Sunday, September 30, 2007

Sunday Roundup

The CyclingNews says that the city of Stuttgart refuses to pay the UCI the rest of the money owed it, righteous indignation abounds:

"We will not hand over taxpayers' money to any organisation that is not fighting seriously against doping," Mayor Wolfgang Schuster told the Stuttgarter Nachrichten newspaper according to Eurosport. On the line are 600,000 Euros due to the UCI and 75,000 Euros due to the German Cycling Federation.

The VeloNews
provides another doping item, this one has Paolo Bettini suing the German TV station ZDF for accusing him of supplying PEDs to Patrik Sinkewitz. It sadly seems that more action currently takes place in courtrooms than on the roads:

Bettini had slammed what he termed "a campaign of denigration of which the town of Stuttgart, the organising committee and channel ZDF are responsible." "We've decided to take legal action regarding this campaign of denigration," the cyclist's lawyer Guido Marangoni said. "We're not yet in a position to evaluate the totality of the damage cause to Paolo Bettini."

The Miami Herald
writes about the "dark side of the sports circus" and includes Floyd Landis along with McLaren racing, Michael Vik, and Bill Belichick. It speaks about the rather institutionalized cheating that takes place in a win at all costs time in our history saying that perhaps the current spate of cheater stories is cyclic. The bottom line is that all of the cheating that takes place undermines the integrity of sports.

Blindside posts an entry dedicated to a discussion of what can be good and bad about using the internet. One good thing cited is that vigilant users can expose fraud, and the bad is that unscrupulous people can illegally distribute PEDs. Inevitably it seems Floyd Landis is blamed for making cheating look appealing in some way in that winners take drugs or something. Huh?

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Saturday, September 29, 2007

Saturday Roundup

St Louis notes that the second Tour of Missouri is scheduled to beging next year with approximately the same dates as it did this year, and that would interfere with the proposed super race the Tour of America. The author, Kathleen Nelson, mentions that the Tour of America is not yet sanctioned by the UCI and the only riders who would participate would be those with time on their hands, such as Floyd Landis.

VeloNews reports that Michael Rasmussen was found to have used Dynepo which is thus far not on WADA's banned substances list due to the fact that it is nearly identical to naturally produced human EPO cells:

Traces of Dynepo, a biosimilar EPO, were found in Rasmussen's urine," AFLD President Pierre Bordry told the Reuters news service on Friday. "Rasmussen's test could not be declared positive because of the positivity criteria of the World Anti-Doping Agency (WADA)."

Currently, the EPO test can be declared positive only if the erythropoietin used is the older version of Epogen. Since Dynepo is made from human cells, WADA researchers said the risk of a false positive is too great since it could be mistaken with human EPO.

The NY Times says that Operation Raw Deal, the huge steroid bust made by the DEA earlier this week, doesn't even scratch the surface of the problem and that someone else will now fill in the gaps left by the recent arrests and destruction of clandestine steroid labs.

Rant compares two stories from today on the Rasmussen Dynepo revelation. One version seems to leave out some important information, but both neglect exploration of WHY we even know this information since by WADA rules we should not.

Standard Chuck's View of Everything Around feels that events such as the Landis saga, have tainted sports and we now no longer feel shock when we read about the latest scandal.

Brewers Pub Sports notes that Floyd Landis has lost his tour de France title, after a year of deliberations. No wonder we all feel so tired.

T-Guy J missed a lot while he was on his honeymoon, including the Landis decision. He likely had a lot more fun that the rest of us who missed nothing.

The Science of Sport
reviews several recent doping cases including that of Floyd Landis, and worries about the atmosphere in which we live that could create public apathy about them.

Chicago Bull
talks about promoters trying to stage a Tommy Lee and Kid Rock fight. It got CB thinking about who he would like to see in the octagon and one of the pairings he thought up was Rick Ankeil vs Floyd Landis for the best sports comeback ruined by steroids, keep thinking CB:

In 06' Floyd Landis was a huge success story, and this year it was the reemergence of Rick Ankiel. Both have cheated their way to glory, and now they get to win something they actually have to earn. This fight was over before it began though. Ankiel has 60 pounds on Landis and 3 inches in height (according to perspective websites that I don't believe). Not to mention, Landis probably has been clean now that he still trying to take tests while Ankiel can keep doping up. Ankiel mauls him; Landis cries that he was set up and wants a second fight to no avail

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Friday, September 28, 2007

Retention Times II

I'm having problems editing the earlier post, so this is a continuation in a new one.

Figure 5: IRMS chromatograms stacked; Cal mix, Blank F3, Landis F3

Figure 5 does the same thing we showed in the previous post, theoretically in Figure 3, and practically in Figure 4, which showed how the GCMS peaks were correctly identified. Here we've taken the charts from USADA 361, 345 and 349. We see that the cal mix in this case only contains two peaks that match the urine samples -- the 5aA internal reference, and the first metabolite of interest, the 5bA. These matches are outlined in yellow.

There are no standards in the cal mix for the 5aA or 5bP metabolites, thus no positive identification according to a very strict reading ot TD2003IDCR. This is possibly what Dr. DeBoer meant in his B-Sample observer's report when he said peaks were not identified to "minimal WADA criteria."

It is also puzzling, because LNDD had the right cal mix available with the other metabolites. They did, after all, use it in the GCMS runs, leaving no doubt there.

Absent an end-to-end calibration sample match on the peaks of interest, we are left with two options for identification.
  1. Assume the unmatched peaks in the blank are the peaks of interest, unproven since there is no calibration to back up the claim;
  2. Attempt to match the GCMS that was properly identified to the IRMS that wasn't.
As we've been discussing, there seem to be two ways to do the latter, relying on the "visual gestalt" of the pattern of peaks. This assumes that the peaks are in the same order ("of course" says the Majority), and that no significant peaks appear or disappear between the representations. The panel adopted this approach, even though there is nothing in the technical documents to support it as a methodology. The correct thing would have been to use a cal mix with the right compounds present.

The second method is to attempt to work out the math to map the retention times from the GCMS to the IRMS. The Majority says this can't be done. Herr Doktor Professor is evidently more comfortable with the math and the physics and tried to do this.

Attempting to map the times requires accounting for all the significant differences, and Meier-Augenstein believed he had.

Figure 5: Shimadzu's catalog of relevant factors

Poking at the "details" button on the Shimadzu "relative retention" page, we see why it seemed like a good thing to try:

Figure 6: Shimadzu explains why relative retention is useful

The advantageous point of relative retention is that it depends only on the ratio of distribution coefficients and the effects from some parameters, such as column length and carrier gas flow, are bascially cancelled out.

However, there are some limiations for relative retention. Measurement of errors will increase for target peaks located far from the reference peak.

(emphasis added).

Are relative retention times useful for comparing results across instruments, which the Majority denied?

This journal abstract suggests otherwise:
Using experimental RRT data for 126 PBDE congeners from the literature, predictive regression models were built for seven individual GC capillary columns differing in stationary phases. Each model includes four descriptors which included Wiener index, Randic index, polarity parameter, etc., selected by CODESSA. High predictability was obtained. High multiple correlation coefficients R2 indicated that >98.5% (except for stationary phase CP-Sil 19) of the total variation in the predicted RRTs is explained by the fitted models.

Or this one:

Phenolic acids and related compounds were separated by gas chromatography using three separate columns. One of these columns was coupled to a Fourier transform infrared spectrometer. The trimethylsilyl derivatives could be separated and identified by comparing the relative retention times of the three different columns. However, where there was overlap, the accompanying infrared data clearly distinguished between the questionable derivatives, thus enabling characterization of all derivatives.

This one seems particularly apropos:
Since retention times vary with the column length, type of stationary phase and temperature, suitable parameters for comparison include relative retention times and so-called retention indices (RI). Relative retention times are simply the ratios of analyte times to the time of a chosen standard compound.

On values for matches, this EPA lab related document says,

9.8 Qualitative Confirmation- The relative retention time of methyl parathion in samples is tracked by comparing the relative retention time (rrt) of sample to standard within "3 standard deviation. In addition, a second, dissimilar GC column is used to determine if methyl parathion and surrogate were positively identified by both rrts.

The DEA has used relative retention to identify opiates and steroids:

Gas Chromatography (GC): The chromatogram is not shown. Methandrostenolone, dehydrochlormethyltestosterone, and stanozolol eluted at 7.96, 9.32, and 10.29 minutes, respectively. The peak shape for stanozolol was broad in comparison to the other steroids. The mixture in the yellow tablets was not formally quantitated, but was estimated as roughly 100 : 5 : 2.5 dehydrochlormethyltestosterone : methandrostenolone : stanozolol. Table 1 lists the relative retention times for cocaine, heroin, and six other steroids with similar chromatography.

Table 1. GC Relative Retention Times.

Drug (GC)
Cocaine 0.580
Mesterolone 0.813
Testosterone 0.822
Heroin 0.829
Methyltestosterone 0.836
Methandrostenolone 0.854
Testosterone Acetate 0.882
Fluoxymesterone 0.990
Dehydrochlormethyltestosterone 1.000
Stanozolol 1.103
Testosterone Isocaproate 1.188

It therefore appears that the assertion by the Majority in paragraph 188 that use of relative retention times to provide comparisons across instruments is "unsound and without any reasonable scientific basis" may itself be categorized exactly the same way. It suggests the Panel did not understand the science, or chose not to understand the science, and/or was misinformed by the "independant expert" or Brenna's testimony.

It should be noted that an even more accurate methodology is the use of "Kovats indexes", but those are not appropriate for the chromatograms at issue here. Their use requires a pair of internal standards, one at the beginning, and another at the end, after the target peaks. Since LNDD has not provided a later standard, the only methodology available is the use of relative retention times.

How we got here
  1. Brenna, Ayotte and Mongongu testify relative retention time is how peaks are matched between GCMS and IRMS.
  2. LNDD did not use an IRMS calibration standard to unambiguously identify 5aA and 5bP in samples.
  3. LNDD did not use an IRMS calibration standard with a trailing internal standard admitting use of Kovats Indexes.
  4. The only quantitative method available to match the GCMS and the IRMS peaks is the relative retention time.
  5. Herr Doktor Professor calculated the RRT matches, and they are at least 5%.
  6. TD2003IDCR says 1% or 0.2 minutes.
  7. Peak identification appears not to be done in an ISL-acceptable manner.
  8. Brenna changes story, testifies [absolute] retention times can't work for lots of reasons.
  9. Brenna says "relative retention times won't work for reasons I discussed this morning"
  10. Brenna says the match is done visually.
  11. Panel accepts "visual gestalt" as an acceptable peak identification technique, and lambastes Meieir-Augenstein and Davis for suggesting RRTs are relevant.
Is Herr Doktor Professor's math right?

Over at DPF, a number of people who are not in the group generally associated with sympathy towards Landis' arguments have repeated what Meier-Augenstein did, and obtained identical results, down to the 7.2% mismatch of RRTs on the furthest compounds in samples.

[ still working on the math part to get a clear example ]

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Another side of Euro Press

An emailer sends along a babelfish version of a story in the Swiss WeltWoche:

A judgement, which is not
Hanspeter Born

Did he dope now or not? The question, whether Floyd Landis won the route de France only by artificial Testosteron, remains disputed.

After months-long consultation an American arbitral tribunal with 2:1 voices, consisting of three lawyers, found the winner of the route de France 2006, Floyd Landis, guilty of doping with synthetic Testosterone and two years closed. The majority of the committee granted that numerous procedural errors were suffused to the French laboratory LNDD that it made itself guilty “sloppy practices” and that, “if such practices persist”, in the future doping analysises of the laboratory be rejected could. Arbitral tribunal found also that the results of the original doping analysis, with which a too high quotient was determined from Testosterone to Epitestosterone (above 4:1), an examination do not withstand. Nevertheless the arbitral tribunal Landis holds for guilty, because the additional carbon isotope test proved the income of exogenous Testosterone.

The arbitral tribunal majority trusts thereby the scientific experts of the “accusation”, i.e. the US-Anti Doping Agency acting on behalf the World Anti Doping Agency WADA, which regards the results of the carbon isotope test as “unambiguous”. In a deviating minority opinion the third member of the arbitral tribunal, a former olympic Ringer, holds the opinion that the documents submitted by the French laboratory are in such a manner filled with errors “that they do not support an offence against the Doping Rules” and that “Mr Landis should be found innocent”.

The judgement of the arbitral tribunal raises more questions, than it answers. Contrary to (embarrassed) the directors of the Wada laboratories from Landis called scientifically expelled forensic chemists explained the results of the carbon isotope test for “unreliably”. One this expert, who had Andrologist John Amory, stated that the “strange” raised from the LNDD would contradict, from day to day varying values the results of all scientific studies, in which exogenous Testosterone was given to subjects. The arbitral tribunal majority did not deal with this argument. On the other hand it called from the experts of the defense, Dr. Wolfram Meier eye stone and Dr. Simon Davis, in the field offered proofs “scientifically completely unacceptable and fundamentally flawed”. These two with the devices chemists trusted used with the tests closely will not simply swallow this honour-active reproach.

Landis invested over two million dollar into the procedure. If it wants to further-pull the decision to the Lausanner sport arbitral tribunal TAS, it this dollar will cost estimated 800000. For the set off route winner, who still regards itself as a “legal winner”, the Anti Doping System is “corrupt, inefficient and unfair”. With this opinion he does not stand alone. In a thorough analysis of the submitted evidence the forensic chemist Robert D comes. Blackledge (in the specialized organ the California Association OF Criminalists) in the end: “The data of the LNDD in an actual criminal procedure before jurors in the American court system were submitted, bet I that the procedure would not even reach the stage that of conclusion final speech. After conclusion of the proof of the public prosecutor's office the judge would find that the accusation had not furnished a Prima-facie-proof, and the jurors to instruct to impose a non--guilty verdict.”

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Friday Roundup

The NY Times this morning says that it appears there may be no known professional or Olympic athletes involved, either as distributors or users, in the steroid network busted earlier this week by the DEA. However distribution of steroids by an athlete would be viewed by USADA and WADA as just as ,if not more, serious an offense as a failed doping control:

Gary I. Wadler, a member of the World Anti-Doping Agency and an associate professor at New York University School of Medicine, said that every drug policy should explain that failing a drug test should not be necessary to receive a sanction. The penalty for receiving, distributing or buying banned drugs should be the same as using them, he said, following the WADA’s code.

“Sure, we’ve talked about Floyd Landis and his failed drug test, but the paradigm has changed,” Wadler said. “So much of the story now deals with stings and federal investigations and law enforcement, and the leagues have to specifically address that shift in their drug policies. They can’t just view doping as a positive test. Those days are long gone.”

The Deseret Morning News
interviews Levi Leipheimer about his future plans, he is rumored to be heading to Astana, and inevitably asks him about doping in cycling which unfortunately brings up Floyd Landis' name:

The Floyd Landis saga, particularly, has been a challenge to deal with. Questions about doping haunt cyclists everywhere they go, and Leipheimer has heard just about all of them.

"Yep, that's pretty much all we talk about," he said, only half sarcastically over dinner. "I hope now that Floyd's deal is kind of over, that we can move on. Everyone acts like we're the dirtiest athletes in the world, when I think the reality is we are the cleanest. We get tested all the time. They show up at your door unannounced and test you. We're tested before races and after races. We're tested all the time.

The Daily Cardinal points out the many examples of cheating in sports that seem to abound now and explores what motivates those who cheat to do so. Floyd Landis is included on the list and the piece warns that he has much more to be concerned about than just losing his Tour de France title.

The Tracy Press
has plenty to say about cheating too.

The North County Times posts an editorial on the dangers of steroids to young athletes, and uses Floyd Landis' current woes as "exhibit A" as a warning to kids considering getting an edge on the competition.

Sportingo reviews the doping controversies leading up to this year's World Cycling Championships.

The CyclingNews
opens up it's Friday mailbag to reveal lots of letters commenting on last week's decision in the Landis case. Most of the letters expressed dismay at the ambiguity of the decision wondering how the majority arbitrators could criticize the lab as they did , but still uphold a suspension for Landis.

And the CyclingNews is full of more "UCI vs everyone else" news, and this includes the mayor of Stuttgart who has gotten in on the act. It also publishes the now rather confusing Pro Tour calendar, and the usual unfortunate doping updates.

The National Lampoon Splog makes an unoriginal crack about the Landis family. Funny it's not, but at least this one got the right religion.

Rog has two things on his mind this AM about Floyd Landis. One is that he hopes that Floyd is innocent, because if not Rog feels like a sucker. The second thing is that he hopes Floyd saves his money and doesn't appeal last week's decision, after all they can't take Floyd's memories. He also stole David Walsh's book "From Landis to Landis". Walsh may be a good writer, but he lies by omission, and it's only 1% Landis anyways. So don't buy it, though following Rog's advice on how to get the book may get you in trouble with Mr. Bookman.

High Voltage Report speaks about the dangers of riding, even in groups, and the Floyd Landis decision which has him more convinced than ever that Floyd got the shaft. Thanks for the plug!

Rant equates today's version of professional cycling to the "soap opera" it has become, without the sex that is.

Net.wars does a nice job of writing about doping enforcement and how it has been misapplied in some cases. She read "Positively False" and feels Floyd Landis did a better job than she expected in explaining the inaccuracies of the tests that showed he was positive for PEDs. She feels no one, including Dick Pound, can claim any glory:

Landis has, I think legitimately, pointed out flaws in the anti-doping system as it's presently constituted. For one thing, its courts are not governed by the due process and civil liberties that normally apply. The testing regime is privacy-invasive: urine or blood samples may be demanded at any time, without notice, and a missed test is treated as a positive test. In the case of a positive test, athletes can only call on assistance from experts who are not part of the WADA system – which means almost all the experts on the subject. Finally, the system is set up to presume guilt.

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Thursday, September 27, 2007

Thursday Roundup

The Cycling News reports that the CAS ruled in favor of Alejandro Valverde thus allowing him to take part in the World Championships in Stuttgart. The ruling is a setback for UCI president Pat McQuaid who had forbidden the participation of Valverde based on alleged ties to OP. This also opens the door to Australian Allan Davis and the Czech Rene Andrle who were in circumstances similar to that of Valverde. The UCI made its decision for "reasons of equity" after the CAS ruled in Valverde's favor. In the meantime Paolo Bettini has been accused of distributing testosterone gel, and the city of Stuttgart is threatening legal action against the UCI if Danilo Di Luca and Paolo Bettini start in Sunday's World Championship road race. Sounds like a mess for Dr Phil.

CNN reports that the folks at the World Cycling Championships won't have Danilo Di Liua to kick around any more, he's left the building:

"It's a scandal," Di Luca said. "I'm going home without ever being banned, after months of sacrifice. (The decision) only served to prevent me from racing the world championship. ... I will be cleared 100 percent."

After a three-month wait, cycling's world governing body, the UCI, gave CONI permission on Wednesday to compare that abnormal test with his other drugs tests given during the Giro.

CONI would not divulge the results on Thursday, but indicated the findings warranted a suspension. The case now moves to CONI's disciplinary panel and they could recommend Di Luca loses his Giro crown.

The CyclingNews
also has a "news flash" on the Di Luca story. And in earlier CyclingNews UCI president Pat McQuaid is criticized for not protecting cycling's legends.

The VeloNews
is on the Di Luca story as well, and Bettini may be out too, stay tuned.

The Canadian Press reports Dick Pound's comments on cycling and doping made in Beijing today. Pound says cycling can come back from the brink, but that it needs to get its' collective head out of he sand and get its' act together about doping:

He called on participants to ask themselves "what is the problem, what is the paradigm shift that we need to take in order to go from where we are now . . . to something that will give the world confidence that we've dealt with the problem."

"I think they've now realized that they've let this go too far and they're fighting their way back from the brink."

I don't Care says everyone loves an update, but the trouble is in the details. There's lots there, you'll have to hunt for Landis commentary which is a bit off as far as facts are concerned. Blogs posted one a few days ago that we missed. It's about atonement in the season of Yom Kippur, and not to be overly dramatic but Michael Connelly thinks that Floyd Landis' family and friends should keep an eye on him.

Jenn Martinelli snarks that Floyd Landis is an ass, not only that but he is also pathetic, shady, and stupid. Jenn says it's her blog and no one can argue with her, wanna bet?

WADAwatch notes the power struggle in process for the leadership of WADA after "lame duck" Dick Pound vacates his position.

makes mention of the Landis arbitration decision that came down 2-1 against him a week ago.

Rant makes a couple of points based on the CAS ruling in favor of Alejandro Valverde. Cyclists who have not been proven to have doped must not be punished, and those who run the store need to cease using cyclists as pawns to score political points. Amen!

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Wednesday, September 26, 2007

Discussion about Relative Retention Times

Over in the thread about visual identification of peaks (Discussion with BustinBilly), there have been some comments that lead naturally into a discussion about the applicability of relative retention time across two instruments.

As we know, Paragraph 185 of the Majority Award declared that it wasn't possible, therefore Landis' complaints about the RTTs not being within spec of TD2003IDCR didn't apply.

In the discussion of visual identification, I tried to show that some of the math used in paragraph 185 was incorrect:

M wrote:

Indeed, the majority decision in their mathematical example seems to suggest that what TBV is doing can never result in a match.

They say the retention times of the IRMS GC take longer than the GC-MS machine by some constant amount of time. They use the example of a relative retention time ratio of 10 to 5, becoming 11 to 6, after you add a 1 minute constant.

Well if in fact the IRMS retention times are off by some ADDITIVE constant relative to the GCMS machine, then you can't correct for that by MULTIPLYING in some proportionality correction. By stretching the scale I assume TBV is doing some multiplying. At least that is how I understand the example and the math.

TBV wrote:
The panel got their "math" example wrong. If they'd figured it out correctly, the example they gave as "broken" worked just fine. You are supposed to subtract the fixed offset before you do the multiplcation, so (11-1) / (6-1) works out to 10/5 just like they said it didn't.

M responded:

What is the authority for these two statements:

1. "You are supposed to subtract the fixed offset before you do the multiplcation"

2 "and then scaling (doing the proportional multiplication)." (I asked before, on what basis are you claiming you are entitled to do proportional scaling?

Kevin answered:

You can google "relative retention time chromatography", and the first link you find ( will take you to a pdf document entitled " Retention Parameters in Column Chromatography". It has a section (p.2) describing the Adjusted Retention Volume (Time). It then goes on to discuss Relative Retention (r) on p. 4. For those who are interested, IUPAC is International Union of Pure and Applied Chemistry. This is pretty standard stuff.
Another reference I've found is a tutorial at the Shimadzu web site, unfortunately in Flash.

(also some interesting stuff at
Although many consider GC/MS to be the "gold standard" in scientific analysis, GC/MS does have some limitations. Because great faith is maintained in GC/MS analysis, erroneous results are not expected and hard to dispute. However, false positives and false negatives are possible.

I'll confess that I've never quite understood some things about RTT. It's been represented to me that it does solve the problem in question (identifying peaks) across different runs, which might include different machines. The Majority of the Panel asserts this is not the case.

Let's explore together the same way we did with "visual gestalt". I'll post some things as I understand them, then comments can react and tell me what I've gotten wrong. I'll collect the ones I think are most relevant here and we'll see where we end up.

Before going on, commenter "M" writes, quoting the iupac reference above:
On the other hand, the unadjusted relative retention (and "relative retention time") values are only reproducible within a single chromatographic system."

There's an implication that RRTs are therefore not valid, except that we are dealing with a single chromatographic system, despite various caveats:
The GC column is, of course, the same in both instruments

-Majority award paragraph 188

So, we'll work through it as best we can and see who is hot-dogging who.

Let's illustrate some terms, shamelessly borrowed from the Shimadzu tutorial, also from an Agilent document on terms.

Figure 1: Basic Parameters

Time zero is the injection, then there is plumbing delay (see majority award para 184).

The "Retention Time" is from injection to the peak detection.

The unretained compound peak seems to be time at which a test substance that won't be delayed by the column is injected until when it gets out. It goes through the column as fast as anything possible can, and becomes a fixed reference for this run.

The "Adjusted Retention Time" is the retention time less the hold-up time.

Figure 2: Relative Retention

In the simplest case, we have two sample peaks, a known reference, and a target that follows. The RRT is the ratio of the adjusted retention times of the target and reference, and shown as the "alpha" symbol.

The figure also introduces K symbols, which are Retention Factors. The retention factor for a peak is the adjusted retention time divided by the hold up time. As a special case, the retention factor of the unretained peak is defined to be zero, to avoid a divide-by-zero.

Figure 3: Compound identification by Time

Figure 3 shows how retention time is used to identify compounds. Given the times observed in a sample with known substances, the times can be compared with times of unknowns in a target sample.

This is how we know in the GCMS that the labeled peaks are what they are -- there was reference run in the GCMS with standards that identified the substances in question, and the retention times there were matched within TD2003IDCR of the Landis target samples.

Figure 4: Example matches of USADA 309, Cal Mix Acetate and USADA 321 Landis F3 f.

Figure 4 shows the kind of match done in Figure 3 with the LNDD calibration sample and the Landis F3. The target peaks line up well, within TD2003IDCR. We note at the left edge by the known standard that the circled peaks of the standard in the cal mix acetate is very different height than it is in the Landis sample. If we'd gone on peak heights alone rather than look at the times, we might have lined the Landis next peak to the right with the cal mix.

Figure 5: IRMS chromatograms from '474 B: Cal Mix, Blank F3, Landis F3.

[ coming, cal mix in the IRMS and the Landis F3 ]

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Wednesday Roundup

The CyclingNews has more this morning on the bitter disaapointment felt by Pat McQuaid over Paolo Bettini's refusal to sign the UCI "pledge". In other UCI news Andrey Kashechkin is beginning legal proceedings against the UCI for invasion of privacy on the same day the UCI case against him went to court in Liege. Also the President of the Spanish Sport Superior Council Jaime Lissavetzky has responded to Pat McQuaid's accusations that Spain is the source of the most of sport's doping problems. Lissavetzky's comments come after McQuaid criticized the nation for having a "reluctance to completely clean the problem out". Lissavetzky stated that he does not answer to the UCI or Pat McQuaid. Sounds like the UCI has its' hands full with non competition matters, and one wonders if any of this recent outspoken behavior by athletes and governing bodies alike has any connection to the way the UCI has treated Floyd Landis and his reaction to that treatment .

The Collegian Online
says the most distressing thing about the Floyd Landis saga is not the drug use itself, but Landis' utter lack of remorse for his actions. On the other hand if one's conscience is clear, remorse need not be an issue.

FoxSports Australia picks up the Reuter's version Landis statement to the FFF on Monday, as have many outlets this AM. reports that Floyd Landis was supported, after the arbitration decision that went against him 2-1, by the home folks who they describe as "Amish". It wouldn't hurt to do a little fact checking now and then, would it?

The Herald Sun
quotes the "disgraced" Floyd Landis that it is the anti doping establishment and not Landis who failed to play by the "rules".

The Gilroy Dispatch took calls and votes and decided that cycling may be a sport after all, and that the doping in cycling is not all related to Floyd Landis. Bless that garlic.

Bike Biz says "round one" to USADA, and thanks for the continuing plugs:

There are inconsistencies in both documents. Legal eagles – and those experts dissed in the two decisions – will likely be reading these documents closely, with possible fireworks to follow

VeloNews has a flash from Interbike that a North Carolina sports management firm will finance a "Tour of America". The 27 stage 22 state race will invite 25 of the world's most elite cycling teams. No firm dates or routes have been made available but the prize money is listed at 11milion dollars:

"This event will be the greatest international cycling event in the world," said Aqu, Inc. President Frank Arokiasamy. "The Tour of America will provide the largest prize pool to international cyclists ever offered in history and will ensure quality competition from beginning to end. We are excited to finally bring one of the world's largest spectator sports to the United States through a major international competition."

Floyd posts the same message of thanks to supporters that was first seen on the FFF web site.

Phantom Reflections says that in light of the smear campaign against Floyd Landis America has stood up on it's hind legs and said "no more", and thus is born the "Tour of America".

The Mighty Quinn has Floyd Landis as the answer to a trivia quiz question.

Elipongo's Blog did a Yahoo News search for "sleep" and got the quote from Floyd Landis that he is not losing any over his recent arbitration decision.

Epic Carnival
discusses PEDs and says he is sick of reading about doping athletes all the time. He says several American Olympians ,who tested positive for banned substances, were allowed to compete and states the USOC covered it up.

Dave's Room of Words wants Floyd Landis to take sodium pentothal, truth serum, then we will "know" the truth. Sounds like Dave has watched too many episodes of "Mission Impossible".

131 Days got Floyd Landis right after the Tour de France last year, and he was fun at first. But he's now been farmed out so he can run and play to his heart's content without annoying anyone.

Pedal Harder
has a few choice, very colorful words for Floyd Landis' hip, I'll say no more.

Petaluma 360 asks, "Floyd Landis, Victim or Villain"? Good question as Rick Moeller explores sports, what they mean to us and why we expect so much from those we idolize:

We want heroes. Nice clean, shiny, moral, ethical, paragons of virtue that we can hold up as examples of the unblemished nature of humanity. Thus by extension, all the rest of "us" are heroes too. Nice dream, if logically, not to mention genetically, flawed.

Rant covers the Paolo Bettini vs Pat McQuaid story, which reveals the UCI "pledge" for what it is, a PR stunt. Rant goes further to speak about the damage mere accusations can do to a cyclist's reputation, not to mention a positive doping control, or even a finding of guilt such as in the Landis case. Why would anyone want to sign it?:

Who, in their right mind, would want to sign such a document? Especially knowing that the system is so riddled with flaws that his or her career and reputation could be ruined by the mere accusation of doping as a result of a leaked test result, long before the case is heard and an arbitration panel has convicted a person of doping.

Perhaps Bettini understands that signing a worthless piece of paper is of no matter in the fight against doping, especially when there are other, bigger problems that need attention in the anti-doping world. Doping in cycling has been a problem for a long time. Signing “The Pledge” won’t put an end to the problem.

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Tuesday, September 25, 2007

Tuesday Roundup

The San Bernardino County Sun posts comments from local friends and fellow cyclists who feel depressed and disappointed in the 2-1 arbitration decision that went against Murrieta resident Floyd Landis last week. Bike shop owner Scott McAfee , who had held a fund raising event for Landis in June said:

"If you're going to ruin someone's career,you better have your procedures straight."


The NYT further expands yesterday's story of a DEA crackdown on steroid labs which have an extensive connection to China.

ESPN has Pat McQuaid quoted as saying that Spain may be the root of many doping evils and needs to not only enact laws on doping but vigorously enforce them as well.

The Times Argus had Floyd Landis as the answer to an obscure clue in a sort of word game. You'll need to look far down the piece to find it.

The San Diego Union Tribune says that even though no one in golf is likely using steroids or HGH it's a good idea to test since, "line between honor and cheating these days is as thin as Floyd Landis' yellow jersey." Seems you gotta get your cheap shots in where you can these days.

The Boulder Report comes to the conclusion that after all the time, money, drama, heartache, and PR disasters, what the Landis case taught us is that the anti doping system no longer works:

I have written before about how disappointed I was with Floyd’s defense, which I saw to be aggressive to a fault, overly technical and relying too much on public relations. The circumstantial evidence surrounding cycling indicates that it’s entirely likely that he did use synthetic testosterone. I still think all of that is true. However, after the trial, and looking at the opinions, I think the case could as easily have gone Floyd’s way and, in the interest of the system’s integrity, maybe it should have. Did he do it? I don’t know. But neither can I be sure that the anti-doping community convincing proved its case. And that we all must live with that question is unacceptable. The problem that remains then is whether we have the political will to change the establishment, and if so, what would we do?

It's rather long winded but worth the read.

posts an AP Eddie Pells piece which dissects the Floyd Landis statement of appreciation to donors that was posted on the FFF yesterday.

The Glenwood Springs Post Independent asks various readers which sport is doing the best job of policing itself where doping is concerned. Jeremy Simon seems to have a reasonable answer, but a lot of the respondents think that cycling is the worst.

GMA News TV posts a chronology of the Landis case, from the beginning.

The VeloNews Tuesday Eurofile has plenty to say covering the Bettini vs McQuaid story, as well as the idea that the pro cycling teams have agreed to cover the significant costs for the testing of their riders. This latest anti-doping initiative was suggested by the International Professional Cycling Teams (IPCT) association and is in part a reaction to the internal programs established by CSC and Slipstream. The silence of "the Lance" is also covered

The IHT reads like a soap opera script as it describes the machinations that accompany the beginning of the World Cycling Championships. Paolo Bettini won't sign "the pledge" which has the UCI's Pat McQuaid in a snit. Meanwhile McQuaid is still trying to keep Alejandro Valverde from participating, but if the CAS rules in Valverde's favor McQuaid concedes that he will be allowed to ride. And, local officials in Stuttgart are crying out for the exclusion of admitted/reformed doper Erik Zabel. Sounds like fun.

CFA unequivocally states that if Lance Armstrong thinks he is now only a cancer crusader and can spend the rest of life denying he has any interest in cycling, thus allowing him to refuse comment on the Landis decision, he is nuts!:

This is his new mantra, and you better believe it is paying off for him in big ways that have nothing to do with cancer. He is earning himself vast reservoirs of goodwill that insulate him from any and all doping accusations that might still linger and follow him. So good for Lance, he may have suddenly and mysteriously lost any ability to multi-task, but before long he will surely be granted sainthood and permanent lifetime immunity from any and all negative innuendos. He might have been ruthless and arrogant, but he never was dumb.

Veloguy passes on a piece with more non comments from Armstrong

Steroid Nation hops on the "Armstrong will not comment on Landis " bandwagon:

Frequent champion Lance Armstrong, almost as frequently questioned about doping, says he don't know and he don't care about his former bud Floyd Landis' doping conviction last week.

Thoughts of Hazel Mae calls Floyd Landis a chump and then is chagrined to not be able to come up with a good punchline. That's OK,really.

Chuck the Cyclist
fears that he sadly may have to look for another American hero.

cwdtrek82 has too much to write about and too little time now, so comments on Floyd Landis will have to wait. But there was time to write lots about the current Genesis tour and Dad.

Edocblog got to hang with mountain biker Dave Wiens,winner of this year's Leadville 100 where Floyd Landis came in second . Kent and Dave were manning an aid station together at the Vapor Trail event and Kent got to hear the blow by blow of the battle between Landis and Wiens at Leadville.

sent another open letter to all of the WADA laboratories urging reform in light of the Landis ruling and the upcoming WADA summit in November.

In further ZENmud news, a new blog is born. WADAwatch will concentrate on WADA news and discussions and leave the old CrystalZENmud blog to talk politics and other current issues. WADAwatch will keep its' eye trained on WADA.

team raceAthlete provides three perspectives on the Landis arbitration decision. One is pro Landis, one thinks Floyd got what he well deserved, and the third one is that oldie but goodie (?) from "The Onion" about a drug free Tour de France.

Rant puts together the "The Science of it all" giving a GC/MS/IRMS primer for the scientifically challenged with descriptions of how the tests work, and highlighting as well potential problems with retention times ect. Rant explains the relevance of this to several internet discussions that have ensued since the announcement of the Landis decision.

Clearly Sports
obviously thinks that for Floyd Landis it's all about the dollars, claiming that not only was Landis rumored to have been a rampant drug user before the 2006 Tour de France began, but that Floyd is also so arrogant he assumes the public will just believe him when he says he is innocent. To say this is "snarkworthy" would be a gross understatement, but it's obviously representative of at least some sports fans.

The Outdoor Weblog
notes that Floyd Landis continues to maintian his innocence.

Where I Stand thinks that Floyd Landis deserved punishment. No one feels sorry for Landis now who must face the consequences of his actions. That's one way to look at it.

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Monday, September 24, 2007

Floyd Landis' Message

This is a message from Floyd Landis sent out to friends and supprters via the FFF home page

Dear Friends and Supporters,

I’m of course disappointed and in fact angry about the split decision ruling against me last week.

If any good has come out of this, we have shown that the anti-doping system is corrupt, inefficient and unfair. The content of this decision unfortunately highlights this once again. The straightforward and clear dissent in support of my case contrasts sharply with the scientifically flawed and illogical majority decision against me – not to mention the nonsensical ruling regarding when my proposed two-year suspension should start. I still have hope that the system can, and will be, changed so that no other athlete has to suffer through this process only to be denied a clean chance at justice.

I can sleep well at night knowing that I won the 2006 Tour de France fair and square. I hope that my campaign to clear my name still means something to all of you who have kindly donated to my legal defense fund. Every single contribution to the FFF made a real difference. For your constant support and generosity, I thank you.

At the end of the day, I am proud of what I accomplished in winning the Tour and I’ll always consider myself the rightful winner of the Tour. Whatever the way ahead, it will be good to be moving forward with my life, and at this point I will take some time to review my options.

Thank you for all of the support and encouragement,


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Monday Roundup

The CyclingNews posts that the policy making arm of WADA has banned several news substances for 2008:

New for 2008 will be "new classes of substances such as selective androgen receptor modulators (SARMs), a family of nonsteroidal molecules that has the same effect as anabolic steroids, and agents modifying myostatin functions including but not limited to myostatin inhibitors" the organisation announced.
The committee also approved the prohibition of intravenous infusions unless they are used to treat an acute medical condition.

reports that a number of underground streoid operations have been busted by a coordinated effort on the part of the DEA:

In a four-day series of daylight raids that ended Sunday, Drug Enforcement Administration agents shut down 26 underground steroid labs and made more than 50 arrests across the country, capping what agents are calling the largest performance-enhancing drug crackdown in U.S. history. The DEA also has identified 37 Chinese factories that purportedly supplied the raw materials for the labs, a DEA spokesman told ESPN.
The investigation also focused on message boards where advice is traded about obtaining raw materials, as well as on the Web sites that help the labs sell finished products to the public. Hundreds of thousands of e-mails were intercepted, according to Dan Simmons, a San Diego-based special agent for the DEA. Simmons said that no professional athletes have been implicated so far but that the e-mails are being compiled into a massive database of names and are being analyzed.

In a separate investigation in Albany, NY over two dozen doctors and pharmacists were busted for running illegal prescription mills for HGH revealing the huge extent to which it is being used by athletes.

ESPN's Page 2
has Jim Caple thinking that Floyd Landis got hosed when the arbitration panel from his hearing last May voted 2-1 against him:

Imagine your reputation, your career and the prize to which you devoted half your life are on trial. You present your side of the story and the prosecution presents theirs. When you've both finished, the judge nods and says he'll get back to you sometime in the future; he won't say when. A week passes. A month passes. Another month passes. Another two months pass. Finally, four agonizing months after your trial, the judge announces his decision.

Floyd Landis waited four months before receiving the bad news.
The fingerprint evidence against you, he says, was unreliable. And the lab analyzing the DNA evidence, he acknowledges, did shoddy work.
And then he delivers the verdict. You're still guilty.
That's pretty much how it worked for Floyd Landis, who just lost his arbitration case over his positive testosterone result in the 2006 Tour de France.

The St. Cloud Times posts an op-ed by John D Reep in which he expresses outrage and concern over the 2-1 verdict against Floyd Landis . He fears for the rights of athletes everywhere due to the arbitration panel's decision:

In our judicial system, Landis would have won in a romp. Much of USADA's case would have been inadmissible.
But in WADA world things are different. WADA sets the rules, acts as prosecutor, and appoints a best friend as judge. It's a fixed game. If you are accused you will lose.
Most people won't bother to read the 84-page arbitration award or the 23-page dissenting opinion. They'll assume it must be correct because someone who sounds kind of important wrote it, and it's awfully long.

After reading the decision, I'm convinced the mental gymnastics required to find Landis guilty are worthy of a gold medal. They ignore compelling scientific evidence and scores of lab errors.
The lab was sloppy and incompetent. Staffers didn't understand the equipment, violated procedures and standards repeatedly, failed to properly track chain of custody, reran tests, cherry-picked results and covered their ineptitude by overwriting the computer files.
It is any wonder they have had three times as many positive tests than the other 32 WADA labs, while actually doing fewer tests?

The Cleveland Plain Dealer's "Ask the Slouch" has more to complain about than a "jobbed" Floyd Landis does, he tore up his betting slip that had Oscar Pereiro winning the TdF.

PezCyclingNews provides a short report on the announcement that Oscar Pereiro was declared the 2006 TdF winner by the UCI.

The Province quotes Landis Armstrong on the Floyd Landis affair during yesterday's cancer fund raiser ride in BC:

"I'm not in that business," said Armstrong, adding he's focused on finding a cure for cancer now. "I only have the ability to focus on one thing at a time."

The Tucson Citizen publishes alleged "humor" by Argus Hamilton.

Bicycling's La Scene reports Oscar Pereiro seems to be getting little respect as the newly declared 2006 Tour de France winner.

The VeloNews Monday Mailbag has dedicated the entire column to responses about the Landis verdict. As one might expect some are outraged at the treatment Floyd Landis received by what one letter percieves as an unqualified panel of arbitrators. Some letters are outraged that anyone would still believe Floyd Landis did not dope as he is clearly a cheater, and so it goes.

Yahoo Eurosport posts a piece which comtains yesterday's non comments on the Landis case from Lance Armstrong, but it also includes a short statement on a possible press conference from a Landis representative:

Meanwhile Peal Piatt, a spokeswoman for Landis, said she doesn't expect the San Diego-based cyclist to hold a news conference to address the arbitration panel's decision to strip him of his title and slap him with a two-year ban for using synthetic testosterone.
"I don't know if we are going to have a (news conference)," Piatt said. "He's just taking it all in."

Biking Bis makes note of Lance Armstrong's non response to the Landis verdict.

CrystalZENmud read the Landis decision twice this weekend and came away with the opinion that the majority in the decision never fairly considered the minority opinion of arbitrator Christopher Campbell:

The best example of this, from my first, early analysis of a total of 103 relevant pages (of some 110 total), is found in the Campbell Dissent, and concerns the topic of 'cherry picking through separate sequences for ICRS evidence' (see Campbell, paras. 4 – 12).

In the majority's Decision, there is no mention of 'cherry picking' of evidence from the vital testing sequences that resulted in the Floyd decision of positive. Why not? Why ignore the most powerful statements made by the third member of this Arbitration panel?

In an update Zen tells us why the process Floyd Landis has found himself in for the past 14 months took so long, and what needs to be done to solve this problem.

NPA Think Tank is full of Dick Pound news, and wants to know what planet Dick Pound lives on where lab procedures do not matter if they ultimately find a positive test? NPA also wonders how in the world WADA doesn't hold itself to the same high standard that it holds athletes to? Good question. He ends his piece with what he considers to be good news.

Mom the Baby Nurse doesn't know what to think about the Landis case.

Carbolic Smoke Ball
has Floyd Landis morphing into the "Incredible Hulk" after learning of the arbitration decision that went against him. Nice Photoshop work.

The World According to Nick
wonders how the lab in the Landis case can get the initial testing wrong and then be trusted to do more complicated testing right. He also answers a friend's question asking whether the Tour de France can be won clean.

Ask Ryan
gets the "snark of the day" award , even though it's early, for not only insulting Floyd Landis but his family as well.

Steroid Nation
writes about the massive steroid bust by the DEA and in the Yahoo piece he cites it's mentioned that there may be a database of the steroid user's identities.

Baby Hatchetface
compiles a list of highly inappropriate Halloween costumes, one of which would involve Floyd Landis if you were clever, or slightly cruel.

Pommi posts Floyd Landis' statementto FFF supporters from earlier today.

NJ.Com posts a nice picture of Floyd Landis at a recent fund raising event in Bucks county for Anchor House.

The Long Run posts an eclectic blog entry tonight, and one of his comments is an expressed disappointment in the Landis hearing outcome. He is not surprised, but is sitll disappointed. Thanks for the plug BTW.

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Sunday, September 23, 2007

Discussion with BustinBilly on matching GCMS with GC-IRMS

In the Saturday Roundup, BustinBilly made a comment:

Don't debate the retention times just look at the damn plots. They are printed @ UsadaAndLandis-FinalAward20-09-07[1].pdf pages 41, 42. They are exactly the same. No doubt.

I used to believe Floyd until I saw the evidence.

To which I replied:
Excellent, not [meant "now"] we can have some useful discussion.

I'm sure you understand that only the F3 fractions are relevant; why the others were included is a mystery.

Your commend say the plots are "exactly the same"

In what ways do you think they are the same? Once you identify some of those we'll have something to talk about.


And BB replied:
The F3 is the 5-alpha-androstandiol-5beta-pregnandiol difference this whole shebang is about. The A sample F3 is @ pages 35, 36. The GC/MS and GC/C/IRMS plots are identical. The two metabolites above and the 5-beta-androstandiol are the 3 peaks in the middle of the GC/C/IRMS plot.

with clarification

I meant the 3 big peaks in the middle.

Because this is important, I've given this discussion it's own post here, and expect to carry on in comments below. Warning: I will be merciless deleting off-topic comments.

I believe BB is referring to the the following chromatograms. First the GCMS of the blank, the Landis F3, then the two overlaid to show what Brenna testified, the retention times line up. This was never disputed.

Figure 1:
Blank F3 GCMS plot, labeled by compound; very clean chromatogram.
click for full size

Figure 1a:
Landis F3 GCMS

labeled by compound
click for bigger

Figure 1b:
Blank F3 and Landis F3 GCMS overlaid
Scaling isn't perfect, but the identified compounds line up within TD2003IDCR by time.

(Note the very messy and sloping background in the Landis compared to the blank, and the extra peaks it contains.)

And then the GC-IRMS plot:

Figure 2:
Landis F3 GC-IRMS chromatogram,
labeled by retention time and CIR.
click for full size

To make things clear, below are versions that put the things on top of each other, going along with BB's (and USADA/Majority) claim that the big peaks in the middle are absolutely the ones in question. That is, one is lined up, and the scale adjusted linearly so the other peak lines up as well. This anchors the highest middle peak, and adjusts the scale so the rightmost big peaks line up. These are the "peaks of interest" for the measurements.

Figure 3:
blank F3 GCMS and Landis F3 GC-IRMS
chromatograms overlaid.
click for full size

Figure 3a:
Landis F3 GCMS and GC-IRMS overlaid.

Asserted -28.79/5bA aligned, scale adjusted so 5bPreg matches.
click for bigger.

To make sure I've understood BB's claims, I'll ask now, did I get this right? Please answer in comments below and we'll carry on the dialogue. When needed, we'll add more figures to this post, and if BB wants to add some, we'll include whatever he provides.

Billy writes:

There you have it. The three peaks are the same.

I reply:

OK. Remember what we did, we adjusted the horizontal scale to make those three peaks line up, so we think linear (proportional) adjustment is correct.

Now, look at figure 4, a zoom of the left hand side of figure 3a, where the "anchor" internal standard is supposed to be located.

There doesn't appear to be very good alignment with those peaks is there?

With the linear scaling we used to get the peaks in the middle and right to align, we don't have alignment on the peaks on the left.

How should we try to correct it, by changing the scaling factor, or shifting the left peaks into better alignment?

Figure 4:
zooms in on Figure 3a.
click for bigger

Figure 4a:
Zoom in on figure 3.

Click for bigger.

If these zooms aren't clear, please suggest what I can try to make them better. Alternatively, try these manipulations yourself with Photoshop/Gimp and the previous figures. I do it by making one a background layer, and the other a transparent layer on top, which can be scaled and moved around.

Billy Answers:

There is nothing to correct. It is a qualitative issue. said...

By what do you mean "qualitative?"

Should the internal standard align in the GCMS and GC-IRMS the way the analytes of interest line up or not?

BustinBilly said...

It is qualitative. For identification only. Which is different from a quantitative issue, e. g. the T/E quantification that was negated. The identification of the three metabolites is quite obvious. What more is there to say?

docnzym said...

But the internal standards are suppose to be lined up or why would you call them an internal standard (other than for extraction efficiency purposes) By just looking at these three peaks and nothing else then it would seem that you are forcing the answer

BustinBilly said...

What does it matter if the quantified peak-internal standard difference is changed by 0.3-0.4 minutes? The patterns are the same. The peaks were identified in the GC/MS plot.

The plots are from different machines with corresponding columns. A difference is expected.

BustinBilly said...

Look, there are two pertinent points I haven't seen anybody argue away.
1.The substances were identified correctly in the F3 GC/MS plots.
2.The F3 GC/C/IRMS plots for both the A&B samples are nearly identical to the GC/MS plots. The three metabolites of interest are almost exactly identical.

The panel of judges was right when they decided this issue.

TBV adds some figures:

Figure 5:
Lined up on the SI peaks on the left, scaled horizonally so the 5bP lines up.
This is interesting.
Click for bigger.
Figure 6:
Scaling from Figure 4a slid left so SI peak aligns.
5bP on right is way off.
Click for bigger

Figure 7:
Zoom of Figure 5 (not 6) showing 5bPdiol peak alignment
I believe the peaks align.

Figure 8:
Zoom of Figure 5 (not 6) showing 5bPdiol baseline match.
It's not as good as the peak which is why both are shown.

Figure 9:
Zoom of Figure 5 (not 6) showing baseline in the middle.

TBV saaid

[...] responding to BB's 5:45 comment.

1. The GCMS identification isn't in question; that's not in dispute here.

2. This is what we are discussing, and we'll see if it gets argued away or not.

In the comment that Billy started with, he said "They are exactly the same".

We've shown with overlays they are not exactly the same, and Billy has changed to using "nearly identical" for the whole chart and saying the metabolites of interest are "exactly identical".

He says the lack if exact match on the low end near the SI is not relevant. We'll leave this aside for now.

I do want to offer two more versions of overlays for comparison.

Figure 5 is a version of the overlay where the SI is aligned, and the axis linearly expanded so the 5bP aligns. In this, we see a significant left shift of the 5bA and 5bP peaks.

Figure 6 is one where the overlay scaling of Figure 4a is left shifted so the SI seems to align. In this case, it doesn't appear anything on the middle or right aligns, so that might be pointless to pursue.

Figure 7 is a zoom of the 5bP peak [in Fig 5] to show how it was aligned at the top. Figure 8 shows that the bottom alignment might be questioned, but the trailing peaks look OK.

Figure 9 is a zoom [in Fig 5] of what we think is the region of interest. In it, things are not quite as clear to me as they appear to be for BB. Here we see the peak identified as 5bA might align as well with a low GC-IRMS peak as with the one originally claimed, and the one labelled 5aA might align with the GC-IRMS peak that is ostensibly the 5bA.

Are the identifications of the GC-IRMS peaks still as obviously correct on visual examination as they seemed at first?

BustinBilly said...

Yes the identifications are as obviously correct as they seemed at first.

A good analogy would be different sized fonts. If you type the same sentence in the same font in Photoshop, the two sentences will overlay perfectly. Type the same sentence again in the same font-using a slightly larger point. A few letters will line up well on overlay, the rest will not. However it will still be the same sentence.

I hope that analogy helps. I don't see how quibbling over the overlay makes any difference. said...

Please be patient while I try to figure out what is obvious to you, and not yet to me.

In Figure 9, we can see that innaccurate horizontal alignment can result in peaks being completely misidentified. The GCMS peak for 5bA is closer to a small GC-IRMS peak just short of 15:00 minutes that has not had it's CIR measured. The GCMS peak identified as the 5aA peak nearly sits on top of the GC-IRMS peak that is measured to be the 5bA peak.

How is that potential misidentification not a problem?

If that misidentification can't happen, what criteria are you using to decide which peak in that region aligns with which peak in the other chromatogram?

[ There's some discussion I'll capture in a bit, but for now, moving on ]

Figure 11:
Landis A sample F2 GCMS
click for bigger

Figure 12:
Landis A sample G2 IRMS
click for bigger

Figure 13:
Figures 11 and 12 overlaid, and scaled so anchor and rightmost labeled peak align.
click for bigger.

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