnostic tool (i.e., the laboratory is not required to calculate signal-tonoise ratio (s/n), but the peak must be observable). If the peak is not observable, the 

laboratory shall take the appropriate action (e.g., raise the LOD, re-inject the standard, 

etc.). For laboratories that use in-matrix calibration standards, the LOD standard shall 

also be in-matrix. For laboratories that do not use in-matrix calibration standards, the 

LOD standard shall be in the same solution as the calibration standards.

7.2 Retention Time Criteria (Selective Detection and MS Systems)
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Title: Data and Instrumentation

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7.2.1 GC and LC Retention Time

7.2.1.1 If an external standard is used, the retention time (RT) of the compound of 

interest in the standard and the RT of the same compound in the sample shall be 

within 0.1

1 minutes.

7.2.1.2 If an internal standard is used, the relative retention time (RRT) of the 

compound of interest to the internal standard within the reference standard and the 

RRT of the compound of interest to the internal standard within the sample shall 

be within 0.01 minutes.

7.2.2 MS Screening for Identification

In order to maximize the number of compounds screened by MS systems while maximizing 

the number of scans per second and dwell times, it may be desirable to perform the initial 

identification and quantification using fewer than three ions for some or all of the 

compounds. Presumptive-positive samples shall be re-injected or data reprocessed to meet 

all MS confirmation criteria.

7.3 MS Confirmation Criteria

7.3.1 GC/MS and LC/MS Confirmation Criteria

 

7.3.1.1 A minimum of three structurally significant ions (meeting the 3:1 s/n 

ratio) are required for confirmation. For GC/MS, because the molecular ion is the 

most structurally significant ion in a mass spectrum, if it is present and meets the 

1The laboratory may perform instrument-specific retention time studies to verify stipulation of different retention time 

window criteria than those specified in this SOP. It is expected that a generally accepted method of retention time 

window calculation be used and documented to establish these criteria.
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3:1 s/n ratio, it is preferable that it be included as one of the three ions.

Note: If instrument conditions and/or ionization techniques limit the number of 

ions available, the laboratory shall request a deviation from MPD in order to 

report results under these conditions.

7.3.1.2 A pair of isotopic cluster ions may be used as two of the three structurally 

significant ions required for confirmation.

7.3.1.3 Use of fragment ions resulting from water loss to meet the three 

structurally significant ions requirement is discouraged.

7.3.1.4 The confidence limits of the relative abundance of structurally significant 

ions used for SIM and/or full scan identification shall be ± 30% (relative) when 

compared to the same relative abundances observed from a standard solution 

injection made during the same analytical run.

7.3.1.5 MS spectra produced by “soft” ionization techniques (e.g., GC/MS -

chemical ionization and for LC/MS – APCI, APPI, ESI, etc.) may require 

additional evidence for confirmation. If the isotope ratio of the ion(s) or the 

chromatographic profile of isomers of the analyte is highly characteristic, there 

may be sufficient information for confirmation. Additional evidence may consist 

of MS/MS data, use of a different ionization technique, use of a different 

chromatographic separation system, and for LC/MS systems, altering 

fragmentation by changing ionization conditions. If available, High Resolution 

MS (HRMS) may be used for additional confirmation.

7.3.1.6 GC/MS: Fragmentation that results from “soft” ionization techniques is 

highly dependent on instrument design and the conditions applied (i.e., the 

obtained spectra can widely differ). Commercially available spectral libraries 

bundled with GC/MS instruments may contain spectra generated under standard 

70eV EI conditions; therefore, the use of library search software for spectra from 

“soft” ionization techniques could result in identification errors and is 

discouraged.
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Title: Data and Instrumentation

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7.3.2 GC/MS/MS and LC/MS/MS Confirmation Criteria

7.3.2.1 Target analyte confirmation shall be performed by either (1) monitoring 

the transition of one precursor ion to at least two product ions, OR (2) monitoring 

at least two precursor-to-product ion transitions.

Multipeak compound confirmation may be based on the largest peak or the sum of 

all the peaks. If it is based on the sum of all the peaks, one or two of the constituents 

can be used for both transitions.

Note: If instrument conditions and/or ionization techniques limit the number of 

transitions available, the laboratory shall request a deviation from MPD in order 

to report results under these conditions.

7.3.2.2 The abundance of the signal from the precursor-to-product ion transition 

shall meet the 3:1 s/n ratio requirement.

7.3.2.3 The relative abundances of ion transitions used for compound 

identification in the sample shall be ± 30% (relative) when compared to the same 

relative abundances observed from a standard solution analyzed during the same 

analytical run if more than one precursor-to-product ion transition is monitored.

The ion ratio tolerance shall be calculated using the following example: If the ion 

ratio (qualifier area count/target area count) is 15%, the acceptable range will be 

15%+/-4.5 or 10.5% to19.5%.

7.3.2.4 Use of product ions resulting from water loss for identification is 

discouraged.

Note: Any information that provides a contraindication of identity of the residue 

will be addressed in the internal SOP by the laboratory.

7.3.3 When more than one confirmation method has been utilized, the method with the 
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higher level of confidence shall be entered in the Confirmation Method 1 field and the 

method with the next highest level of confidence should be entered in the Confirmation 

Method 2 field. For example, if a residue is confirmed using an alternate column and 

mass selective detector, the laboratory would most likely enter “M” in the Confirmation 

Method 1 field and “C” in the Confirmation Method 2 field of the RDE. The decision 

regarding the level of confidence of a particular confirmation is left to the discretion of 

the Technical Program Manager.

Note: The Ident Points (identification points) field of the RDE is an optional field that may 

be used to record the degree of confirmation.

7.4 MS Documentation Criteria

Structurally significant ions and/or precursor-to-product ion transitions used for confirmation shall 

be documented.

8. Data Handling:

8.1 Raw Data Handling

8.1.1 Hardcopy raw data are defined as any laboratory worksheets, logbooks, records, 

notes, chromatograms, calculations, instrument printouts, and any other data, which are 

the result of original observations and activities. Electronic raw data are the files 

generated by the instrument system.

8.1.2 For manual entry, hardcopy raw data shall be recorded directly, promptly, and 

legibly in permanent ink. Pencil or erasable pen is not acceptable. All data entries shall 

be dated on the date of entry and signed or initialed by the person entering the data. Each 

individual error shall be corrected using a single-line cross out (no white-out). It is 

recommended, but not required, that the reason for the correction be indicated. Each 

correction shall be dated and initialed. Documented error codes may be used to explain 

errors. Correction of multiple errors may be accomplished in the following manner:
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• On first occurrence of the error, or on a summary sheet, make/indicate the 

appropriate correction, including date, initials, explanation of error/error code, and 

all affected subsequent entries.

• Each subsequent occurrence of the error must then be corrected, dated, and 

initialed.

8.1.3 Each participating laboratory shall ensure sample and data traceability for raw and 

electronic data collection and processing. Chromatograms that have been reprocessed 

through the data system shall be clearly labeled.

8.1.4 Each participating laboratory shall maintain a log of names, initials, and 

signatures for all individuals who are responsible for signing or initialing any laboratory 

record.

8.2 Hardcopy Data Package Requirements

8.2.1 Routine sample data packages, PT data, and method validation data packages 

retained by the participant laboratory shall consist of laboratory records (i.e., worksheets 

and/or completed forms), USDA collection and report forms (where applicable), and 

supporting technical data in the form of chromatograms and integration reports, 

calculations, and derived data. Data requirements consist of two types, instrument and 

chromatographic. The following information shall be included in the data package.

8.2.1.1 The instrument method shall be included or referenced. Instrument 

information shall be traceable. Examples may consist of instrument type and 

identifier, detector type, injection volume, temperature parameters (injector, 

detector, oven), analytical column parameters (phase, film thickness, diameter, 

length), and instrument parameters (integration threshold, attenuation, timed 

events).

8.2.1.2 Chromatographic information shall be traceable. Examples may consist of 

sample ID, analyst name, dilution information, and date and time of injection.

8.2.2 At a minimum, hardcopies of data sets shall include the following:
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Pesticide Data Program

SOP No.: PDP-DATA Page 17 of 32

Title: Data and Instrumentation

Revision: 11 Replaces: 03/01/23 Effective: 03/01/24

• Instrument methods or references to them (data acquisition, 

calibration/standardization, and data analysis parameters)

• Injection sequences

• Chromatograms and/or instrument reports of samples, standards, reagent 

blanks, matrix blanks, and matrix spikes

• PDP Sample Information Forms (SIFs) [if paper SIFs were submitted by the 

Sample Collector]

• Matrix blank, reagent blank, matrix spike, and sample results

• Documentation of technical and QA review

Note: Laboratories that choose to retain electronic data sets as PDF or Excel files shall

ensure all requirements for QA, traceability, etc. are met. Nothing shall be lost in the 

electronic domain that would normally be captured on paper, and all markups of the 

original chromatogram shall also be retained.

9. Data Reporting:

9.1 Calculations and Significant Figures

9.1.1 Each laboratory shall have an internal SOP describing the data processing steps 

taken to reach the final reported concentration. Data shall not be ignored without a 

written explanation (e.g., instrument malfunction, wrong standard used, co-eluting peak, 

etc.). 

9.1.2 In calculations, at least one significant figure in excess of the reporting 

requirements shall be carried through the calculation. When rounding is required, values 

greater than or equal to 5 shall be rounded up.

9.1.3 Percent recoveries shall be reported to two significant figures if less than 100 or to 

three significant figures if greater than 100.

9.1.4 Concentrations shall be reported to at least two significant figures in parts per 

million (ppm), parts per billion (ppb), or parts per trillion (ppt). MPD requests that 
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Pesticide Data Program

SOP No.: PDP-DATA Page 18 of 32

Title: Data and Instrumentation

Revision: 11 Replaces: 03/01/23 Effective: 03/01/24

laboratories report as many significant figures as they are able to determine is appropriate

for each commodity/pesticide pair using a given method.

9.1.5 Individual peaks may be reported for multiple peak compounds. If separate 

standards are available for separate isomers, it is preferable to report the isomers 

separately.

9.2 Determination of Residue Concentrations for PDP Reporting Purposes

9.2.1 A laboratory may elect to set LOD = LOQ provided all of the following 

conditions are met: 

• the analyses are completely performed via MS systems (i.e., quantification and selfconfirmation) and

• the qualifier ions are at least 3 x s/n and

• the quantification ions have a response at least 10 x s/n.

The laboratory shall code the findings (both detects and non-detects) as “Z” [LOD equals 

LOQ] in the “Test Class” section of the RDE analytical results section only if the actual 

LOQ value is not entered for the findings.

9.2.2 Do not report residue concentrations less than the verified LOD.

9.2.3 Compounds appearing on the analytical results list for which results are 

not/cannot be reported shall be coded as “M” [not analyzed (e.g., compound not in 

standard, used as marker only)] or “UD” [unable to determine (e.g., matrix interference, 

method failure)] in the mean result field of the RDE analytical results section.

9.2.4 Numeric concentrations below the LOQ are considered low confidence values 

associated with a qualitative finding. A concentration value is not required when a 

pesticide is detected at or above the determined LOD and below the determined LOQ. 

The laboratory shall code the finding as “Q” (residue BQL) in the “Annotated Info.” 

section of the RDE analytical results section. The concentration will be converted to 1⁄2 

LOQ in the PDP database for reporting purposes.
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SOP No.: PDP-DATA Page 19 of 32

Title: Data and Instrumentation

Revision: 11 Replaces: 03/01/23 Effective: 03/01/24

9.2.5 All detections shall be coded as:

• “O” (detect – original extraction value);

• “A” (detect – average of original and re-extraction analyses values); or

• “R” (detect – re-extraction analysis value) 

in the mean result field of the RDE analytical results section (refer to Attachment 2,

Flowchart for Reporting Codes).

9.2.6 Validated Pesticide/Commodity Pairs

A pesticide/commodity pair is considered validated when all applicable modules in SOP 

PDP-QC have been met.

9.2.6.1 Results less than the verified LOD shall be coded as “ND” (non-detect, 

well-recovered analyte) in the mean result field of the RDE analytical results 

section.

9.2.6.2 Residue concentrations greater than or equal to the LOQ shall be reported 

on the RDE analytical results section. If there are no qualifications of the data 

(i.e., estimate, marginal performing analyte, unvalidated compound), the 

quantification field shall be left blank. If the data is an estimate (e.g., has failed 

linearity, calibration integrity or spike recovery), then the results shall be coded as 

“E” (estimate) in the quantification field of the RDE analytical results section

(refer to Attachment 2, Flowchart for Reporting Codes).

9.2.7 Validated Marginal Performing Analytes

Marginal Performing Analytes are identified and documented during method validation or 

during ongoing QC.

9.2.7.1 Results less than the verified LOD shall be coded as “NP” (non-detect, 

marginal performing analyte) in the mean result field of the RDE analytical 

results section.
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SOP No.: PDP-DATA Page 20 of 32

Title: Data and Instrumentation

Revision: 11 Replaces: 03/01/23 Effective: 03/01/24

9.2.7.2 Residue concentrations greater than or equal to the LOQ shall be reported 

on the RDE analytical results section. Results shall be coded as “P” (marginal 

performing analyte) in the quantification field of the RDE analytical results 

section (refer to Attachment 2, Flowchart for Reporting Codes).

9.2.8 Unvalidated Pesticide/Commodity Pairs

As a rule, unvalidated residues should not be reported. However, unvalidated residues 

may be reported on a case-by-case basis. For example, identification and tentative 

quantification of a compound not currently included in the analytical screen or preliminary 

results for special projects. Procedures to be followed in these instances are as follows:

9.2.8.1 Results less than the estimated LOD shall be coded as “NU” (non-detect, 

unvalidated residue) in the mean result field of the RDE analytical results section.

9.2.8.2 Residue concentrations greater than or equal to the LOQ shall be reported 

on the RDE analytical results section. Results shall be coded as “U” (unvalidated 

analyte) in the quantification field of the RDE analytical results section (refer to 

Attachment 2, Flowchart for Reporting Codes).

9.2.9 In cases where calibration integrity exceeds 20%, the laboratory shall use best 

professional judgment to determine whether or not to report positive findings as follows:

• Report positive findings using quantification codes: “E” (Estimate), “P” (Marginal 

Performing Analyte), or “U” (Unvalidated Compound). The use of code “E” does 

not require a deviation letter and should be determined on a set-to-set basis, using 

best professional judgment. It could be used when the calibration integrity, 

linearity, or the spike recovery fail.

• Report results that could not be quantified as non-detects using mean result code 

“UD” (unable to determine)(refer to Attachment 2, Flowchart for Reporting 

Codes).
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Pesticide Data Program

SOP No.: PDP-DATA Page 21 of 32

Title: Data and Instrumentation

Revision: 11 Replaces: 03/01/23 Effective: 03/01/24

9.3 Administrative Reporting Level

The Administrative Reporting Level is a level below which results shall be reported as not 

detected. For all commodities, it is 1 ppb (parts per billion). A laboratory's reported LOD may be 

at or above this level, but not below.

9.4 PDP Tolerance Table

9.4.1 MPD maintains a PDP Tolerance Table that lists established pesticide tolerances 

for food commodities currently in the program. The table lists pesticides registered for 

use on current PDP commodities and metabolites applicable to PDP testing, and includes 

food handling, interim, regional, and Section 18 emergency tolerances. FDA action levels 

for pesticides with revoked tolerances are also included as these chemicals may persist in 

the environment. Blank spaces in the table indicate that no tolerance is established for 

that commodity. Compounds listed in the PDP Tolerance Table may or may not coincide 

with those listed in a specific Commodity Compound List Memorandum provided to the 

lab by MPD. The PDP Tolerance Table is updated approximately quarterly to reflect new 

commodities entering the program and to remove outgoing commodities from the list. 

Laboratories are encouraged to notify MPD if they become aware of any newly registered 

pesticides or find errors in the PDP Tolerance Table. The table is available to PDP 

participants on the PDP SharePoint site. 

9.4.2 The PDP Tolerance Table is intended to be used only as a general guide and is 

prepared for the convenience of the participants. The tolerance information should not be 

used for enforcement, or domestic/international trade issues, without verifying the 

completeness and accuracy of this tolerance information. The information may be out-ofdate because new pesticide tolerances may be promulgated by EPA at any time and 

existing tolerances may be revised/revoked at any time following EPA review. EPA's 

new/revised/revoked tolerances are published as issued in the daily Federal Register. 

9.5 Non-Violative Results
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Pesticide Data Program

SOP No.: PDP-DATA Page 22 of 32

Title: Data and Instrumentation

Revision: 11 Replaces: 03/01/23 Effective: 03/01/24

Non-violative results for PDP reporting purposes are residue determinations that do not exceed a 

stated tolerance. A tolerance is the maximum amount of a pesticide residue that is permitted in or 

on a food. All concentrations shall be reported on the RDE analytical results section.

• A detected residue concentration is considered to be non-violative if it is equal to or less 

than the 40 CFR 180 tolerance for the given commodity.

• If no commodity tolerance exists, then the group tolerance (if available) should be used.

• If no commodity or group tolerance is established or Section 18 reference noted, the 

tolerance shall be considered zero.

9.6 Presumptive Tolerance Violations (PTV)

Tolerances are established for food commodities by EPA under the authority of the Federal Food, 

Drug, and Cosmetic Act (FFDCA) and are listed in 40 CFR 180. Tolerances can be established 

for a specific commodity; however, tolerances may also be established by the commodity 

groupings established by EPA in 40 CFR 180 or Section 18 tolerances may apply.

9.6.1 A residue is considered to exceed the 40 CFR 180 tolerance when the reported 

value exceeds the tolerance by one number in the second significant figure, or in the case 

of a single significant figure in the tolerance expression, by one number in that significant 

figure. For example, if the tolerance is 20 ppm, then a “presumptive violation” would 

occur at 21 ppm. If the tolerance is 1.0 ppm, then a “presumptive violation” would occur 

at 1.1 ppm. If the tolerance is 0.01 ppm, then a “presumptive violation” would occur at 

0.02 ppm.

9.6.2 If the pesticide residue exceeds the established tolerance or does not have an 

established tolerance, the laboratory shall report the appropriate code in the annotated 

information field of the RDE analytical results section (refer to Attachment 1 –

Laboratory Information Form (LIF) Codes).

9.6.3 PTV Notification Policy
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SOP No.: PDP-DATA Page 23 of 32

Title: Data and Instrumentation

Revision: 11 Replaces: 03/01/23 Effective: 03/01/24

PTVs shall be transmitted via RDE during normal data submission process. MPD shall 

notify HQ FDA. If States have a cooperative agreement with local FDA, MPD will also 

send a State-specific report to the laboratories, if requested.

9.7 Tolerance Interpretation for Processed Commodities

9.7.1 MPD shall follow the guideline of the EPA Office of Prevention, Pesticides and 

Toxic Substances (OPPTS) 860.1520, processed food/feed, section (b), which states in 

part:

“If residues do concentrate in a processed commodity, a food or feed additive tolerance 

must be established under section 409 of the Federal Food, Drug and Cosmetic Act 

(FFDCA) (or a section 701 Maximum Residue Limit (MRL) in some cases). However, if 

residues do not concentrate in processed commodities, the tolerance for the raw agricultural 

commodity (RAC) itself applies to all processed food or feed derived from it.”

9.7.2 When a specific tolerance for a compound is listed for a processed commodity in 

the Code of Federal Regulations (CFR), that tolerance will be stated in the quarterly 

tolerance tables. For example, 40 CFR 180.472 lists a specific tolerance for imidacloprid

in tomato paste at 6.0 parts per million (ppm). This is the tolerance that would be listed 

for tomato paste in the tolerance table released by MPD.

9.7.3 If a specific tolerance for a compound is not listed in the CFR for a processed 

commodity, then the tolerance for the RAC will be listed in the PDP tolerance table. For 

example, 40 CFR 180.303 does not list a specific tolerance for oxamyl in tomato paste; 

however, there is a tolerance of 2 ppm for oxamyl on tomatoes, the RAC. A tolerance of 

2 ppm for oxamyl would be listed for tomato paste in the tolerance table released by 

MPD.

9.7.4 For juices, the tolerances for the RAC will be listed in the tolerance tables unless 

specific tolerances for juices are listed in the CFR. When adding water to juice 

concentrate, do not back-calculate for the water added. Reconstituted juices should be 

treated the same as ready-to-serve (RTS) juices. MPD will apply the RAC tolerance for a 

compound, as is, to RTS juice unless there is a specific juice tolerance in the CFR. For 
United States Department of Agriculture

Agricultural Marketing Service, Science & Technology

Pesticide Data Program

SOP No.: PDP-DATA Page 24 of 32

Title: Data and Instrumentation

Revision: 11 Replaces: 03/01/23 Effective: 03/01/24

example, 40 CFR 180.671 lists a tolerance for fenpyrazamine in grape juice at 4 ppm. 

This tolerance applies to both the RTS juice and the grape juice concentrate, after it is 

reconstituted. A tolerance of 4 ppm for fenpyrazamine in grape juice would be reflected 

in the tolerance table released by MPD. Another example is that 40 CFR 180.114 does 

not list a specific tolerance for ferbam in grape juice. However, there is a specific 

tolerance listed at 4.0 ppm for grapes, the RAC. A tolerance of 4.0 ppm for ferbam for 

the RAC would be reflected for RTS grape juice and grape juice concentrate, after it is 

reconstituted, in the tolerance table released by MPD.

9.8 Reporting Proficiency Testing (PT) Results

Results for PT rounds issued by the CDFA-QAU and FAPAS shall be reported according 

to the provider’s instructions. Laboratories also may report PDP PT results to MPD via 

RDE. 

10. Data Review:

Each data package shall undergo review by the technical and QA sections for accuracy 

and completeness, adherence to PDP criteria, and integrity of the overall quality system. 

The QAU shall have access to all documentation necessary to achieve this objective. 

Both technical and QA reviews shall be documented.

Following QAU review of a data package, that data shall not be changed by any 

laboratory personnel unless as a response to comments/concerns/recommendations by the 

QAU. Actions taken as a result of technical and/or QA findings shall be documented.

11. Remote Data Entry (RDE) System:

11.1 RDE System Administration

11.1.1 Each laboratory and/or TPM shall designate an individual or individuals to 

administer applicable aspects of the RDE system. An existing laboratory system 

administrator can grant system administrator privileges to other users or MPD can 
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SOP No.: PDP-DATA Page 25 of 32

Title: Data and Instrumentation

Revision: 11 Replaces: 03/01/23 Effective: 03/01/24

provide a temporary account/password that connects directly to the RDE System Admin 

menu so that system administrator privileges can be granted to any user.

11.1.2 The laboratory system administrator shall contact MPD to request new RDE user 

accounts for laboratory personnel. MPD shall create the user account in the central RDE 

database, then generate and send the laboratory a text data file holding the new account 

information. The laboratory system administrator shall then import the text data file to 

add the user using the Import New User feature on the RDE Manage User Accounts 

screen. Each user account shall be assigned one or more roles, which serve as defined 

permissions to access the different RDE options, based on position requirements.

11.1.3 The laboratory system administrator may reset passwords and unlock accounts as 

needed using the Manage User Accounts option in the RDE System and shall disable the 

RDE user account when an individual terminates employment with the organization.

Note: The RDE system will automatically deactivate any account not accessed in the past 

90 days.

11.1.4 The laboratory system administrator shall import updates to standardized code 

look-up tables, like the commodity and site tables, using text data files provided by MPD

and the Import Look-up Table Updates option on the RDE System Admin menu. MPD

shall provide those updates quarterly in response to scheduled program changes or 

immediately if a new required code is added. 

11.2 RDE System Access

11.2.1 The distributed RDE system requires Microsoft Office 2013 (V15.0) or newer, 

either 32-bit or 64-bit, installed on each client computer to run the application, including 

Access, Excel (for data exports), and Outlook (for data transmits). For optimal 

performance, the front-end application files should be installed on each client computer 

with connections to the single set of shared back-end database files. 

11.2.2 The RDE system requires an assigned user account and password to gain access. 
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Pesticide Data Program

SOP No.: PDP-DATA Page 26 of 32

Title: Data and Instrumentation

Revision: 11 Replaces: 03/01/23 Effective: 03/01/24

Laboratory personnel shall contact the assigned laboratory system administrator to 

resolve problems with accessing the RDE system, such as a locked account or forgotten 

password. If the laboratory system administrator is not available, MPD may be contacted 

to provide a one-day temporary password that will unlock and re-activate the account.

11.3 RDE Data Entry

11.3.1 The laboratory shall create analytical sets, referred to as Groups in RDE, so that 

all samples related to the corresponding set’s QA Recovery Data, are included under one 

unique Group identification number. Multiple Groups for the same commodity and 

month are acceptable.

11.3.2 Matrix Spike Recovery data that are associated with all samples in the Group 

shall be entered as specified in SOP PDP-QC.

11.3.3 Sample identity information for collected and non-collected samples shall be 

entered from a paper SIF or attached to the Group if an electronic SIF was submitted.

Ensure that the sample identification information matches the information that is 

recorded in RDE. 

11.3.4 Analytical Results data shall be entered for each sample as specified in this SOP.

11.3.5 Process Control spike recovery data shall be entered for each sample as specified 

in SOP PDP-QC.

11.3.6 Data may be entered, maintained, and signed-off on a Laboratory Information 

Management System (LIMS), but shall be imported into the RDE System for 

transmission to MPD.

11.3.7 Refer to the latest RDE System documentation for further information. The User 

Guide can be accessed with a link on the RDE system’s main menu. The latest version 

can be downloaded from the RDE Shared folder on the PDP SharePoint site.
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SOP No.: PDP-DATA Page 27 of 32

Title: Data and Instrumentation

Revision: 11 Replaces: 03/01/23 Effective: 03/01/24

11.4 RDE Data Sign-off and Transmission

11.4.1 The data must go through a multi-level review and sign-off process prior to 

submission to MPD (the RDE system provides for up to three reviewer sign-offs for each 

analytical set). The first level sign-off is optional, while the TPM and Quality Assurance 

Officer sign-offs are required before the analytical set is allowed to be transmitted. A 

proxy sign-off for the TPM and/or QAO can be done for data sets that are imported from 

a LIMS provided that the TPM and QAO have both reviewed and approved the data. 

Data may be maintained on a LIMS, but must be transmitted through the RDE system.

11.4.2 Data shall be electronically transmitted to MPD as described in this SOP using the 

Transmit option in the RDE System. Analytical data on any other media shall not be 

submitted without prior authorization from MPD.

11.4.3 Participating laboratories shall submit electronic results for routine data sets to

MPD via RDE within 90 days of receipt of the last sample in the set according to 

established procedures as detailed in this SOP. If the 90-day reporting requirement is not 

met, the laboratory shall send the MPD Director and Laboratory Liaison monthly updates 

detailing the reason for the delay and a projected schedule for data delivery. In addition to 

the updates, the laboratory shall make a special report for any samples held unanalyzed 

for over 90 days.

11.4.4 MPD and the laboratory will come to a written agreement, on a case-by-case 

basis, regarding any changes to be made to program data after it has been reported to the 

PDP database. The laboratory shall be responsible for making any changes to hardcopies 

and their own internal database/records.
United States Department of Agriculture

Agricultural Marketing Service, Science & Technology

Pesticide Data Program

SOP No.: PDP-DATA Page 28 of 32

Title: Data and Instrumentation

Revision: 11 Replaces: 03/01/23 Effective: 03/01/24

Revised By: Chantal Rollerson Date

PDP Chemist

Monitoring Programs Division 

1400 Independence Ave, SW

Washington, DC 20250

(202) 572-8172

Reviewed By: Sarva Balachandra Date

Presiding Member of PDP Technical Advisory Group

California Department of Food and Agriculture

3292 Meadowview Rd

Sacramento, CA 95832

(916) 228-6857

Approved By: Brenda Foos Date

Monitoring Programs Division Director

1400 Independence Ave, SW

Washington, DC 20250

(202) 572-8167

Original signed by Chantal Rollerson 2/28/2024

Original signed by Sarva Balachandra 3/1/2024

Original signed by Brenda Foos 2/29/2024
United States Department of Agriculture

Agricultural Marketing Service, Science & Technology

Pesticide Data Program

SOP No.: PDP-DATA Page 29 of 32

Title: Data and Instrumentation

Revision: 11 Replaces: 03/01/23 Effective: 03/01/24

Revision 11 March 2024 Monitoring Programs Division

• Made minor grammatical and formatting updates throughout document

• Clarified peak summation verbiage in section 6.4

• Added a statement on HRMS to section 7.3.1.5

• Removed section 8.2.3 as it is no longer relevant

• Removed section 9.4 on OPP reporting due to insufficient reasoning for OPP to have special reporting 

requirements. Section numbering was updated for section 9

• Updated the examples in section 9.6.1 and 9.7.4

• Updated the section numbering for section 10

Revision 10 March 2023 Monitoring Programs Division

• Updated footers of attachment documents

• Updated “revised by PDP Chemist” signature line

• Updated the presiding member of the Technical Advisory Group

• Removed the U.S. Tolerance Tracker from the references section as it has been retired

• Removed “hardcopy” from section 5.4.3

• Removed redundant term from section 6.1.2

• Changed “quantitated” to “quantified” in section 6.1.3

• Clarified language in section 6.2.1

• Added “but not all” in regards to reporting peaks that are BQL in section 6.4

• Clarified language in section 6.4

• Removed section 7.3 due to outdated methodology

• Added PT data to section 8.2.1

• Updated language in section 9.1.4

• Defined abbreviations in sections 9.2.8.1 and 9.2.9

• Deleted reference to the U.S. Tolerance Tracker in section 9.5.2 as it has been retired

• Clarified language in section 9.8.4

• Added the need of a special report for samples held unanalyzed over 90 days in section 11.4.3

• Minor grammatical and formatting updates throughout

Revision 9 March 2022 Monitoring Programs Division

• Updated footers of attachment documents

• Updated “revised by PDP Chemist” signature line

• Changed USDA/AMS Extranet to PDP SharePoint site throughout the document

• Replaced USDA/AMS with MPD throughout the document where applicable

• Added links to refences in section 4
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Agricultural Marketing Service, Science & Technology

Pesticide Data Program

SOP No.: PDP-DATA Page 30 of 32

Title: Data and Instrumentation

Revision: 11 Replaces: 03/01/23 Effective: 03/01/24

• Reference “Agro AgriBusiness US Tolerance Tracker” changed to “IHS Markit, US Tolerance 

Tracker, and link updated

• Updated section 6.2.1 with definition of LOQ (Limit of Quantitation)

• Updated section 6.2.5 with definition of QAU (Quality Assurance Unit)

• Updated section 8.2.3 to limit the submission of hardcopies

• Updated section 9.5.1 the description of the PDP Tolerance Table was updated

• Removed mention in section 9.5.1 of Commodity Compound List Memorandums on Sharepoint site

• Updated section 9.5.2 to reflect tolerance tracker updates are no longer monthly

• Updated section 9.8.2 to remove the specificity of timing

• Updated section 9.8.3 to remove the specificity of timing 

• Updated section 9.8.4 for clarification on the tolerance table

• Updated section 11.3.2 wording for clarification

• Added “LT” and “T” to Confirmation Codes table in Attachment 1

• Removed reference to “PDP-Data-03.5.7” in Confirmation Method description for code “S” in 

Confirmation Codes table in Attachment 1

• Added “69” to Determinative Codes table in Attachment 1

• Added “600” and “904” to Extraction Codes table in Attachment 1

Revision 8 March 2021 Monitoring Programs Division

• Added cross referencing throughout the document

• Updated the web link to FDA’s Center for Veterinary Medicine Guidance for Industry Document 18

and added a note indicating references were consulted in the preparation of the SOP in section 4

• Added reference sections from the ADMIN SOP to section 5.4.4

• Updated section 7.2.1 by combining LC and GC retention time criteria 

• Removed section 7.2.2 and renumbered section 7.2.3 to 7.2.2.

• Added confirmation method reporting for positive residue detects only in section 7.3.1

• Added user guide access information for the RDE system in section 11.3.7 

• Removed reference to web based RDE system in section 11.4.1

Revision 7 March 2020 Monitoring Programs Division

• Removed reference to the Pesticide Chemical News Guide in section 4 and replaced it with the US 

Tolerance Tracker

• Renumbered sections 6.2.1 through 6.2.4 so that the sections are now numbered 6.2.2 through 6.2.5

• Added a new section 6.2.1 to provide incurred residue subtraction language for matrix matched 

standards

• Updated language for reporting a Z code only if LOQ is not entered in section 9.2.1

• Updated language for new name of PCNG service in section 9.5.2
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SOP No.: PDP-DATA Page 31 of 32

Title: Data and Instrumentation

Revision: 11 Replaces: 03/01/23 Effective: 03/01/24

• Updated language for account management in the new local RDE system in section 11.1.1

• Removed italicized note from section 11.1.1 as it does not apply to the local RDE system

• Updated language for account creation in the local RDE system in section 11.1.2

• Updated language for the user management option name in section 11.1.3

• Added section 11.1.4 for updating look-up tables in the local RDE system

• Updated language for system requirements for the local RDE system in section 11.2.1

• Updated language for user access for the local RDE system in section 11.2.2

• Updated language for allowed data sign-off in LIMS in section 11.3.6

• Updated section 11.4.3 by changing the PDP Technical Director to MPD Director and adding 

notification to the Laboratory Liaison when there is a delay in data delivery 

Revision 6 April 2018 Monitoring Programs Division

• Changed GC and LC ion ratio criteria to +/- 30% relative in sections 7.4.1.4 and 7.4.2.3

• Added analyte confirmation language and ion ratio tolerance example calculation to section 7.4.2

• Added electronic data retention requirement to section 8.2.2

• Updated language for PT reporting in section 9.9 

• Removed sections 9.9.1 and 9.9.2

• Updated language to address restricted access to RDE in section 11.2.2

• Added new codes for determinative method to Attachment 1

Revision 5 April 2017 Monitoring Programs Division

• Added multipeak confirmation criteria to section 7.4.2.1 

• Clarified sample identity information in section 11.3.3

Revision 4 February 2016 Monitoring Programs Division

• Updated language for quantification of multi-peak compounds in section 6.4

• Updated language for quantification of spikes in section 6.5

• Changed GC and LC retention time criteria to 0.1 minutes in section 7.2

• Clarified tolerances for metabolites are based on parent levels in section 9.5

Revision 3 November 2014 Monitoring Programs Division

• Updated MPD address

• Updated procedures for method validation package submission to section 8.2.3

• Updated PDP Tolerance Table procedures to section 9.5

• Updated RDE System Access procedures to section 11.2

• Added new codes for determinative method, extraction, and test class to Attachment 1
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SOP No.: PDP-DATA Page 32 of 32

Title: Data and Instrumentation

Revision: 11 Replaces: 03/01/23 Effective: 03/01/24

Revision 2 August 2013 Monitoring Programs Division

• Updated MPO to USDA/AMS throughout document

• Changed requirement for calibration integrity to 30% for residues not detected in routine samples in 

sections 6.13 and 7.1.1

• Clarified reporting exceptions in section 6.5

• Added requirement for name/initials/signature log to section 8.1.4

Revision 1 April 2011 Monitoring Programs Office

• Added paragraph regarding sample dilution in section 6.2.4.

• Added specification about incurred residues in section 6.5.3.

• Added sections 6.5.5-6.5.8 regarding spike coding in RDE.

• Updated section 7.1.1 for redundant information.

• Changed “shall” with “should” in section 7.3.2 to reflect MPO needs.

• Updated section 7.4.2.3.

• Updated section 9.1.1 by taking out “best two out of three” requirement.

• Updated section 9.8.4 with relevant pesticide example.

• Updated Attachments 1 and 2 with QA Codes

Original Revision April 2010 Monitoring Programs Office

• Combined all PDP DATA (03, 07, 09) and INSTR (04, 06) into a single document as follows:

– PDP – INSTR 04 is section 7.1

– PDP – INSTR 06 is section 5 (Instrumentation)

– PDP – DATA 03 is section 6 (Calibration)

– PDP – DATA 07 is spread over sections 8 (Data Handling), 9 (Data Reporting), 10 (Data 

Review) and 11 (RDE System)

– PDP – DATA 09 is section 7 (Generating Raw Data)

• Removed requirements to check instruments performance verification before/during analysis from old

PDP - INSTR 06, section 5.4.b.

• Removed requirements to include comment in SIF field when using “E” code, from old PDP – DATA 

03, section 5.1.c.1, currently section 9.2.9.

• Moved and reworded section 5.1.c from old PDP – DATA 03 to chapter 9 (Data Reporting), section 

9.2.9 of current PDP – DATA.

• Updated section 5.3.b from old PDP – DATA 07 (currently section 8.2.2)

• Reworded section 5.5 from old PDP – DATA 07 (currently section 9.3)

• Updated section 5.16.c from old PDP – DATA 07 (currently section 11.4.3)
Pesticide Data Program

Laboratory Information Form Codes

CODE CONFIRMATORY METHOD: Instrumental method used to confirm analyte identity

A GC/AED - Gas Chromatography with Atomic Emission Detector 

C GC or LC Alternate Column

CD GC or LC Alternate Column and Alternate Detector

D GC or LC Alternate Detector

F Liquid Chromatography with Fluorescence Detector

GF GC/TOF - Gas Chromatography with Time of Flight Mass Spectrometry

GI GC/MS/MS - Gas Chromatography with Tandem Mass Spectrometry - ion trap

GN GC/MSD w/ Negative Chemical Ionization (NCI)

GT GC/MS/MS - Gas Chromatography with Tandem Mass Spectrometry - triple quadrupole

HR GC or LC High Resolution Mass Spectrometry

I GC/IT - Gas Chromatography with Ion Trap Mass Spectrometry - single stage

IA Immunoassay

LF LC/TOF - Liquid Chromatography with Time of Flight Mass Spectrometry

LI LC/MS - Liquid Chromatography with Ion Trap Mass Spectrometry - single stage

LL LC/MS/MS - Liquid Chromatography with Tandem Mass Spectrometry - ion trap

LS LC/MS - Liquid Chromatography with Mass Spectrometry - single quadrupole

LT LC/MS/MS - Liquid Chromatography with Tandem Mass Spectometry

LU LC/MS/MS - Liquid Chromatography with Tandem Mass Spectrometry - triple quadrupole

M GC/MS - Gas Chromatography with Mass Spectrometry - single quadrupole

MO Quantitation & Confirmation by GC/MS only

MR GC or LC Mid Resolution Mass Spectrometry

P LC-AMP - Liquid Chromatography Alternate Mobile Phase 

R LC-DAD - Liquid Chromatography with Diode Array Detector 

S GC or LC -MS Alternate Detector

T GC/MS/MS - Gas Chromatography with Tandem Mass Spectometry

Z Other

CODE ANNOTATED INFORMATION: Additional information about analyte finding

Q Residue at Below Quantifiable Level (BQL)

QV Residue at <BQL> with a Presumptive Violation - No Tolerance

QX Residue at <BQL> with a Presumptive Violation - Exceeds Tolerance

V Residue with a Presumptive Violation - No Tolerance

X Residue with a Presumptive Violation - Exceeds Tolerance

CODE QUANTITATION: Method used to calibrate, quantitate or validate analyte

(none/blank) No qualifications of data or non-detect

E Estimate

P Marginal performing analyte

U Unvalidated compound

CODE MEAN RESULT: Summary of analyte findings and how they were determined

O Detect: original extraction value

R Detect : re-extraction analysis value

A Detect: average of original and re-extraction analyses values

ND Non-detect: validated, well-recovered analyte

NP Non-detect: marginal performing analyte

NU Non-detect: unvalidated residue

M Not analyzed (not in standard, used as a marker only)

UD Unable to determine (matrix interference, method failure)

CONFIRMATION CODES

ANNOTATION CODES

QUANTITATION CODES

MEAN RESULT CODES

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PDP DATA Attachment 1

Revision 11 - Effective March 1, 2024
Pesticide Data Program

Laboratory Information Form Codes

CODE QA/QC EXCEPTION: Exceptional finding/notation of spike recovery 

I Incurred residue when levels>2xLOQ

N Not recovered

S Incurred subtracted

E Estimate

M Matrix interference

P Marginal performing analyte

U Unvalidated

CODE DETERMINATIVE METHOD: Instrumental method used to quantitate analyte 

01 GC/ECD - Electron Capture Detector

02 GC/FPD - Flame Photometric Detector in Phosphorus Mode

03 GC/FPD - Flame Photometric Detector in Sulfur Mode

04 GC/ELCD - Electrolytic Conductivity Detector in Nitrogen Mode

05 GC/ELCD - Electrolytic Conductivity Detector in Halogen Mode

06 GC/FID - Flame Ionization Detector

07 GC/MS - Gas Chromatography with Mass Spectrometry - single quadrupole

08 GC/IT - Gas Chromatography with Ion Trap Mass Spectrometry - single stage

09 TLC - Thin Layer Chromatography

10 LC/FL - Liquid Chromatography with Fluorescence Detector

11 LC/UV - Liquid Chromatography with UV Detector

12 Liquid Chromatography with Post-Column Derivatization & Fluorescence Detection 

14 GC/NPD - Phosphorus Mode

15 GC/NPD - Nitrogen Mode

16 GC/NPD - Nitrogen/Phosphorus Detector

18 GC/FPD - Flame Photometric Detector in Nitrogen Mode

19 Liquid Chromatography with Pre-Column Derivatization & Fluorescence Detection

27 GC/AED - Atomic Emission Detector

28 AED - Element Selective GC/AED

30 GC/ELCD - Electrolytic Conductivity Detector in Sulfur Mode

35 GC/MS/MS - Gas Chromatography with Tandem Mass Spectrometry - triple quadrupole

51 LC/MS - Liquid Chromatography with Mass Spectrometry - single quadrupole

52 LC/MS/MS - Liquid Chromatography with Tandem Mass Spectrometry - triple quadrupole

58 GC - Gas Chromatography w/ Detector other than Listed

59 LC - Liquid Chromatography w/ Detector other than Listed

60 GC/XSD - Halogen Specific Detector 

63 Second LC/MS

64 Second LC/MS/MS

65 GC/Micro ECD - Micro Electron Capture Detector

66 GC/PFPD - Pulsed Flame Photometric Detector

67 Third LC/MS/MS

68 Second GC/ECD

69 LC/MS/MS - Ion Trap

70 Fourth LC/MS/MS

71 Second GC/Micro ECD

72 GC/MSD with Negative Chemical Ionization (NCI)

73 GC/MS/MS - Gas Chromatography with Tandem Mass Spectrometry - ion trap

74 LC/MS - Liquid Chromatography with Ion Trap Mass Spectrometry - single stage

75 LC/MS/MS - Liquid Chromatography with Tandem Mass Spectrometry - ion trap

76 GC/TOF - Gas Chromatography with Time of Flight Mass Spectrometry

77 LC/TOF - Liquid Chromatography with Time of Flight Mass Spectrometry

DETERMINATIVE CODES

QA/QC EXCEPTION CODES

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PDP DATA Attachment 1

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Pesticide Data Program

Laboratory Information Form Codes

78 Second GC/MS - single quadrupole

79 GC/HRMS-Gas Chromatography with High Resolution Mass Spectrometry

80 LC/HRMS-Liquid Chrmatography with High Resolution Mass Spectrometry

98 Immunoassay Screen

99 OTHER

CODE EXTRACTION METHOD: Extraction method used for this analyte 

000 No Extraction Necessary

015 Modified Luke Extraction Method without Cleanup for Multi-Residues & Carbamates

550 CDFA Lee et al C-18 Extraction Method

551 CDFA Chlorinated ACN Florisil SPE Extraction Method

552 CDFA MSD Aminopropyl Extraction Method

553 CDFA Carbamate SPE Extraction Method

554 CDFA Organophosphate Florisil SPE Extraction Method

555 CDFA Chlorinated Aminopropyl SPE Extraction Method

556 CDFA LC compounds Florisil SPE Extraction Method

600 LIB 3217 Extraction Method for Benomyl, MBC and Thiophanate-Methyl

800 FL-Modified CDFA C-18 Extraction Method (P-fraction)

801 FL-Modified CDFA C-18 Extraction Method Aminopropyl SPE Cleanup

802 FL-Modified CDFA C-18 Extraction Method w/ Florisil SPE Cleanup

803 GIPSA Modifed Method for Extraction of Multi-Residues in Grains

804 GIPSA Modified Method for Determination of Triazole Metabolites in Wheat Flour (SPE, LC/MS-MS)

805 Modified Quecher's Method

806 NYS Modifed SPE Method (F&V)

807 NYS Modified Method for Determination of Triazoles and Metabolites in Peaches (SPE, LC/MS-MS)

808 WSDA Modified Method for Determination of Triazoles and Metabolites in Apples (SPE, LC/MS-MS)

809 NSL Butter Extraction Method

810 Montana SPE Triazole Extraction Method for Water

811 Montana SPE Extraction Method for Polar Pesticides (Water)

812 Montana Liquid/Liquid Extraction Method for Non-Polar Pesticides

813 NSL Dairy Product Method

814 WA-Modified CDFA C-18 Extraction Method (P-fraction)

815 WA-Modified CDFA C-18 Extraction Method Aminopropyl SPE Cleanup

816 WA-Modified CDFA C-18 Extraction Method w/Florisil SPE Cleanup

817 FL Aminopropyl SPE Extraction Method

818 NSL Animal Tissue Extraction Method

819 EPA Extraction Method

820 Phenoxy Extraction Method

821 NSL Honey Extraction Method

822 CDFA-Modified QuEChERS Method

823 WSDA Animal Tissue Extraction Method

900 Liquid/Liquid Method

901 NYS Modification of USGS Method 2001/2002 (SPE, GC)

902 NYS Modification of USGS Method 9060 (SPE, LC)

903 NYS Modification of USGS Method for Chloroacetanilide Metabolites (SPE, LC)

904 NYS SPE method for Bottled Water

997 OTHER Methods Used for Determination of Single Components

998 OTHER Single-Analysis Methods

999 OTHER Multi-Residue Methods

CODE TEST CLASS: Test classification for analyte 

A Halogenated

 TEST CLASS CODES

EXTRACTION CODES

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PDP DATA Attachment 1

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Pesticide Data Program

Laboratory Information Form Codes

B Benzimidazole

C Organophosphorus

D Avermectin

E Carbamate

F Organonitrogen

G 2,4-D / Acid Herbicides

H Formetanate HCL

I Other Compounds

J Imidazolinone

K Sulfonyl Urea Herbicides

L Conazoles / Triazoles

M Dithiocarbamates

N Imidazoles

O Pyrethroids

P Thiocarbamates

Q QA only (for RDE)

R Triazines

S Triazine, Non-Halogenated

T Nitrile

U Uracil

V Pyrimidone

W Morpholine

X Natural Pesticides

Z LOD equals LOQ (for RDE)

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PDP DATA Attachment 1

Revision 11 - Effective March 1, 2024
SOP PDP-DATA

Flowchart for Reporting Codes

Detect?

Blank (no qualifications) Met: 

Calibration Integrity ( 6.1), Linearity 

(6.2) and Spike recovery (6.5); or 

Single point Comparison used due 

to linearity or calibration integrity 

failure (6.3).

E: estimate Use on set-to-set 

basis, based on best 

professional judgment, if 

failed: linearity & single point 

used, or calibration integrity or 

spike recovery (9.2.6.2)*

P: marginal performing 

analyte - identified 

during validation (9.2.7 

& PDP-QC 5.18.1.3**)

U: unvalidated 

compound (9.2.8)

 * does NOT require deviation letter

** requires letter of deviation

Detect?

Yes

O: Detect - Original Extraction 

Value (9.2.5)

R: Detect - Re-extraction 

Analysis Value (9.2.5)

A: Detect - Average of 

Original and Reextraction Analyses 

Values (9.2.5)

ND: non-detect, 

validated, wellrecovered analyte 

(9.2.6.1)

NP: non-detect, 

marginal 

performing 

analyte (9.2.7.1)

NU: non-detect, 

unvalidated 

residue (9.2.8.1)

M: not analyzed 

(not in standard, 

used as marker 

only) (9.2.3)

UD: unable to 

determine (matrix 

interference, method 

failure) (9.2.3)

I: incurred residue when levels 

> 2 x LOQ (6.5.3)

N: not recovered 

(6.5.4)

S: incurred 

subtracted (6.5.1) E: estimate (6.5.5)

M: matrix 

interference 

(6.5.6)

P: marginal 

performing 

analyte (6.5.7)

U: unvalidated 

(6.5.8)

1) Sample Results (LIF Codes)

2) QA/QC Results (QA/QC Codes)

Exception Codes

No

No

Quantitation Codes

Mean Result Codes

Blank

Yes

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PDP-DATA, Attachment 2

Revision 11 - Effective March 1, 2024
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Pesticide Data Program

Glossary of Mass Spectrometry Terms and Acronyms

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Adduct ion: Ion formed by the interaction of the molecular ion and another compound or 

element (e.g., ammonium, hydrogen, sodium, etc.) as a result of van der Waals forces.

Atmospheric pressure chemical ionization (APCI): Ionization process where an aerosol of 

sample solution is sprayed at atmospheric pressure into a heated region creating a reaction 

between a reagent ion and a neutral molecule to create a charged ionic form of the molecule. 

Atmospheric pressure ionization (API): Ionization process carried out at atmospheric pressure 

by any of several procedures including a radioactive source, electrical discharges, light sources, 

and high voltage electric fields. The main types are APCI, APPI, and ESI.

Atmospheric pressure photo ionization (APPI): Ionization process where an aerosol of sample 

solution is sprayed at atmospheric pressure into an area with a light source creating a reaction 

between photons and a neutral molecule to create a charged ionic form of the molecule. 

Atomic mass unit (amu): An arbitrarily defined unit in terms of which the masses of individual 

atoms are expressed. One amu is exactly 1/12 of the mass of an atom of the nuclide 12C (the 

predominant isotope of carbon). 

Base peak: The ion with the most intense peak in the mass spectrum (full scan). The relative 

abundance of the base peak is assigned a value of 100%, and the abundance of all other ions 

plotted in that reference spectrum are normalized to that value.

Chemical ionization (CI): Ionization process initiated by the reaction of a reagent ion and a 

neutral molecule to create a charged ionic form of the molecule.

Collision induced dissociation (CID): Process by which an isolated ion is fragmented, producing 

an MS/MS spectrum. CID is sometimes called collision activated dissociation. 

Confidence limits: The upper and lower boundaries in the range of values which includes (with 

a pre-assigned probability called the confidence level) the true value of a parameter.

“Absolute” confidence limits: Confidence limits determined for relative abundances of 

structurally significant ions by adding ± the pre-assigned confidence level. For example, 

an absolute confidence limit of 15%, for ion 149 with a relative abundance of 45%, the

confidence interval would be 30% to 60%.

“Relative” confidence limits: Confidence limits determined for relative abundances of 

structurally significant ions by multiplying ± the pre-assigned confidence level. For 

example, a relative confidence limit of 15% for ion 149 with a relative abundance of 

45%, the confidence interval would be 38% [45×(100-15)/100] to 52%

[45×(100+15)/100]. 
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Confirmation: Verification of a previous analyte identification that is performed by another 

analytical system.

Deconvolution: Process to extract clean spectra from a complex mixture of overlapping peaks 

using mathematical algorithms.

Diagnostic ion(s): Ion(s) used to identify and quantitate the target compound. Diagnostic ions 

include the molecular ion, characteristic adduct ions, characteristic fragment ions (structurally 

significant ions), and isotope ions. 

Electron ionization (EI): Ionization process initiated by the interaction of the gas-phase 

molecule with an energetic electron to create a charged ionic form of the molecule. Electron 

ionization is sometimes called electron impact.

Electrospray ionization (ESI): Ionization process where a sample solution is pumped into a 

capillary which is held at high potential causing a reaction between a reagent ion and a neutral 

molecule to create a charged ionic form of the molecule. The solution emerges from the 

capillary as a mist which is sprayed at atmospheric pressure into the mass spectrometer. 

Fragment ion(s): Ion(s) formed when the precursor or product ion fractures after undergoing 

CID. All fragment ion(s) are product ion(s), but not all product ion(s) are fragment ion(s)

Full scan: The practice of monitoring and recording a wide range of ion mass-to-charge ratios 

(m/z) produced following sample ionization. 

Ion trap: Type of mass analyzer consisting of two end caps and a ring electrode forming a threedimensional quadrupole that stores ions at its center. An additional electrical signal is used to 

selectively eject ions to an external detector.

IonsprayTM ionization: Pneumatically assisted ESI. Ionspray ionization is also called turbospray 

ionization. 

Internal standard: A substance not contained in the test sample with physical and chemical 

properties as similar as possible to those of the target analyte to be identified. An isotope-labeled 

form of the target analyte can also serve as an internal standard. The internal standard is added 

to each test sample as well as to each calibration standard at the beginning of the analytical 

process and used in the quantitative determination of the target analyte by taking into account the 

recovery of the internal standard. 

Matrix-assisted laser desorption ionization (MALDI): Ionization process where sample 

molecules are mixed with an excess of energy-absorbing matrix. The subsequent mixture is co-
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crystallized in a thin film on an inert support. Repetitive irradiation with a pulsed laser releases 

ions from the surface.

Molecular ion: An ion formed by the removal or addition of one or more electrons to a molecule 

without fragmentation; the peak representing the ionized molecule that contains only the isotopes 

of greatest natural abundance. 

Mass spectrometry (MS): Analytical technique used to identify compounds based on their 

chemical structures’ fragmentation patterns. MS instruments are called mass spectrometers.

Mass spectrometry/mass spectrometry (MS/MS): A form of mass spectrometry whereby ions are 

separated according to their mass-to-charge ratio in the first stage and are then fragmented by 

collisionally-induced dissociation, and the resultant fragment ions separated and measured in the 

second stage. MS/MS is also referred to as tandem mass spectrometry.

MSn: MS/MS reactions recurring over multiple steps.

MS spectrum: Graphical representation of ion intensity vs. m/z data at a single point in time. 

MS/MS spectrum: Graphical representation of ion intensity vs. m/z data at a single point in time 

produced by an isolated mass undergoing CID. 

Multiple reaction monitoring: Selected reaction monitoring for more than one precursor-toproduct ion transition. 

m/z: A ratio of mass-to-charge.

Precursor ion: An abundant, structurally significant ion selected from the full scan spectrum to 

be isolated and subsequently subjected to CID. A precursor ion may be a molecular ion or a 

fragment ion. The precursor ion is sometimes called the parent ion. 

Precursor ion scan: The practice of using the second stage mass analyzer in an MS/MS 

experiment to select a specific product ion and then using the first stage mass analyzer to scan 

for the precursor ion(s). The term parent ion scan is also used.

Product ion(s): Ion(s) formed from the reaction of the precursor ion. The reaction need not 

involve fragmentation through CID (e.g., the reaction involves a change in the number of 

charges carried by the precursor ion). If the reaction does involve CID, the product ion is also a 

fragment ion. Product ion(s) are sometimes called daughter ion(s). 
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Product ion scan: The practice of using the first stage mass analyzer in an MS/MS experiment to 

select a specific precursor ion and then using the second stage mass analyzer to scan for the 

resulting product ions. The term daughter ion scan is also used. 

Quadrupole: Type of mass analyzer consisting of four parallel rods arranged in a square array. 

Radio frequency and direct current voltages are applied to the rods creating a hyperbolic field 

that filters ions based on their mass-to-charge ratio. 

Qualifier ion(s): Structurally significant ion(s) chosen from the reference spectrum to show 

consistent relative abundances when compared to the target ion. Qualifier ion(s) are sometimes 

called secondary ion(s).

Quantitation ion: A structurally significant ion that demonstrates a linear response over a broad 

range of concentrations. It is typically the target ion. 

Reconstructed ion chromatogram: A plot of the intensity of specific ions in a MS or MS/MS 

spectrum (based on m/z) versus time.

Reference spectrum: Graphical representation of ion intensity vs. m/z data at a single point in 

time.

Relative abundance: The abundance of an ion relative to that of the most abundant ion, or base 

peak, in the spectrum.

Selected ion monitoring (SIM): Data acquisition technique of monitoring and recording one or 

more ion mass-to-charge ratios (m/z) rather than monitoring and recording the full MS spectra 

(i.e., a wide range of m/z values). This technique can greatly improve instrument sensitivity, 

albeit at a cost of reduced specificity. The term single ion monitoring is sometimes used.

Selected reaction monitoring (SRM): The MS/MS techniques of monitoring and recording one 

or more precursor-to-product ion transitions rather than monitoring and recording the full 

MS/MS spectra (i.e., all precursor or product ions). This practice can serve to greatly increase 

signal-to-noise by reducing noise. 

“Soft” ionization: Low energy ionization process that typically results in little or no molecule 

fragmentation. The ions are usually either protonated (M+H)+ or deprotonated (M-H)-. Soft 

ionization processes include (but are not limited to) CI, ESI, APCI, and APPI. 

Structurally significant ion: Ion with a mass-to-charge ratio (m/z) which indicates a 

characteristic structural grouping formed by the fragmentation of a molecule.
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Target ion: A structurally significant ion selected from the reference spectrum, typically the 

most abundant ion, to be used to generate relative abundance ratios with qualifier ions. The 

target ion is sometimes called the primary ion.

Time-of-flight (TOF) mass analyzer: Type of mass analyzer that uses the flight time of an ion 

over a fixed distance to measure its mass. Lower mass ions will move through fixed distance 

faster than higher mass ions.

Total ion current: A plot of the summed intensity of all acquired ions in a MS or MS/MS 

spectrum versus time. The term total ion chromatogram is also used.